annotate hd.py @ 29:6b15b3b6405c draft

planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
author mheinzl
date Wed, 24 Jul 2019 05:58:15 -0400
parents 1fa7342a140d
children 46bfbec0f9e6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
1 #!/usr/bin/env python
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
2
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
3 # Hamming distance analysis of SSCSs
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
4 #
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
5 # Author: Monika Heinzl, Johannes-Kepler University Linz (Austria)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
6 # Contact: monika.heinzl@edumail.at
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
7 #
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
8 # Takes at least one TABULAR file with tags before the alignment to the SSCS and
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
9 # optionally a second TABULAR file as input. The program produces a plot which shows a histogram of Hamming distances
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
10 # separated after family sizes, a family size distribution separated after Hamming distances for all (sample_size=0)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
11 # or a given sample of SSCSs or SSCSs, which form a DCS. In additon, the tool produces HD and FSD plots for the
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
12 # difference between the HDs of both parts of the tags and for the chimeric reads and finally a CSV file with the
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
13 # data of the plots. It is also possible to perform the HD analysis with shortened tags with given sizes as input.
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
14 # The tool can run on a certain number of processors, which can be defined by the user.
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
15
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
16 # USAGE: python hd.py --inputFile filename --inputName1 filename --sample_size int /
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
17 # --only_DCS True --FamilySize3 True --subset_tag True --nproc int --minFS int --maxFS int
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
18 # --nr_above_bars True/False --output_tabular outptufile_name_tabular
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
19
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
20 import argparse
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
21 import itertools
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
22 import operator
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
23 import sys
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
24 from collections import Counter, defaultdict
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
25 from functools import partial
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
26 from multiprocessing.pool import Pool
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
27 import random
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
28 import os
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
29
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
30 import matplotlib.pyplot as plt
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
31 import numpy
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
32 from matplotlib.backends.backend_pdf import PdfPages
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
33
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
34 plt.switch_backend('agg')
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
35
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
36
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
37 def plotFSDwithHD2(familySizeList1, maximumXFS, minimumXFS, originalCounts,
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
38 subtitle, pdf, relative=False, diff=True, rel_freq=False):
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
39 if diff is False:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
40 colors = ["#e6194b", "#3cb44b", "#ffe119", "#0082c8", "#f58231", "#911eb4"]
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
41 labels = ["HD=1", "HD=2", "HD=3", "HD=4", "HD=5-8", "HD>8"]
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
42 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
43 colors = ["#93A6AB", "#403C14", "#731E41", "#BAB591", "#085B6F", "#E8AA35", "#726C66"]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
44 if relative is True:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
45 labels = ["d=0", "d=0.1", "d=0.2", "d=0.3", "d=0.4", "d=0.5-0.8", "d>0.8"]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
46 else:
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
47 labels = ["d=0", "d=1", "d=2", "d=3", "d=4", "d=5-8", "d>8"]
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
48
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
49 fig = plt.figure(figsize=(6, 7))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
50 ax = fig.add_subplot(111)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
51 plt.subplots_adjust(bottom=0.1)
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
52 p1 = numpy.bincount(numpy.concatenate(familySizeList1))
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
53 maximumY = numpy.amax(p1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
54
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
55 if len(range(minimumXFS, maximumXFS)) == 0:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
56 range1 = range(minimumXFS - 1, minimumXFS + 2)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
57 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
58 range1 = range(0, maximumXFS + 2)
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
59
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
60 if rel_freq:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
61 w = [numpy.zeros_like(data) + 1. / len(numpy.concatenate(familySizeList1)) for data in familySizeList1]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
62 counts = plt.hist(familySizeList1, label=labels, weights=w, color=colors, stacked=True,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
63 rwidth=0.8, alpha=1, align="left", edgecolor="None", bins=range1)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
64 plt.ylabel("Relative Frequency", fontsize=14)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
65 plt.ylim((0, (float(maximumY) / sum(p1)) * 1.1))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
66 else:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
67 counts = plt.hist(familySizeList1, label=labels, color=colors, stacked=True,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
68 rwidth=0.8, alpha=1, align="left", edgecolor="None", bins=range1)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
69 if len(numpy.concatenate(familySizeList1)) != 0:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
70 plt.ylim((0, max(numpy.bincount(numpy.concatenate(familySizeList1))) * 1.1))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
71 plt.ylabel("Absolute Frequency", fontsize=14)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
72 plt.ylim((0, maximumY * 1.2))
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
73 plt.legend(loc='upper right', fontsize=14, frameon=True, bbox_to_anchor=(1.45, 1))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
74 plt.suptitle(subtitle, y=1, x=0.5, fontsize=14)
2
316fbf91dd12 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f9d5547849dabb59a33a5e998bda4730323d62a9
mheinzl
parents: 1
diff changeset
75 plt.xlabel("Family size", fontsize=14)
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
76 ticks = numpy.arange(0, maximumXFS + 1, 1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
77 ticks1 = map(str, ticks)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
78 if maximumXFS >= 20:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
79 ticks1[len(ticks1) - 1] = ">=20"
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
80 plt.xticks(numpy.array(ticks), ticks1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
81 [l.set_visible(False) for (i, l) in enumerate(ax.get_xticklabels()) if i % 5 != 0]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
82 plt.xlim((0, maximumXFS + 1))
21
9919024d7778 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6
mheinzl
parents: 20
diff changeset
83 legend = "\nfamily size: \nabsolute frequency: \nrelative frequency: "
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
84 plt.text(0.15, -0.08, legend, size=12, transform=plt.gcf().transFigure)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
85
11
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
86 count = numpy.bincount(originalCounts) # original counts
21
9919024d7778 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6
mheinzl
parents: 20
diff changeset
87 if max(originalCounts) >= 20:
9919024d7778 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6
mheinzl
parents: 20
diff changeset
88 max_count = ">= 20"
9919024d7778 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6
mheinzl
parents: 20
diff changeset
89 else:
9919024d7778 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6
mheinzl
parents: 20
diff changeset
90 max_count = max(originalCounts)
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
91 legend1 = "{}\n{}\n{:.5f}".format(max_count, p1[len(p1) - 1], float(p1[len(p1) - 1]) / sum(p1))
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
92 plt.text(0.5, -0.08, legend1, size=12, transform=plt.gcf().transFigure)
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
93 legend3 = "singletons\n{:,}\n{:.5f}".format(int(p1[1]), float(p1[1]) / sum(p1))
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
94 plt.text(0.7, -0.08, legend3, transform=plt.gcf().transFigure, size=12)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
95 plt.grid(b=True, which='major', color='#424242', linestyle=':')
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
96 pdf.savefig(fig, bbox_inches="tight")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
97 plt.close("all")
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
98
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
99
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
100 def plotHDwithFSD(list1, maximumX, minimumX, subtitle, lenTags, pdf, xlabel, relative=False,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
101 nr_above_bars=True, nr_unique_chimeras=0, len_sample=0, rel_freq=False):
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
102 if relative is True:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
103 step = 0.1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
104 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
105 step = 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
106
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
107 fig = plt.figure(figsize=(6, 8))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
108 plt.subplots_adjust(bottom=0.1)
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
109 p1 = numpy.array([v for k, v in sorted(Counter(numpy.concatenate(list1)).iteritems())])
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
110 maximumY = numpy.amax(p1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
111 if relative is True: # relative difference
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
112 bin1 = numpy.arange(-1, maximumX + 0.2, 0.1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
113 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
114 bin1 = maximumX + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
115
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
116 if rel_freq:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
117 w = [numpy.zeros_like(data) + 1. / len(numpy.concatenate(list1)) for data in list1]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
118 counts = plt.hist(list1, bins=bin1, edgecolor='black', linewidth=1, weights=w,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
119 label=["FS=1", "FS=2", "FS=3", "FS=4", "FS=5-10", "FS>10"], rwidth=0.8,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
120 color=["#808080", "#FFFFCC", "#FFBF00", "#DF0101", "#0431B4", "#86B404"],
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
121 stacked=True, alpha=1, align="left", range=(0, maximumX + 1))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
122 plt.ylim((0, (float(maximumY) / sum(p1)) * 1.2))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
123 plt.ylabel("Relative Frequency", fontsize=14)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
124 bins = counts[1] # width of bins
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
125 counts = numpy.array(map(float, counts[0][5]))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
126
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
127 else:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
128 counts = plt.hist(list1, bins=bin1, edgecolor='black', linewidth=1,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
129 label=["FS=1", "FS=2", "FS=3", "FS=4", "FS=5-10", "FS>10"], rwidth=0.8,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
130 color=["#808080", "#FFFFCC", "#FFBF00", "#DF0101", "#0431B4", "#86B404"],
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
131 stacked=True, alpha=1, align="left", range=(0, maximumX + 1))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
132 maximumY = numpy.amax(p1)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
133 plt.ylim((0, maximumY * 1.2))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
134 plt.ylabel("Absolute Frequency", fontsize=14)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
135 bins = counts[1] # width of bins
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
136 counts = numpy.array(map(int, counts[0][5]))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
137
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
138 plt.legend(loc='upper right', fontsize=14, frameon=True, bbox_to_anchor=(1.45, 1))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
139 plt.suptitle(subtitle, y=1, x=0.5, fontsize=14)
2
316fbf91dd12 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f9d5547849dabb59a33a5e998bda4730323d62a9
mheinzl
parents: 1
diff changeset
140 plt.xlabel(xlabel, fontsize=14)
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
141 plt.grid(b=True, which='major', color='#424242', linestyle=':')
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
142 plt.xlim((minimumX - step, maximumX + step))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
143 # plt.axis((minimumX - step, maximumX + step, 0, numpy.amax(counts) + sum(counts) * 0.1))
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
144 plt.xticks(numpy.arange(0, maximumX + step, step))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
145
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
146 if nr_above_bars:
14
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
147 bin_centers = -0.4 * numpy.diff(bins) + bins[:-1]
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
148 for x_label, label in zip(counts, bin_centers): # labels for values
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
149 if x_label == 0:
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
150 continue
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
151 else:
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
152 if rel_freq:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
153 plt.annotate("{:,}\n{:.3f}".format(int(round(x_label * len(numpy.concatenate(list1)))),
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
154 float(x_label)),
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
155 xy=(label, x_label + len(numpy.concatenate(list1)) * 0.0001),
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
156 xycoords="data", color="#000066", fontsize=10)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
157 else:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
158 plt.annotate("{:,}\n{:.3f}".format(x_label, float(x_label) / sum(counts)),
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
159 xy=(label, x_label + len(numpy.concatenate(list1)) * 0.01),
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
160 xycoords="data", color="#000066", fontsize=10)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
161
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
162 if nr_unique_chimeras != 0:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
