Mercurial > repos > iuc > variant_analyzer
annotate read2mut.py @ 1:3556001ff2db draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 60dc8db809909edf44d662683b1f392b9d5964bf"
author | iuc |
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date | Wed, 04 Dec 2019 16:21:17 -0500 |
parents | 8d29173d49a9 |
children | 3f1dbd2c59bf |
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8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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1 #!/usr/bin/env python |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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2 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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3 """read2mut.py |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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4 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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5 Author -- Gundula Povysil |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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6 Contact -- povysil@bioinf.jku.at |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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7 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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8 Looks for reads with mutation at known |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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9 positions and calculates frequencies and stats. |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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10 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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11 ======= ========== ================= ================================ |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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12 Version Date Author Description |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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13 0.2.1 2019-10-27 Gundula Povysil - |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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14 ======= ========== ================= ================================ |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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15 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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16 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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17 USAGE: python read2mut.py --mutFile DCS_Mutations.tabular --bamFile Interesting_Reads.trim.bam |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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18 --inputJson tag_count_dict.json --sscsJson SSCS_counts.json |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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19 --outputFile mutant_reads_summary_short_trim.xlsx --thresh 10 --phred 20 --trim 10 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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20 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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21 """ |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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22 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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23 from __future__ import division |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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24 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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25 import argparse |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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26 import json |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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27 import operator |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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28 import os |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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29 import re |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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30 import sys |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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31 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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32 import numpy as np |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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33 import pysam |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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34 import xlsxwriter |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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35 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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36 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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37 def make_argparser(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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38 parser = argparse.ArgumentParser(description='Takes a tabular file with mutations, a BAM file and JSON files as input and prints stats about variants to a user specified output file.') |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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39 parser.add_argument('--mutFile', |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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40 help='TABULAR file with DCS mutations.') |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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41 parser.add_argument('--bamFile', |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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42 help='BAM file with aligned raw reads of selected tags (FASTQ created by mut2read.py - trimming with Trimmomatic - alignment with bwa).') |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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43 parser.add_argument('--inputJson', |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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44 help='JSON file with data collected by mut2read.py.') |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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45 parser.add_argument('--sscsJson', |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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46 help='JSON file with SSCS counts collected by mut2sscs.py.') |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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47 parser.add_argument('--outputFile', |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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48 help='Output xlsx file of mutation details.') |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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49 parser.add_argument('--thresh', type=int, default=0, |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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50 help='Integer threshold for displaying mutations. Only mutations occuring less than thresh times are displayed. Default of 0 displays all.') |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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51 parser.add_argument('--phred', type=int, default=20, |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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52 help='Integer threshold for Phred score. Only reads higher than this threshold are considered. Default 20.') |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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53 parser.add_argument('--trim', type=int, default=10, |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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54 help='Integer threshold for assigning mutations at start and end of reads to lower tier. Default 10.') |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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55 return parser |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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56 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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57 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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58 def safe_div(x, y): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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59 if y == 0: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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60 return None |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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61 return x / y |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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62 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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63 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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64 def read2mut(argv): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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65 parser = make_argparser() |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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66 args = parser.parse_args(argv[1:]) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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67 file1 = args.mutFile |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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68 file2 = args.bamFile |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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69 json_file = args.inputJson |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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70 sscs_json = args.sscsJson |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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71 outfile = args.outputFile |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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72 thresh = args.thresh |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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73 phred_score = args.phred |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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74 trim = args.trim |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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75 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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76 if os.path.isfile(file1) is False: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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77 sys.exit("Error: Could not find '{}'".format(file1)) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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78 if os.path.isfile(file2) is False: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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79 sys.exit("Error: Could not find '{}'".format(file2)) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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80 if os.path.isfile(json_file) is False: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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81 sys.exit("Error: Could not find '{}'".format(json_file)) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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82 if thresh < 0: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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83 sys.exit("Error: thresh is '{}', but only non-negative integers allowed".format(thresh)) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