163 if (relative and ((counts[len(counts)-1] / nr_unique_chimeras) == 2)) or \
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
164 (sum(counts) / nr_unique_chimeras) == 2:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
165 legend = "nr. of tags = {:,}\nsample size = {:,}\nnr. of data points = {:,}\nnr. of CF = {:,} ({:,})"\
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
166 .format(lenTags, len_sample, len(numpy.concatenate(list1)), nr_unique_chimeras, nr_unique_chimeras * 2)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
167 else:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
168 legend = "nr. of tags = {:,}\nsample size = {:,}\nnr. of data points = {:,}\nnr. of CF = {:,}".format(
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
169 lenTags, len_sample, len(numpy.concatenate(list1)), nr_unique_chimeras)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
170 else:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
171 legend = "nr. of tags = {:,}\nsample size = {:,}\nnr. of data points = {:,}".format(
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
172 lenTags, len_sample, len(numpy.concatenate(list1)))
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
173
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
174 plt.text(0.14, -0.07, legend, size=12, transform=plt.gcf().transFigure)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
175 pdf.savefig(fig, bbox_inches="tight")
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
176 plt.close("all")
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
177 plt.clf()
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
178
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
179
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
180 def plotHDwithDCS(list1, maximumX, minimumX, subtitle, lenTags, pdf, xlabel, relative=False,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
181 nr_above_bars=True, nr_unique_chimeras=0, len_sample=0, rel_freq=False):
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
182 step = 1
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
183 fig = plt.figure(figsize=(6, 8))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
184 plt.subplots_adjust(bottom=0.1)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
185 p1 = numpy.array([v for k, v in sorted(Counter(numpy.concatenate(list1)).iteritems())])
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
186 maximumY = numpy.amax(p1)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
187 bin1 = maximumX + 1
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
188 if rel_freq:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
189 w = [numpy.zeros_like(data) + 1. / len(numpy.concatenate(list1)) for data in list1]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
190 counts = plt.hist(list1, bins=bin1, edgecolor='black', linewidth=1, weights=w,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
191 label=["DCS", "ab", "ba"], rwidth=0.8, color=["#FF0000", "#5FB404", "#FFBF00"],
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
192 stacked=True, alpha=1, align="left", range=(0, maximumX + 1))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
193 plt.ylim((0, (float(maximumY) / sum(p1)) * 1.2))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
194 plt.ylabel("Relative Frequency", fontsize=14)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
195 bins = counts[1] # width of bins
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
196 counts = numpy.array(map(float, counts[0][2]))
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
197
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
198 else:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
199 counts = plt.hist(list1, bins=bin1, edgecolor='black', linewidth=1,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
200 label=["DCS", "ab", "ba"], rwidth=0.8, color=["#FF0000", "#5FB404", "#FFBF00"],
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
201 stacked=True, alpha=1, align="left", range=(0, maximumX + 1))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
202 plt.ylim((0, maximumY * 1.2))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
203 plt.ylabel("Absolute Frequency", fontsize=14)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
204 bins = counts[1] # width of bins
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
205 counts = numpy.array(map(int, counts[0][2]))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
206
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
207 plt.legend(loc='upper right', fontsize=14, frameon=True, bbox_to_anchor=(1.45, 1))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
208 plt.suptitle(subtitle, y=1, x=0.5, fontsize=14)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
209 plt.xlabel(xlabel, fontsize=14)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
210 plt.grid(b=True, which='major', color='#424242', linestyle=':')
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
211 plt.xlim((minimumX - step, maximumX + step))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
212 # plt.axis((minimumX - step, maximumX + step, 0, numpy.amax(counts) + sum(counts) * 0.1))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
213 plt.xticks(numpy.arange(0, maximumX + step, step))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
214
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
215 if nr_above_bars:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
216 bin_centers = -0.4 * numpy.diff(bins) + bins[:-1]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
217 for x_label, label in zip(counts, bin_centers): # labels for values
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
218 if x_label == 0:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
219 continue
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
220 else:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
221 if rel_freq:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
222 plt.annotate("{:,}\n{:.3f}".format(int(round(x_label * len(numpy.concatenate(list1)))),
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
223 float(x_label)),
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
224 xy=(label, x_label + len(numpy.concatenate(list1)) * 0.0001),
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
225 xycoords="data", color="#000066", fontsize=10)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
226 else:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
227 plt.annotate("{:,}\n{:.3f}".format(x_label, float(x_label) / sum(counts)),
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
228 xy=(label, x_label + len(numpy.concatenate(list1)) * 0.01),
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
229 xycoords="data", color="#000066", fontsize=10)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
230
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
231 if nr_unique_chimeras != 0:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
232 if (sum(counts) / nr_unique_chimeras) == 2:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
233 legend = "nr. of tags = {:,}\nsample size = {:,}\nnr. of data points = {:,}\nnr. of CF = {:,} ({:,})".\
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
234 format(lenTags, len_sample, len(numpy.concatenate(list1)), nr_unique_chimeras, nr_unique_chimeras * 2)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
235 else:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
236 legend = "nr. of tags = {:,}\nsample size = {:,}\nnr. of data points = {:,}\nnr. of CF = {:,}".format(
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
237 lenTags, len_sample, len(numpy.concatenate(list1)), nr_unique_chimeras)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
238 else:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
239 legend = "nr. of tags = {:,}\nsample size = {:,}\nnr. of data points = {:,}".format(
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
240 lenTags, len_sample, len(numpy.concatenate(list1)))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
241 plt.text(0.14, -0.07, legend, size=12, transform=plt.gcf().transFigure)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
242
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
243 legend2 = "SSCS ab = {:,}\nSSCS ba = {:,}\nDCS = {:,}".format(len(list1[1]), len(list1[2]), len(list1[0]))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
244 plt.text(0.6, -0.047, legend2, size=12, transform=plt.gcf().transFigure)
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
245
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
246 pdf.savefig(fig, bbox_inches="tight")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
247 plt.close("all")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
248 plt.clf()
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
249
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
250
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
251 def plotHDwithinSeq(sum1, sum1min, sum2, sum2min, min_value, lenTags, pdf, len_sample, rel_freq=False):
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
252 fig = plt.figure(figsize=(6, 8))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
253 plt.subplots_adjust(bottom=0.1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
254
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
255 ham_partial = [sum1, sum1min, sum2, sum2min, numpy.array(min_value)] # new hd within tags
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
256 maximumX = numpy.amax(numpy.concatenate(ham_partial))
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
257 minimumX = numpy.amin(numpy.concatenate(ham_partial))
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
258 maximumY = numpy.amax(numpy.array(numpy.concatenate(map(lambda x: numpy.bincount(x), ham_partial))))
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
259
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
260 if len(range(minimumX, maximumX)) == 0:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
261 range1 = minimumX
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
262 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
263 range1 = range(minimumX, maximumX + 2)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
264
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
265 if rel_freq:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
266 w = [numpy.zeros_like(data) + 1. / len(data) for data in ham_partial]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
267 plt.hist(ham_partial, align="left", rwidth=0.8, stacked=False, weights=w,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
268 label=["HD a", "HD b'", "HD b", "HD a'", "HD a+b', a'+b"],
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
269 bins=range1, color=["#58ACFA", "#0404B4", "#FE642E", "#B40431", "#585858"],
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
270 edgecolor='black', linewidth=1)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
271 plt.ylabel("Relative Frequency", fontsize=14)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
272 # plt.ylim(-0.1, (float(maximumY) / len(numpy.concatenate(ham_partial))) * 1.2)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
273 else:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
274 plt.hist(ham_partial, align="left", rwidth=0.8, stacked=False,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
275 label=["HD a", "HD b'", "HD b", "HD a'", "HD a+b', a'+b"],
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
276 bins=range1, color=["#58ACFA", "#0404B4", "#FE642E", "#B40431", "#585858"],
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
277 edgecolor='black', linewidth=1)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
278 plt.ylabel("Absolute Frequency", fontsize=14)
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
279
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
280 plt.legend(loc='upper right', fontsize=14, frameon=True, bbox_to_anchor=(1.55, 1))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
281 plt.suptitle('Hamming distances within tags', fontsize=14)
14
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
282 plt.xlabel("HD", fontsize=14)
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
283 plt.grid(b=True, which='major', color='#424242', linestyle=':')
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
284 plt.xlim((minimumX - 1, maximumX + 1))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
285 # plt.axis((minimumX - 1, maximumX + 1, 0, maximumY * 1.2))
2
316fbf91dd12 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f9d5547849dabb59a33a5e998bda4730323d62a9
mheinzl
parents: 1
diff changeset
286 plt.xticks(numpy.arange(0, maximumX + 1, 1.0))
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
287 legend = "nr. of tags = {:,}\nsample size = {:,}\nnr. of data points = {:,}".format(
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
288 lenTags, len_sample, len(numpy.concatenate(ham_partial)))
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
289 plt.text(0.14, -0.05, legend, size=12, transform=plt.gcf().transFigure)
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
290 pdf.savefig(fig, bbox_inches="tight")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
291 plt.close("all")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
292 plt.clf()
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
293
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
294
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
295 def createTableFSD2(list1, diff=True):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
296 selfAB = numpy.concatenate(list1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
297 uniqueFS = numpy.unique(selfAB)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
298 nr = numpy.arange(0, len(uniqueFS), 1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
299 if diff is False:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
300 count = numpy.zeros((len(uniqueFS), 6))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
301 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
302 count = numpy.zeros((len(uniqueFS), 7))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
303 state = 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
304 for i in list1:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
305 counts = list(Counter(i).items())
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
306 hd = [item[0] for item in counts]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
307 c = [item[1] for item in counts]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
308 table = numpy.column_stack((hd, c))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
309 if len(table) == 0:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
310 state = state + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
311 continue
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
312 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
313 if state == 1:
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
314 for k, l in zip(uniqueFS, nr):
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
315 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
316 if j[0] == uniqueFS[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
317 count[l, 0] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
318 if state == 2:
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
319 for k, l in zip(uniqueFS, nr):
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
320 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
321 if j[0] == uniqueFS[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
322 count[l, 1] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
323 if state == 3:
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
324 for k, l in zip(uniqueFS, nr):
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
325 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
326 if j[0] == uniqueFS[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
327 count[l, 2] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
328 if state == 4:
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
329 for k, l in zip(uniqueFS, nr):
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
330 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
331 if j[0] == uniqueFS[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
332 count[l, 3] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
333 if state == 5:
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
334 for k, l in zip(uniqueFS, nr):
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
335 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
336 if j[0] == uniqueFS[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
337 count[l, 4] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
338 if state == 6:
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
339 for k, l in zip(uniqueFS, nr):
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
340 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
341 if j[0] == uniqueFS[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
342 count[l, 5] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
343 if state == 7:
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
344 for k, l in zip(uniqueFS, nr):
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
345 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
346 if j[0] == uniqueFS[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
347 count[l, 6] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
348 state = state + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
349 sumRow = count.sum(axis=1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
350 sumCol = count.sum(axis=0)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
351 uniqueFS = uniqueFS.astype(str)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
352 if uniqueFS[len(uniqueFS) - 1] == "20":
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
353 uniqueFS[len(uniqueFS) - 1] = ">20"
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
354 first = ["FS={}".format(i) for i in uniqueFS]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
355 final = numpy.column_stack((first, count, sumRow))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
356 return (final, sumCol)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
357
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
358
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
359 def createFileFSD2(summary, sumCol, overallSum, output_file, name, sep, rel=False, diff=True):
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
360 output_file.write(name)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
361 output_file.write("\n")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
362 if diff is False:
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
363 output_file.write("{}HD=1{}HD=2{}HD=3{}HD=4{}HD=5-8{}HD>8{}sum{}\n".format(
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
364 sep, sep, sep, sep, sep, sep, sep, sep))
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
365 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
366 if rel is False:
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
367 output_file.write("{}diff=0{}diff=1{}diff=2{}diff=3{}diff=4{}diff=5-8{}diff>8{}sum{}\n".format(
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
368 sep, sep, sep, sep, sep, sep, sep, sep, sep))
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
369 else:
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
370 output_file.write("{}diff=0{}diff=0.1{}diff=0.2{}diff=0.3{}diff=0.4{}diff=0.5-0.8{}diff>0.8{}sum{}\n".
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
371 format(sep, sep, sep, sep, sep, sep, sep, sep, sep))
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
372 for item in summary:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
373 for nr in item:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
374 if "FS" not in nr and "diff" not in nr:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
375 nr = nr.astype(float)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
376 nr = nr.astype(int)
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
377 output_file.write("{}{}".format(nr, sep))
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
378 output_file.write("\n")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
379 output_file.write("sum{}".format(sep))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
380 sumCol = map(int, sumCol)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
381 for el in sumCol:
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
382 output_file.write("{}{}".format(el, sep))
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
383 output_file.write("{}{}".format(overallSum.astype(int), sep))
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
384 output_file.write("\n\n")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
385
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
386
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
387 def createTableHD(list1, row_label):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
388 selfAB = numpy.concatenate(list1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
389 uniqueHD = numpy.unique(selfAB)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
390 nr = numpy.arange(0, len(uniqueHD), 1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
391 count = numpy.zeros((len(uniqueHD), 6))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
392 state = 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
393 for i in list1:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
394 counts = list(Counter(i).items())
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
395 hd = [item[0] for item in counts]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
396 c = [item[1] for item in counts]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
397 table = numpy.column_stack((hd, c))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
398 if len(table) == 0:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
399 state = state + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
400 continue
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
401 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
402 if state == 1:
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
403 for k, l in zip(uniqueHD, nr):
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
404 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
405 if j[0] == uniqueHD[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
406 count[l, 0] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
407 if state == 2:
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
408 for k, l in zip(uniqueHD, nr):
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
409 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
410 if j[0] == uniqueHD[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
411 count[l, 1] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
412 if state == 3:
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
413 for k, l in zip(uniqueHD, nr):
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
414 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
415 if j[0] == uniqueHD[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
416 count[l, 2] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
417 if state == 4:
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
418 for k, l in zip(uniqueHD, nr):
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
419 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
420 if j[0] == uniqueHD[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
421 count[l, 3] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
422 if state == 5:
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
423 for k, l in zip(uniqueHD, nr):
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
424 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
425 if j[0] == uniqueHD[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
426 count[l, 4] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
427 if state == 6:
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
428 for k, l in zip(uniqueHD, nr):
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
429 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
430 if j[0] == uniqueHD[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
431 count[l, 5] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
432 state = state + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
433 sumRow = count.sum(axis=1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
434 sumCol = count.sum(axis=0)
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
435 first = ["{}{}".format(row_label, i) for i in uniqueHD]
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
436 final = numpy.column_stack((first, count, sumRow))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
437 return (final, sumCol)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
438
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
439
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
440 def createTableHDwithTags(list1):
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
441 selfAB = numpy.concatenate(list1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
442 uniqueHD = numpy.unique(selfAB)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
443 nr = numpy.arange(0, len(uniqueHD), 1)
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
444 count = numpy.zeros((len(uniqueHD), 5))
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
445 state = 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
446 for i in list1:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
447 counts = list(Counter(i).items())
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
448 hd = [item[0] for item in counts]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
449 c = [item[1] for item in counts]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
450 table = numpy.column_stack((hd, c))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
451 if len(table) == 0:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
452 state = state + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
453 continue
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
454 else:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
455 if state == 1:
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
456 for k, l in zip(uniqueHD, nr):
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
457 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
458 if j[0] == uniqueHD[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
459 count[l, 0] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
460 if state == 2:
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
461 for k, l in zip(uniqueHD, nr):
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
462 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
463 if j[0] == uniqueHD[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
464 count[l, 1] = j[1]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
465 if state == 3:
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
466 for k, l in zip(uniqueHD, nr):
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
467 for j in table:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
468 if j[0] == uniqueHD[l]:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
469 count[l, 2] = j[1]
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
470 if state == 4:
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
471 for k, l in zip(uniqueHD, nr):
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
472 for j in table:
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
473 if j[0] == uniqueHD[l]:
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
474 count[l, 3] = j[1]
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
475 if state == 5:
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
476 for k, l in zip(uniqueHD, nr):
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
477 for j in table:
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
478 if j[0] == uniqueHD[l]:
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
479 count[l, 4] = j[1]
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
480 state = state + 1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
481 sumRow = count.sum(axis=1)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
482 sumCol = count.sum(axis=0)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
483 first = ["HD={}".format(i) for i in uniqueHD]
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
484 final = numpy.column_stack((first, count, sumRow))
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
485 return (final, sumCol)
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
486
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
487
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
488 def createTableHDwithDCS(list1):
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
489 selfAB = numpy.concatenate(list1)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
490 uniqueHD = numpy.unique(selfAB)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
491 nr = numpy.arange(0, len(uniqueHD), 1)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
492 count = numpy.zeros((len(uniqueHD), len(list1)))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
493 state = 1
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
494 for i in list1:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
495 counts = list(Counter(i).items())
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
496 hd = [item[0] for item in counts]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
497 c = [item[1] for item in counts]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
498 table = numpy.column_stack((hd, c))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
499 if len(table) == 0:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
500 state = state + 1
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
501 continue
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
502 else:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
503 if state == 1:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
504 for k, l in zip(uniqueHD, nr):
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
505 for j in table:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
506 if j[0] == uniqueHD[l]:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
507 count[l, 0] = j[1]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
508 if state == 2:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
509 for k, l in zip(uniqueHD, nr):
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
510 for j in table:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
511 if j[0] == uniqueHD[l]:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
512 count[l, 1] = j[1]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
513 if state == 3:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
514 for k, l in zip(uniqueHD, nr):
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
515 for j in table:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
516 if j[0] == uniqueHD[l]:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
517 count[l, 2] = j[1]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
518 state = state + 1
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
519 sumRow = count.sum(axis=1)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
520 sumCol = count.sum(axis=0)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
521 first = ["HD={}".format(i) for i in uniqueHD]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
522 final = numpy.column_stack((first, count, sumRow))
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
523 return (final, sumCol)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
524
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
525
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
526 def createFileHD(summary, sumCol, overallSum, output_file, name, sep):
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
527 output_file.write(name)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
528 output_file.write("\n")
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
529 output_file.write("{}FS=1{}FS=2{}FS=3{}FS=4{}FS=5-10{}FS>10{}sum{}\n".format(
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
530 sep, sep, sep, sep, sep, sep, sep, sep))
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
531 for item in summary:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
532 for nr in item:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
533 if "HD" not in nr and "diff" not in nr:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
534 nr = nr.astype(float)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
535 nr = nr.astype(int)
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
536 output_file.write("{}{}".format(nr, sep))