84 if phred_score < 0: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
85 sys.exit("Error: phred is '{}', but only non-negative integers allowed".format(phred_score)) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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86 if trim < 0: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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87 sys.exit("Error: trim is '{}', but only non-negative integers allowed".format(thresh)) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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|
88 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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89 # 1. read mut file |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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90 with open(file1, 'r') as mut: |
1
3556001ff2db
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 60dc8db809909edf44d662683b1f392b9d5964bf"
iuc
parents:
0
diff
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91 mut_array = np.genfromtxt(mut, skip_header=1, delimiter='\t', comments='#', dtype=str) |
0
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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92 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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93 # 2. load dicts |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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94 with open(json_file, "r") as f: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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95 (tag_dict, cvrg_dict) = json.load(f) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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96 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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97 with open(sscs_json, "r") as f: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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98 (mut_pos_dict, ref_pos_dict) = json.load(f) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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99 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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100 # 3. read bam file |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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101 # pysam.index(file2) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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102 bam = pysam.AlignmentFile(file2, "rb") |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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103 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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104 # 4. create mut_dict |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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105 mut_dict = {} |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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106 mut_read_pos_dict = {} |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
107 mut_read_dict = {} |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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108 reads_dict = {} |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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109 if mut_array.shape == (13, ): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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110 mut_array = mut_array.reshape((1, len(mut_array))) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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111 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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112 for m in range(0, len(mut_array[:, 0])): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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113 print(str(m + 1) + " of " + str(len(mut_array[:, 0]))) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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114 # for m in range(0, 5): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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115 chrom = mut_array[m, 1] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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116 stop_pos = mut_array[m, 2].astype(int) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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117 chrom_stop_pos = str(chrom) + "#" + str(stop_pos) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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118 ref = mut_array[m, 9] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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119 alt = mut_array[m, 10] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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120 mut_dict[chrom_stop_pos] = {} |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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121 mut_read_pos_dict[chrom_stop_pos] = {} |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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122 reads_dict[chrom_stop_pos] = {} |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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123 |
1
3556001ff2db
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 60dc8db809909edf44d662683b1f392b9d5964bf"
iuc
parents:
0
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124 for pileupcolumn in bam.pileup(chrom, stop_pos - 2, stop_pos, max_depth=1000000000): |
0
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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125 if pileupcolumn.reference_pos == stop_pos - 1: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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126 count_alt = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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127 count_ref = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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128 count_indel = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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129 count_n = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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130 count_other = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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131 count_lowq = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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132 n = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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133 print("unfiltered reads=", pileupcolumn.n, "filtered reads=", len(pileupcolumn.pileups), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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134 "difference= ", len(pileupcolumn.pileups) - pileupcolumn.n) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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135 for pileupread in pileupcolumn.pileups: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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|
136 n += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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137 if not pileupread.is_del and not pileupread.is_refskip: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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138 tag = pileupread.alignment.query_name |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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139 nuc = pileupread.alignment.query_sequence[pileupread.query_position] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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140 phred = ord(pileupread.alignment.qual[pileupread.query_position]) - 33 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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141 if phred < phred_score: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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142 nuc = "lowQ" |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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143 if tag not in mut_dict[chrom_stop_pos]: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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144 mut_dict[chrom_stop_pos][tag] = {} |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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|
145 if nuc in mut_dict[chrom_stop_pos][tag]: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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|
146 mut_dict[chrom_stop_pos][tag][nuc] += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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|
147 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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148 mut_dict[chrom_stop_pos][tag][nuc] = 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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|
149 if tag not in mut_read_pos_dict[chrom_stop_pos]: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
150 mut_read_pos_dict[chrom_stop_pos][tag] = np.array(pileupread.query_position) + 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