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
537 output_file.write("\n")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
538 output_file.write("sum{}".format(sep))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
539 sumCol = map(int, sumCol)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
540 for el in sumCol:
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
541 output_file.write("{}{}".format(el, sep))
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
542 output_file.write("{}{}".format(overallSum.astype(int), sep))
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
543 output_file.write("\n\n")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
544
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
545
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
546 def createFileHDwithDCS(summary, sumCol, overallSum, output_file, name, sep):
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
547 output_file.write(name)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
548 output_file.write("\n")
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
549 output_file.write("{}DCS{}SSCS ab{}SSCS ba{}sum{}\n".format(sep, sep, sep, sep, sep))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
550 for item in summary:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
551 for nr in item:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
552 if "HD" not in nr:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
553 nr = nr.astype(float)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
554 nr = nr.astype(int)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
555 output_file.write("{}{}".format(nr, sep))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
556 output_file.write("\n")
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
557 output_file.write("sum{}".format(sep))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
558 sumCol = map(int, sumCol)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
559 for el in sumCol:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
560 output_file.write("{}{}".format(el, sep))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
561 output_file.write("{}{}".format(overallSum.astype(int), sep))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
562 output_file.write("\n\n")
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
563
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
564
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
565 def createFileHDwithinTag(summary, sumCol, overallSum, output_file, name, sep):
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
566 output_file.write(name)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
567 output_file.write("\n")
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
568 output_file.write("{}HD DCS{}HD b'{}HD b{}HD a'{}HD a+b', a'+b{}sum{}\n".format(sep, sep, sep, sep, sep, sep, sep))
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
569 for item in summary:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
570 for nr in item:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
571 if "HD" not in nr:
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
572 nr = nr.astype(float)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
573 nr = nr.astype(int)
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
574 output_file.write("{}{}".format(nr, sep))
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
575 output_file.write("\n")
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
576 output_file.write("sum{}".format(sep))
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
577 sumCol = map(int, sumCol)
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
578 for el in sumCol:
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
579 output_file.write("{}{}".format(el, sep))
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
580 output_file.write("{}{}".format(overallSum.astype(int), sep))
1
7414792e1cb8 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents: 0
diff changeset
581 output_file.write("\n\n")
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
582
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
583
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
584 def hamming(array1, array2):
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
585 res = 99 * numpy.ones(len(array1))
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
586 i = 0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
587 array2 = numpy.unique(array2) # remove duplicate sequences to decrease running time
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
588 for a in array1:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
589 dist = numpy.array([sum(itertools.imap(operator.ne, a, b)) for b in array2]) # fastest
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
590 res[i] = numpy.amin(dist[dist > 0]) # pick min distance greater than zero
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
591 i += 1
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
592 return res
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
593
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
594
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
595 def hamming_difference(array1, array2, mate_b):
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
596 array2 = numpy.unique(array2) # remove duplicate sequences to decrease running time
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
597 array1_half = numpy.array([i[0:(len(i)) / 2] for i in array1]) # mate1 part1
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
598 array1_half2 = numpy.array([i[len(i) / 2:len(i)] for i in array1]) # mate1 part 2
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
599 array2_half = numpy.array([i[0:(len(i)) / 2] for i in array2]) # mate2 part1
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
600 array2_half2 = numpy.array([i[len(i) / 2:len(i)] for i in array2]) # mate2 part2
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
601
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
602 # diff11 = 999 * numpy.ones(len(array2))
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
603 # relativeDiffList = 999 * numpy.ones(len(array2))
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
604 # ham1 = 999 * numpy.ones(len(array2))
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
605 # ham2 = 999 * numpy.ones(len(array2))
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
606 # min_valueList = 999 * numpy.ones(len(array2))
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
607 # min_tagsList = 999 * numpy.ones(len(array2))
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
608 # diff11_zeros = 999 * numpy.ones(len(array2))
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
609 # min_tagsList_zeros = 999 * numpy.ones(len(array2))
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
610
8
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
611 diff11 = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
612 relativeDiffList = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
613 ham1 = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
614 ham2 = []
14
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
615 ham1min = []
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
616 ham2min = []
8
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
617 min_valueList = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
618 min_tagsList = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
619 diff11_zeros = []
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
620 min_tagsList_zeros = []
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
621 max_tag_list = []
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
622 i = 0 # counter, only used to see how many HDs of tags were already calculated
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
623 if mate_b is False: # HD calculation for all a's
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
624 half1_mate1 = array1_half
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
625 half2_mate1 = array1_half2
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
626 half1_mate2 = array2_half
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
627 half2_mate2 = array2_half2
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
628 elif mate_b is True: # HD calculation for all b's
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
629 half1_mate1 = array1_half2
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
630 half2_mate1 = array1_half
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
631 half1_mate2 = array2_half2
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
632 half2_mate2 = array2_half
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
633
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
634 # half1_mate1, index_halves = numpy.unique(half1_mate1, return_index=True)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
635 # print(len(half1_mate1))
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
636 # half2_mate1 = half2_mate1[index_halves]
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
637 # array1 = array1[index_halves]
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
638
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
639 for a, b, tag in zip(half1_mate1, half2_mate1, array1):
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
640 # exclude identical tag from array2, to prevent comparison to itself
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
641 sameTag = numpy.where(array2 == tag)[0]
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
642 indexArray2 = numpy.arange(0, len(array2), 1)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
643 index_withoutSame = numpy.delete(indexArray2, sameTag) # delete identical tag from the data
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
644
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
645 # all tags without identical tag
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
646 array2_half_withoutSame = half1_mate2[index_withoutSame]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
647 array2_half2_withoutSame = half2_mate2[index_withoutSame]
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
648 array2_withoutSame = array2[index_withoutSame] # whole tag (=not splitted into 2 halfs)
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
649 # calculate HD of "a" in the tag to all "a's" or "b" in the tag to all "b's"
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
650 dist = numpy.array([sum(itertools.imap(operator.ne, a, c)) for c in
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
651 array2_half_withoutSame])
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
652 min_index = numpy.where(dist == dist.min())[0] # get index of min HD
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
653 min_value = dist.min()
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
654 # min_value = dist[min_index] # get minimum HDs
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
655 # get all "b's" of the tag or all "a's" of the tag with minimum HD
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
656 min_tag_half2 = array2_half2_withoutSame[min_index]
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
657 min_tag_array2 = array2_withoutSame[min_index] # get whole tag with min HD
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
658
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
659 dist_second_half = numpy.array([sum(itertools.imap(operator.ne, b, e)) for e in
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
660 min_tag_half2]) # calculate HD of "b" to all "b's" or "a" to all "a's"
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
661 max_value = dist_second_half.max()
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
662 max_index = numpy.where(dist_second_half == dist_second_half.max())[0] # get index of max HD
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
663 max_tag = min_tag_array2[max_index]
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
664
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
665 # for d, d2 in zip(min_value, max_value):
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
666 if mate_b is True: # half2, corrects the variable of the HD from both halfs if it is a or b
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
667 ham2.append(min_value)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
668 ham2min.append(max_value)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
669 else: # half1, corrects the variable of the HD from both halfs if it is a or b
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
670 ham1.append(min_value)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
671 ham1min.append(max_value)
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
672
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
673 min_valueList.append(min_value + max_value)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
674 min_tagsList.append(tag)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
675 difference1 = abs(min_value - max_value)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
676 diff11.append(difference1)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
677 rel_difference = round(float(difference1) / (min_value + max_value), 1)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
678 relativeDiffList.append(rel_difference)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
679
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
680 # tags which have identical parts:
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
681 if min_value == 0 or max_value == 0:
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
682 min_tagsList_zeros.append(numpy.array(tag))
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
683 difference1_zeros = abs(min_value - max_value) # hd of non-identical part
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
684 diff11_zeros.append(difference1_zeros)
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
685 max_tag_list.append(numpy.array(max_tag))
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
686 else:
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
687 min_tagsList_zeros.append(None)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
688 diff11_zeros.append(None)
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
689 max_tag_list.append(None)
8
e2596a4e1c56 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
mheinzl
parents: 7
diff changeset
690 i += 1
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
691
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
692 # print(i)
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
693 # diff11 = [st for st in diff11 if st != 999]
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
694 # ham1 = [st for st in ham1 if st != 999]
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
695 # ham2 = [st for st in ham2 if st != 999]
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
696 # min_valueList = [st for st in min_valueList if st != 999]
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
697 # min_tagsList = [st for st in min_tagsList if st != 999]
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
698 # relativeDiffList = [st for st in relativeDiffList if st != 999]
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
699 # diff11_zeros = [st for st in diff11_zeros if st != 999]
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
700 # min_tagsList_zeros = [st for st in min_tagsList_zeros if st != 999]
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
701 return ([diff11, ham1, ham2, min_valueList, min_tagsList, relativeDiffList, diff11_zeros,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
702 min_tagsList_zeros, ham1min, ham2min, max_tag_list])
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
703
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
704
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
705 def readFileReferenceFree(file):
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
706 with open(file, 'r') as dest_f:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
707 data_array = numpy.genfromtxt(dest_f, skip_header=0, delimiter='\t', comments='#', dtype='string')
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
708 integers = numpy.array(data_array[:, 0]).astype(int)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
709 return(integers, data_array)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
710
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
711
11
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
712 def hammingDistanceWithFS(fs, ham):
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
713 fs = numpy.asarray(fs)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
714 maximum = max(ham)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
715 minimum = min(ham)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
716 ham = numpy.asarray(ham)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
717
11
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
718 singletons = numpy.where(fs == 1)[0]
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
719 data = ham[singletons]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
720
11
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
721 hd2 = numpy.where(fs == 2)[0]
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
722 data2 = ham[hd2]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
723
11
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
724 hd3 = numpy.where(fs == 3)[0]
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
725 data3 = ham[hd3]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
726
11
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
727 hd4 = numpy.where(fs == 4)[0]
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
728 data4 = ham[hd4]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
729
11
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
730 hd5 = numpy.where((fs >= 5) & (fs <= 10))[0]
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
731 data5 = ham[hd5]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
732
11
7adc48c8a03d planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
mheinzl
parents: 10
diff changeset
733 hd6 = numpy.where(fs > 10)[0]
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
734 data6 = ham[hd6]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
735
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
736 list1 = [data, data2, data3, data4, data5, data6]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
737 return(list1, maximum, minimum)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
738
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
739
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
740 def familySizeDistributionWithHD(fs, ham, diff=False, rel=True):
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
741 hammingDistances = numpy.unique(ham)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
742 fs = numpy.asarray(fs)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
743 ham = numpy.asarray(ham)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
744 bigFamilies2 = numpy.where(fs > 19)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
745 if len(bigFamilies2) != 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
746 fs[bigFamilies2] = 20
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
747 maximum = max(fs)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
748 minimum = min(fs)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
749 if diff is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
750 hd0 = numpy.where(ham == 0)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
751 data0 = fs[hd0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
752
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
753 if rel is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
754 hd1 = numpy.where(ham == 0.1)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
755 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
756 hd1 = numpy.where(ham == 1)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
757 data = fs[hd1]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
758
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
759 if rel is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
760 hd2 = numpy.where(ham == 0.2)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
761 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
762 hd2 = numpy.where(ham == 2)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
763 data2 = fs[hd2]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
764
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
765 if rel is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
766 hd3 = numpy.where(ham == 0.3)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
767 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
768 hd3 = numpy.where(ham == 3)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
769 data3 = fs[hd3]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
770
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
771 if rel is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
772 hd4 = numpy.where(ham == 0.4)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
773 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
774 hd4 = numpy.where(ham == 4)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
775 data4 = fs[hd4]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
776
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
777 if rel is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
778 hd5 = numpy.where((ham >= 0.5) & (ham <= 0.8))[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
779 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
780 hd5 = numpy.where((ham >= 5) & (ham <= 8))[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
781 data5 = fs[hd5]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
782
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
783 if rel is True:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
784 hd6 = numpy.where(ham > 0.8)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
785 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
786 hd6 = numpy.where(ham > 8)[0]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
787 data6 = fs[hd6]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
788
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
789 if diff is True:
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
790 list1 = [data0, data, data2, data3, data4, data5, data6]
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
791 else:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
792 list1 = [data, data2, data3, data4, data5, data6]
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
793
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
794 return(list1, hammingDistances, maximum, minimum)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
795
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
796
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
797 def hammingDistanceWithDCS(minHD_tags_zeros, diff_zeros, data_array):
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
798 diff_zeros = numpy.array(diff_zeros)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
799 maximum = numpy.amax(diff_zeros)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
800 minimum = numpy.amin(diff_zeros)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
801 minHD_tags_zeros = numpy.array(minHD_tags_zeros)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
802
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
803 idx = numpy.concatenate([numpy.where(data_array[:, 1] == i)[0] for i in minHD_tags_zeros])
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
804 subset_data = data_array[idx, :]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
805
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
806 seq = numpy.array(subset_data[:, 1])
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
807
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
808 # find all unique tags and get the indices for ALL tags, but only once
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
809 u, index_unique, c = numpy.unique(numpy.array(seq), return_counts=True, return_index=True)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
810 DCS_tags = u[c == 2]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
811 rest_tags = u[c == 1]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
812
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
813 dcs = numpy.repeat("DCS", len(DCS_tags))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
814 idx_sscs = numpy.concatenate([numpy.where(subset_data[:, 1] == i)[0] for i in rest_tags])
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
815 sscs = subset_data[idx_sscs, 2]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
816
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
817 all_tags = numpy.column_stack((numpy.concatenate((DCS_tags, subset_data[idx_sscs, 1])),
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
818 numpy.concatenate((dcs, sscs))))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
819 hd_DCS = []
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
820 ab_SSCS = []
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
821 ba_SSCS = []
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
822
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
823 for i in range(len(all_tags)):
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
824 tag = all_tags[i, :]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
825 hd = diff_zeros[numpy.where(minHD_tags_zeros == tag[0])[0]]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
826
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
827 if tag[1] == "DCS":
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
828 hd_DCS.append(hd)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
829 elif tag[1] == "ab":
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
830 ab_SSCS.append(hd)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
831 elif tag[1] == "ba":
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
832 ba_SSCS.append(hd)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
833
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
834 if len(hd_DCS) != 0:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
835 hd_DCS = numpy.concatenate(hd_DCS)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
836 if len(ab_SSCS) != 0:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
837 ab_SSCS = numpy.concatenate(ab_SSCS)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
838 if len(ba_SSCS) != 0:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
839 ba_SSCS = numpy.concatenate(ba_SSCS)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
840 list1 = [hd_DCS, ab_SSCS, ba_SSCS] # list for plotting
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
841 return(list1, maximum, minimum)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
842
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
843
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
844 def make_argparser():
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
845 parser = argparse.ArgumentParser(description='Hamming distance analysis of duplex sequencing data')
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
846 parser.add_argument('--inputFile',
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
847 help='Tabular File with three columns: ab or ba, tag and family size.')
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
848 parser.add_argument('--inputName1')
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
849 parser.add_argument('--sample_size', default=1000, type=int,
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
850 help='Sample size of Hamming distance analysis.')
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
851 parser.add_argument('--subset_tag', default=0, type=int,
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
852 help='The tag is shortened to the given number.')
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
853 parser.add_argument('--nproc', default=4, type=int,
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
854 help='The tool runs with the given number of processors.')
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
855 parser.add_argument('--only_DCS', action="store_false",
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
856 help='Only tags of the DCSs are included in the HD analysis')
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
857
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
858 parser.add_argument('--minFS', default=1, type=int,
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
859 help='Only tags, which have a family size greater or equal than specified, '
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
860 'are included in the HD analysis')
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
861 parser.add_argument('--maxFS', default=0, type=int,
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
862 help='Only tags, which have a family size smaller or equal than specified, '
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
863 'are included in the HD analysis')
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
864 parser.add_argument('--nr_above_bars', action="store_true",
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
865 help='If False, values above bars in the histograms are removed')
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
866 parser.add_argument('--rel_freq', action="store_false",
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
867 help='If True, the relative frequencies are displayed.')
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
868
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
869 parser.add_argument('--output_tabular', default="data.tabular", type=str,
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
870 help='Name of the tabular file.')
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
871 parser.add_argument('--output_pdf', default="data.pdf", type=str,
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
872 help='Name of the pdf file.')
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
873 parser.add_argument('--output_chimeras_tabular', default="data.tabular", type=str,
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
874 help='Name of the tabular file with all chimeric tags.')
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
875
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
876 return parser
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
877
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
878
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
879 def Hamming_Distance_Analysis(argv):
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
880 # def Hamming_Distance_Analysis(file1, name1, index_size, title_savedFile_pdf, title_savedFile_csv,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
881 # output_chimeras_tabular, onlyDuplicates, minFS=1, maxFS=0, nr_above_bars=True,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
882 # subset=False, nproc=12, rel_freq=False):
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
883 parser = make_argparser()
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
884 args = parser.parse_args(argv[1:])
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
885 file1 = args.inputFile
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
886 name1 = args.inputName1
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
887 index_size = args.sample_size
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
888 title_savedFile_pdf = args.output_pdf
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
889 title_savedFile_csv = args.output_tabular
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
890 output_chimeras_tabular = args.output_chimeras_tabular
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
891 onlyDuplicates = args.only_DCS
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
892 rel_freq = args.rel_freq
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
893 minFS = args.minFS
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
894 maxFS = args.maxFS
14
883e6381ba29 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
mheinzl
parents: 13
diff changeset
895 nr_above_bars = args.nr_above_bars
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
896 subset = args.subset_tag
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
897 nproc = args.nproc
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
898 sep = "\t"
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
899
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
900 # input checks
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
901 if index_size < 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
902 print("index_size is a negative integer.")
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
903 exit(2)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
904 if nproc <= 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
905 print("nproc is smaller or equal zero")
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
906 exit(3)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
907 if subset < 0:
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
908 print("subset_tag is smaller or equal zero.")
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
909 exit(5)
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
910
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
911 # PLOT
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
912 plt.rcParams['axes.facecolor'] = "E0E0E0" # grey background color
10
69aa17354a6e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f01678e9bfead9f9e1b54dd9ecf7141f057dd9de
mheinzl
parents: 9
diff changeset
913 plt.rcParams['xtick.labelsize'] = 14
69aa17354a6e planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f01678e9bfead9f9e1b54dd9ecf7141f057dd9de
mheinzl
parents: 9
diff changeset
914 plt.rcParams['ytick.labelsize'] = 14
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
915 plt.rcParams['patch.edgecolor'] = "#000000"
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
916 plt.rc('figure', figsize=(11.69, 8.27)) # A4 format
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
917 name1 = name1.split(".tabular")[0]
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
918
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
919 with open(title_savedFile_csv, "w") as output_file, PdfPages(title_savedFile_pdf) as pdf:
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
920 print("dataset: ", name1)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
921 integers, data_array = readFileReferenceFree(file1)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
922 data_array = numpy.array(data_array)
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
923 print("total nr of tags:", len(data_array))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
924
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
925 # filter tags out which contain any other character than ATCG
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
926 valid_bases = ["A", "T", "G", "C"]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
927 tagsToDelete = []
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
928 for idx, t in enumerate(data_array[:, 1]):
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
929 for char in t:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
930 if char not in valid_bases:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
931 tagsToDelete.append(idx)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
932 break
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
933
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
934 if len(tagsToDelete) != 0: # delete tags with N in the tag from data
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
935 print("nr of tags with any other character than A, T, C, G:", len(tagsToDelete),
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
936 float(len(tagsToDelete)) / len(data_array))
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
937 index_whole_array = numpy.arange(0, len(data_array), 1)
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
938 index_withoutN_inTag = numpy.delete(index_whole_array, tagsToDelete)
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
939 data_array = data_array[index_withoutN_inTag, :]
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
940 integers = integers[index_withoutN_inTag]
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
941 print("total nr of filtered tags:", len(data_array))
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
942
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
943 int_f = numpy.array(data_array[:, 0]).astype(int)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
944 data_array = data_array[numpy.where(int_f >= minFS)]
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
945 integers = integers[integers >= minFS]
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
946
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
947 # select family size for tags
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
948 if maxFS > 0:
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
949 int_f2 = numpy.array(data_array[:, 0]).astype(int)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
950 data_array = data_array[numpy.where(int_f2 <= maxFS)]
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
951 integers = integers[integers <= maxFS]
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
952
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
953 if onlyDuplicates is True:
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
954 tags = data_array[:, 2]
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
955 seq = data_array[:, 1]
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
956
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
957 # find all unique tags and get the indices for ALL tags, but only once
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
958 u, index_unique, c = numpy.unique(numpy.array(seq), return_counts=True, return_index=True)
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
959 d = u[c == 2]
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
960
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
961 # get family sizes, tag for duplicates
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
962 duplTags_double = integers[numpy.in1d(seq, d)]
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
963 duplTags = duplTags_double[0::2] # ab of DCS
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
964 duplTagsBA = duplTags_double[1::2] # ba of DCS
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
965
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
966 duplTags_tag = tags[numpy.in1d(seq, d)][0::2] # ab
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
967 duplTags_seq = seq[numpy.in1d(seq, d)][0::2] # ab - tags
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
968
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
969 if minFS > 1:
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
970 duplTags_tag = duplTags_tag[(duplTags >= minFS) & (duplTagsBA >= minFS)]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
971 duplTags_seq = duplTags_seq[(duplTags >= minFS) & (duplTagsBA >= minFS)]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
972 duplTags = duplTags[(duplTags >= minFS) & (duplTagsBA >= minFS)] # ab+ba with FS>=3
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
973
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
974 data_array = numpy.column_stack((duplTags, duplTags_seq))
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
975 data_array = numpy.column_stack((data_array, duplTags_tag))
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
976 integers = numpy.array(data_array[:, 0]).astype(int)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
977 print("DCS in whole dataset", len(data_array))
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
978
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
979 print("min FS", min(integers))
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
980 print("max FS", max(integers))
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
981
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
982 # HD analysis for a subset of the tag
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
983 if subset > 0:
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
984 tag1 = numpy.array([i[0:(len(i)) / 2] for i in data_array[:, 1]])
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
985 tag2 = numpy.array([i[len(i) / 2:len(i)] for i in data_array[:, 1]])
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
986
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
987 flanking_region_float = float((len(tag1[0]) - subset)) / 2
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
988 flanking_region = int(flanking_region_float)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
989 if flanking_region_float % 2 == 0:
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
990 tag1_shorten = numpy.array([i[flanking_region:len(i) - flanking_region] for i in tag1])
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
991 tag2_shorten = numpy.array([i[flanking_region:len(i) - flanking_region] for i in tag2])
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
992 else:
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
993 flanking_region_rounded = int(round(flanking_region, 1))
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
994 flanking_region_rounded_end = len(tag1[0]) - subset - flanking_region_rounded
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
995 tag1_shorten = numpy.array(
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
996 [i[flanking_region:len(i) - flanking_region_rounded_end] for i in tag1])
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
997 tag2_shorten = numpy.array(
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
998 [i[flanking_region:len(i) - flanking_region_rounded_end] for i in tag2])
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
999
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1000 data_array_tag = numpy.array([i + j for i, j in zip(tag1_shorten, tag2_shorten)])
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1001 data_array = numpy.column_stack((data_array[:, 0], data_array_tag, data_array[:, 2]))
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
1002
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1003 print("length of tag= ", len(data_array[0, 1]))
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1004 # select sample: if no size given --> all vs. all comparison
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1005 if index_size == 0:
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1006 result = numpy.arange(0, len(data_array), 1)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1007 else:
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1008 numpy.random.shuffle(data_array)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1009 unique_tags, unique_indices = numpy.unique(data_array[:, 1], return_index=True) # get only unique tags
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1010 result = numpy.random.choice(unique_indices, size=index_size,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1011 replace=False) # array of random sequences of size=index.size
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1012
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1013 # result = numpy.random.choice(len(integers), size=index_size,
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1014 # replace=False) # array of random sequences of size=index.size
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1015 # result = numpy.where(numpy.array(random_tags) == numpy.array(data_array[:,1]))[0]
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
1016
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1017 # with open("index_result.pkl", "wb") as o:
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1018 # pickle.dump(result, o, pickle.HIGHEST_PROTOCOL)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
1019
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1020 # save counts
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1021 # with open(data_folder + "index_sampleTags1000_Barcode3_DCS.pkl", "wb") as f:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1022 # pickle.dump(result, f, pickle.HIGHEST_PROTOCOL)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1023 # with open(data_folder + "dataArray_sampleTags1000_Barcode3_DCS.pkl", "wb") as f1:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1024 # pickle.dump(data_array, f1, pickle.HIGHEST_PROTOCOL)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1025 #
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1026 # with open(data_folder + "index_sampleTags100.pkl", "rb") as f:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1027 # result = pickle.load(f)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1028 #
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1029 # with open(data_folder + "dataArray_sampleTags100.pkl", "rb") as f1:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1030 # data_array = pickle.load(f1)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1031
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1032 # with open(data_folder + "index_result.txt", "w") as t:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1033 # for text in result:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1034 # t.write("{}\n".format(text))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1035
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1036 # comparison random tags to whole dataset
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1037 result1 = data_array[result, 1] # random tags
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1038 result2 = data_array[:, 1] # all tags
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1039 print("sample size= ", len(result1))
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
1040
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1041 # HD analysis of whole tag
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1042 proc_pool = Pool(nproc)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1043 chunks_sample = numpy.array_split(result1, nproc)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1044 ham = proc_pool.map(partial(hamming, array2=result2), chunks_sample)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1045 proc_pool.close()
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1046 proc_pool.join()
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1047 ham = numpy.concatenate(ham).astype(int)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1048 # with open("HD_whole dataset_{}.txt".format(app_f), "w") as output_file1:
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1049 # for h, tag in zip(ham, result1):
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1050 # output_file1.write("{}\t{}\n".format(tag, h))
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
1051
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1052 # # HD analysis for chimeric reads
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1053 # result2 = data_array_whole_dataset[:,1]
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1054
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1055 proc_pool_b = Pool(nproc)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1056 diff_list_a = proc_pool_b.map(partial(hamming_difference, array2=result2, mate_b=False), chunks_sample)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1057 diff_list_b = proc_pool_b.map(partial(hamming_difference, array2=result2, mate_b=True), chunks_sample)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1058 proc_pool_b.close()
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1059 proc_pool_b.join()
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1060 HDhalf1 = numpy.concatenate((numpy.concatenate([item[1] for item in diff_list_a]),
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1061 numpy.concatenate([item_b[1] for item_b in diff_list_b]))).astype(int)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1062 HDhalf2 = numpy.concatenate((numpy.concatenate([item[2] for item in diff_list_a]),
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1063 numpy.concatenate([item_b[2] for item_b in diff_list_b]))).astype(int)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1064 minHDs = numpy.concatenate((numpy.concatenate([item[3] for item in diff_list_a]),
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1065 numpy.concatenate([item_b[3] for item_b in diff_list_b]))).astype(int)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1066 HDhalf1min = numpy.concatenate((numpy.concatenate([item[8] for item in diff_list_a]),
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1067 numpy.concatenate([item_b[8] for item_b in diff_list_b]))).astype(int)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1068 HDhalf2min = numpy.concatenate((numpy.concatenate([item[9] for item in diff_list_a]),
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1069 numpy.concatenate([item_b[9] for item_b in diff_list_b]))).astype(int)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
1070
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1071 rel_Diff1 = numpy.concatenate([item[5] for item in diff_list_a])
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1072 rel_Diff2 = numpy.concatenate([item[5] for item in diff_list_b])
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1073 diff1 = numpy.concatenate([item[0] for item in diff_list_a])
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1074 diff2 = numpy.concatenate([item[0] for item in diff_list_b])
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1075
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1076 diff_zeros1 = numpy.concatenate([item[6] for item in diff_list_a])
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1077 diff_zeros2 = numpy.concatenate([item[6] for item in diff_list_b])
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1078 minHD_tags = numpy.concatenate([item[4] for item in diff_list_a])
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1079 minHD_tags_zeros1 = numpy.concatenate([item[7] for item in diff_list_a])
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1080 minHD_tags_zeros2 = numpy.concatenate([item[7] for item in diff_list_b])
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1081
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1082 chimera_tags1 = sum([item[10] for item in diff_list_a], [])
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1083 chimera_tags2 = numpy.concatenate([item[10] for item in diff_list_b])
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1084
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1085 rel_Diff = []
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1086 diff_zeros = []
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1087 minHD_tags_zeros = []
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1088 diff = []
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1089 chimera_tags = []
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1090 for d1, d2, rel1, rel2, zeros1, zeros2, tag1, tag2, ctag1, ctag2 in \
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1091 zip(diff1, diff2, rel_Diff1, rel_Diff2, diff_zeros1, diff_zeros2, minHD_tags_zeros1, minHD_tags_zeros2,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1092 chimera_tags1, chimera_tags2):
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1093 rel_Diff.append(max(rel1, rel2))
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1094 diff.append(max(d1, d2))
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1095
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1096 if all(i is not None for i in [zeros1, zeros2]):
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1097 diff_zeros.append(max(zeros1, zeros2))
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1098 minHD_tags_zeros.append(str(tag1))
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1099 tags = [ctag1, ctag2]
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1100 chimera_tags.append(tags)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1101 elif zeros1 is not None and zeros2 is None:
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1102 diff_zeros.append(zeros1)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1103 minHD_tags_zeros.append(str(tag1))
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1104 chimera_tags.append(ctag1)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1105 elif zeros1 is None and zeros2 is not None:
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1106 diff_zeros.append(zeros2)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1107 minHD_tags_zeros.append(str(tag2))
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1108 chimera_tags.append(ctag2)
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1109
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1110 chimera_tags_new = chimera_tags
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1111 data_chimeraAnalysis = numpy.column_stack((minHD_tags_zeros, chimera_tags_new))
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1112 # chimeras_dic = defaultdict(list)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1113 #
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1114 # for t1, t2 in zip(minHD_tags_zeros, chimera_tags_new):
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1115 # if len(t2) >1 and type(t2) is not numpy.ndarray:
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1116 # t2 = numpy.concatenate(t2)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1117 # chimeras_dic[t1].append(t2)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1118
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1119 checked_tags = []
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1120 stat_maxTags = []
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1121
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1122 with open(output_chimeras_tabular, "w") as output_file1:
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1123 output_file1.write("chimera tag\tfamily size, read direction\tsimilar tag with HD=0\n")
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1124 for i in range(len(data_chimeraAnalysis)):
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1125 tag1 = data_chimeraAnalysis[i, 0]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1126
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1127 info_tag1 = data_array[data_array[:, 1] == tag1, :]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1128 fs_tag1 = ["{} {}".format(t[0], t[2]) for t in info_tag1]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1129
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1130 if tag1 in checked_tags: # skip tag if already written to file
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1131 continue
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1132
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1133 sample_half_a = tag1[0:(len(tag1)) / 2]
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1134 sample_half_b = tag1[len(tag1) / 2:len(tag1)]
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1135
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1136 max_tags = data_chimeraAnalysis[i, 1]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1137 if len(max_tags) > 1 and type(max_tags) is not numpy.ndarray:
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1138 max_tags = numpy.concatenate(max_tags)
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1139 max_tags = numpy.unique(max_tags)
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1140 stat_maxTags.append(len(max_tags))
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1141
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1142 info_maxTags = [data_array[data_array[:, 1] == t, :] for t in max_tags]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1143
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1144 chimera_half_a = numpy.array([t[0:(len(t)) / 2] for t in max_tags]) # mate1 part1
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1145 chimera_half_b = numpy.array([t[len(t) / 2:len(t)] for t in max_tags]) # mate1 part 2
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1146
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1147 new_format = []
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1148 for j in range(len(max_tags)):
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1149 fs_maxTags = ["{} {}".format(t[0], t[2]) for t in info_maxTags[j]]
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1150
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1151 if sample_half_a == chimera_half_a[j]:
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1152 max_tag = "*{}* {} {}".format(chimera_half_a[j], chimera_half_b[j], ", ".join(fs_maxTags))
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1153 new_format.append(max_tag)
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1154
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1155 elif sample_half_b == chimera_half_b[j]:
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1156 max_tag = "{} *{}* {}".format(chimera_half_a[j], chimera_half_b[j], ", ".join(fs_maxTags))
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1157 new_format.append(max_tag)
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1158 checked_tags.append(max_tags[j])
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1159
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1160 sample_tag = "{} {}\t{}".format(sample_half_a, sample_half_b, ", ".join(fs_tag1))
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1161 output_file1.write("{}\t{}\n".format(sample_tag, ", ".join(new_format)))
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1162
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1163 checked_tags.append(tag1)
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1164
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1165 output_file1.write(
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1166 "This file contains all tags that were identified as chimeras as the first column and the "
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1167 "corresponding tags which returned a Hamming distance of zero in either the first or the second "
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1168 "half of the sample tag as the second column.\n"
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1169 "The tags were separated by an empty space into their halves and the * marks the identical half.")
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1170 output_file1.write("\n\nStatistics of nr. of tags that returned max. HD (2nd column)\n")
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1171 output_file1.write("minimum\t{}\ttag(s)\n".format(numpy.amin(numpy.array(stat_maxTags))))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1172 output_file1.write("mean\t{}\ttag(s)\n".format(numpy.mean(numpy.array(stat_maxTags))))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1173 output_file1.write("median\t{}\ttag(s)\n".format(numpy.median(numpy.array(stat_maxTags))))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1174 output_file1.write("maximum\t{}\ttag(s)\n".format(numpy.amax(numpy.array(stat_maxTags))))
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1175 output_file1.write("sum\t{}\ttag(s)\n".format(numpy.sum(numpy.array(stat_maxTags))))
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1176
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1177 lenTags = len(data_array)
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1178 len_sample = len(result1)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
1179
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1180 quant = numpy.array(data_array[result, 0]).astype(int) # family size for sample of tags
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1181 seq = numpy.array(data_array[result, 1]) # tags of sample
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1182 ham = numpy.asarray(ham) # HD for sample of tags
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
1183
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1184 if onlyDuplicates is True: # ab and ba strands of DCSs
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1185 quant = numpy.concatenate((quant, duplTagsBA[result]))
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1186 seq = numpy.tile(seq, 2)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1187 ham = numpy.tile(ham, 2)
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1188 diff = numpy.tile(diff, 2)
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1189 rel_Diff = numpy.tile(rel_Diff, 2)
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1190 diff_zeros = numpy.tile(diff_zeros, 2)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
1191
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1192 nr_chimeric_tags = len(data_chimeraAnalysis)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1193 print("nr of chimeras", nr_chimeric_tags)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1194
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1195 # prepare data for different kinds of plots
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1196 # distribution of FSs separated after HD
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1197 familySizeList1, hammingDistances, maximumXFS, minimumXFS = familySizeDistributionWithHD(quant, ham, rel=False)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1198 list1, maximumX, minimumX = hammingDistanceWithFS(quant, ham) # histogram of HDs separated after FS
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
1199
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1200 # get FS for all tags with min HD of analysis of chimeric reads
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1201 # there are more tags than sample size in the plot, because one tag can have multiple minimas
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1202 if onlyDuplicates:
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1203 seqDic = defaultdict(list)
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1204 for s, q in zip(seq, quant):
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1205 seqDic[s].append(q)
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1206 else:
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1207 seqDic = dict(zip(seq, quant))
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1208
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1209 lst_minHD_tags = []
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1210 for i in minHD_tags:
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1211 lst_minHD_tags.append(seqDic.get(i))
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
1212
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1213 if onlyDuplicates:
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1214 lst_minHD_tags = numpy.concatenate(([item[0] for item in lst_minHD_tags],
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1215 [item_b[1] for item_b in lst_minHD_tags])).astype(int)
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1216 # histogram with absolute and relative difference between HDs of both parts of the tag
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1217 listDifference1, maximumXDifference, minimumXDifference = hammingDistanceWithFS(lst_minHD_tags, diff)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1218 listRelDifference1, maximumXRelDifference, minimumXRelDifference = hammingDistanceWithFS(lst_minHD_tags,
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1219 rel_Diff)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1220 # chimeric read analysis: tags which have HD=0 in one of the halfs
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1221 if len(minHD_tags_zeros) != 0:
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1222 lst_minHD_tags_zeros = []
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1223 for i in minHD_tags_zeros:
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1224 lst_minHD_tags_zeros.append(seqDic.get(i)) # get family size for tags of chimeric reads
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1225 if onlyDuplicates:
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1226 lst_minHD_tags_zeros = numpy.concatenate(([item[0] for item in lst_minHD_tags_zeros],
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1227 [item_b[1] for item_b in lst_minHD_tags_zeros])).astype(int)
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1228
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1229 # histogram with HD of non-identical half
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1230 listDifference1_zeros, maximumXDifference_zeros, minimumXDifference_zeros = hammingDistanceWithFS(
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1231 lst_minHD_tags_zeros, diff_zeros)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1232
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1233 if onlyDuplicates is False:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1234 listDCS_zeros, maximumXDCS_zeros, minimumXDCS_zeros = hammingDistanceWithDCS(minHD_tags_zeros,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1235 diff_zeros, data_array)
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1236
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1237 # plot Hamming Distance with Family size distribution
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1238 plotHDwithFSD(list1=list1, maximumX=maximumX, minimumX=minimumX, pdf=pdf, rel_freq=rel_freq,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1239 subtitle="Hamming distance separated by family size", lenTags=lenTags,
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1240 xlabel="HD", nr_above_bars=nr_above_bars, len_sample=len_sample)
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
1241
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1242 # Plot FSD with separation after
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1243 plotFSDwithHD2(familySizeList1, maximumXFS, minimumXFS, rel_freq=rel_freq,
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1244 originalCounts=quant, subtitle="Family size distribution separated by Hamming distance",
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1245 pdf=pdf, relative=False, diff=False)
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1246
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1247 # Plot HD within tags
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1248 plotHDwithinSeq(HDhalf1, HDhalf1min, HDhalf2, HDhalf2min, minHDs, pdf=pdf, lenTags=lenTags,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1249 rel_freq=rel_freq, len_sample=len_sample)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
1250
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1251 # Plot difference between HD's separated after FSD
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1252 plotHDwithFSD(listDifference1, maximumXDifference, minimumXDifference, pdf=pdf,
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1253 subtitle="Delta Hamming distance within tags", lenTags=lenTags, rel_freq=rel_freq,
25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 22
diff changeset
1254 xlabel="absolute delta HD", relative=False, nr_above_bars=nr_above_bars, len_sample=len_sample)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
1255
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1256 plotHDwithFSD(listRelDifference1, maximumXRelDifference, minimumXRelDifference, pdf=pdf,
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1257 subtitle="Chimera Analysis: relative delta Hamming distance", lenTags=lenTags, rel_freq=rel_freq,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1258 xlabel="relative delta HD", relative=True, nr_above_bars=nr_above_bars,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1259 nr_unique_chimeras=nr_chimeric_tags, len_sample=len_sample)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
1260
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1261 # plots for chimeric reads
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1262 if len(minHD_tags_zeros) != 0:
19
2e9f7ea7ae93 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents: 18
diff changeset
1263 # HD
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1264 plotHDwithFSD(listDifference1_zeros, maximumXDifference_zeros, minimumXDifference_zeros, pdf=pdf,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1265 subtitle="Hamming distance of chimeric families (CF)", rel_freq=rel_freq,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1266 lenTags=lenTags, xlabel="HD", relative=False,
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1267 nr_above_bars=nr_above_bars, nr_unique_chimeras=nr_chimeric_tags, len_sample=len_sample)
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1268
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1269 if onlyDuplicates is False:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1270 plotHDwithDCS(listDCS_zeros, maximumXDCS_zeros, minimumXDCS_zeros, pdf=pdf,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1271 subtitle="Hamming distance of chimeric families (CF)", rel_freq=rel_freq,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1272 lenTags=lenTags, xlabel="HD", relative=False,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1273 nr_above_bars=nr_above_bars, nr_unique_chimeras=nr_chimeric_tags, len_sample=len_sample)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1274
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1275 # print all data to a CSV file
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1276 # HD
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1277 summary, sumCol = createTableHD(list1, "HD=")
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1278 overallSum = sum(sumCol) # sum of columns in table
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1279
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1280 # FSD
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1281 summary5, sumCol5 = createTableFSD2(familySizeList1, diff=False)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1282 overallSum5 = sum(sumCol5)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1283
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1284 # HD of both parts of the tag
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1285 summary9, sumCol9 = createTableHDwithTags([HDhalf1, HDhalf1min, HDhalf2, HDhalf2min, numpy.array(minHDs)])
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1286 overallSum9 = sum(sumCol9)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1287
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1288 # HD
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1289 # absolute difference
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1290 summary11, sumCol11 = createTableHD(listDifference1, "diff=")
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1291 overallSum11 = sum(sumCol11)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1292 # relative difference and all tags
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1293 summary13, sumCol13 = createTableHD(listRelDifference1, "diff=")
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1294 overallSum13 = sum(sumCol13)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1295
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1296 # chimeric reads
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1297 if len(minHD_tags_zeros) != 0:
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1298 # absolute difference and tags where at least one half has HD=0
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1299 summary15, sumCol15 = createTableHD(listDifference1_zeros, "HD=")
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1300 overallSum15 = sum(sumCol15)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
1301
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1302 if onlyDuplicates is False:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1303 summary16, sumCol16 = createTableHDwithDCS(listDCS_zeros)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1304 overallSum16 = sum(sumCol16)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1305
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1306 output_file.write("{}\n".format(name1))
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1307 output_file.write("nr of tags{}{:,}\nsample size{}{:,}\n\n".format(sep, lenTags, sep, len_sample))
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1308
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1309 # HD
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1310 createFileHD(summary, sumCol, overallSum, output_file,
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1311 "Hamming distance separated by family size", sep)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1312 # FSD
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1313 createFileFSD2(summary5, sumCol5, overallSum5, output_file,
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1314 "Family size distribution separated by Hamming distance", sep,
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1315 diff=False)
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
1316
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1317 # output_file.write("{}{}\n".format(sep, name1))
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1318 output_file.write("\n")
21
9919024d7778 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6
mheinzl
parents: 20
diff changeset
1319 max_fs = numpy.bincount(integers[result])
9919024d7778 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6
mheinzl
parents: 20
diff changeset
1320 output_file.write("max. family size in sample:{}{}\n".format(sep, max(integers[result])))
9919024d7778 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6
mheinzl
parents: 20
diff changeset
1321 output_file.write("absolute frequency:{}{}\n".format(sep, max_fs[len(max_fs) - 1]))
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1322 output_file.write(
21
9919024d7778 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6
mheinzl
parents: 20
diff changeset
1323 "relative frequency:{}{}\n\n".format(sep, float(max_fs[len(max_fs) - 1]) / sum(max_fs)))
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1324
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1325 # HD within tags
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1326 output_file.write(
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1327 "The Hamming distances were calculated by comparing the first halve against all halves and selected the "
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1328 "minimum value (HD a).\nFor the second half of the tag, we compared them against all tags which resulted "
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1329 "in the minimum HD of the previous step and selected the maximum value (HD b').\nFinally, it was possible "
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1330 "to calculate the absolute and relative differences between the HDs (absolute and relative delta HD).\n"
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1331 "These calculations were repeated, but starting with the second half in the first step to find all "
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1332 "possible chimeras in the data (HD b and HD For simplicity we used the maximum value between the delta "
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1333 "values in the end.\nWhen only tags that can form DCS were allowed in the analysis, family sizes for the "
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1334 "forward and reverse (ab and ba) will be included in the plots.\n")
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1335
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1336 output_file.write("\nlength of one half of the tag{}{}\n\n".format(sep, len(data_array[0, 1]) / 2))
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1337
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1338 createFileHDwithinTag(summary9, sumCol9, overallSum9, output_file,
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1339 "Hamming distance of each half in the tag", sep)
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1340 createFileHD(summary11, sumCol11, overallSum11, output_file,
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1341 "Absolute delta Hamming distance within the tag", sep)
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1342
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1343 createFileHD(summary13, sumCol13, overallSum13, output_file,
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1344 "Chimera analysis: relative delta Hamming distance", sep)
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1345
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1346 if len(minHD_tags_zeros) != 0:
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
1347 output_file.write(
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1348 "All tags were filtered: only those tags where at least one half was identical (HD=0) and therefore, "
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1349 "had a relative delta of 1 were kept. These tags are considered as chimeric.\nSo the Hamming distances "
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1350 "of the chimeric tags are shown.\n")
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1351 createFileHD(summary15, sumCol15, overallSum15, output_file,
29
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1352 "Hamming distance of chimeric families separated after FS", sep)
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1353
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1354 if onlyDuplicates is False:
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1355 createFileHDwithDCS(summary16, sumCol16, overallSum16, output_file,
6b15b3b6405c planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit 5b3ab8c6467fe3a52e89f5a7d175bd8a0189018a-dirty
mheinzl
parents: 28
diff changeset
1356 "Hamming distance of chimeric families separated after DCS and single SSCS", sep)
22
7e570ba56b83 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents: 21
diff changeset
1357
20
b084b6a8e3ac planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents: 19
diff changeset
1358 output_file.write("\n")
0
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
1359
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
1360
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
1361 if __name__ == '__main__':
239c4448a163 planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff changeset
1362 sys.exit(Hamming_Distance_Analysis(sys.argv))