151 reads_dict[chrom_stop_pos][tag] = len(pileupread.alignment.query_sequence) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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|
152 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
153 mut_read_pos_dict[chrom_stop_pos][tag] = np.append( |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
154 mut_read_pos_dict[chrom_stop_pos][tag], pileupread.query_position + 1) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
155 reads_dict[chrom_stop_pos][tag] = np.append( |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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156 reads_dict[chrom_stop_pos][tag], len(pileupread.alignment.query_sequence)) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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157 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
158 if nuc == alt: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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|
159 count_alt += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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160 if tag not in mut_read_dict: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
161 mut_read_dict[tag] = {} |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
162 mut_read_dict[tag][chrom_stop_pos] = alt |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
163 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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|
164 mut_read_dict[tag][chrom_stop_pos] = alt |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
165 elif nuc == ref: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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|
166 count_ref += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
167 elif nuc == "N": |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
168 count_n += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
169 elif nuc == "lowQ": |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
170 count_lowq += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
171 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
172 count_other += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
173 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
174 count_indel += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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175 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
176 print("coverage at pos %s = %s, ref = %s, alt = %s, other bases = %s, N = %s, indel = %s, low quality = %s\n" % (pileupcolumn.pos, count_ref + count_alt, count_ref, count_alt, count_other, count_n, count_indel, count_lowq)) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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|
177 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
178 for read in bam.fetch(until_eof=True): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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179 if read.is_unmapped: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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|
180 pure_tag = read.query_name[:-5] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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|
181 nuc = "na" |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
182 for key in tag_dict[pure_tag].keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
183 if key not in mut_dict: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
184 mut_dict[key] = {} |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
185 if read.query_name not in mut_dict[key]: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
186 mut_dict[key][read.query_name] = {} |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
187 if nuc in mut_dict[key][read.query_name]: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
188 mut_dict[key][read.query_name][nuc] += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
189 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
190 mut_dict[key][read.query_name][nuc] = 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
191 bam.close() |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
192 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
193 # 5. create pure_tags_dict |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
194 pure_tags_dict = {} |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
195 for key1, value1 in sorted(mut_dict.items()): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
196 i = np.where(np.array(['#'.join(str(i) for i in z) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
197 for z in zip(mut_array[:, 1], mut_array[:, 2])]) == key1)[0][0] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
198 ref = mut_array[i, 9] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
199 alt = mut_array[i, 10] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
200 pure_tags_dict[key1] = {} |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
201 for key2, value2 in sorted(value1.items()): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
202 for key3, value3 in value2.items(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
203 pure_tag = key2[:-5] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
204 if key3 == alt: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
205 if pure_tag in pure_tags_dict[key1]: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
206 pure_tags_dict[key1][pure_tag] += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
207 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
208 pure_tags_dict[key1][pure_tag] = 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
209 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
210 # 6. create pure_tags_dict_short with thresh |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
211 if thresh > 0: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
212 pure_tags_dict_short = {} |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
213 for key, value in sorted(pure_tags_dict.items()): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
214 if len(value) < thresh: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
215 pure_tags_dict_short[key] = value |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
216 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
217 pure_tags_dict_short = pure_tags_dict |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
218 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
219 whole_array = [] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
220 for k in pure_tags_dict.values(): |
1
3556001ff2db
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 60dc8db809909edf44d662683b1f392b9d5964bf"
iuc
parents:
0
diff
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|
221 whole_array.extend(k.keys()) |
0
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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|
222 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
223 # 7. output summary with threshold |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
224 workbook = xlsxwriter.Workbook(outfile) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
225 ws1 = workbook.add_worksheet("Results") |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
226 ws2 = workbook.add_worksheet("Allele frequencies") |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
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|
227 ws3 = workbook.add_worksheet("Tiers") |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
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|
228 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
229 format1 = workbook.add_format({'bg_color': '#BCF5A9'}) # green |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
230 format2 = workbook.add_format({'bg_color': '#FFC7CE'}) # red |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
231 format3 = workbook.add_format({'bg_color': '#FACC2E'}) # yellow |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
232 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
233 header_line = ('variant ID', 'tier', 'tag', 'mate', 'read pos.ab', 'read pos.ba', 'read median length.ab', |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
234 'read median length.ba', 'DCS median length', |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
235 'FS.ab', 'FS.ba', 'FSqc.ab', 'FSqc.ba', 'ref.ab', 'ref.ba', 'alt.ab', 'alt.ba', |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
236 'rel. ref.ab', 'rel. ref.ba', 'rel. alt.ab', 'rel. alt.ba', |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
237 'na.ab', 'na.ba', 'lowq.ab', 'lowq.ba', |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
238 'SSCS alt.ab', 'SSCS alt.ba', 'SSCS ref.ab', 'SSCS ref.ba', |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
239 'other mut', 'chimeric tag') |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
240 ws1.write_row(0, 0, header_line) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
241 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
242 counter_tier11 = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
243 counter_tier12 = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
244 counter_tier21 = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
245 counter_tier22 = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
246 counter_tier23 = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
247 counter_tier24 = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
248 counter_tier31 = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
249 counter_tier32 = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
250 counter_tier41 = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
251 counter_tier42 = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
252 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
253 row = 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
254 tier_dict = {} |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
255 for key1, value1 in sorted(mut_dict.items()): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
256 counts_mut = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
257 if key1 in pure_tags_dict_short.keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
258 i = np.where(np.array(['#'.join(str(i) for i in z) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
259 for z in zip(mut_array[:, 1], mut_array[:, 2])]) == key1)[0][0] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
260 ref = mut_array[i, 9] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
261 alt = mut_array[i, 10] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
262 dcs_median = cvrg_dict[key1][2] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
263 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
264 tier_dict[key1] = {} |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
265 values_tier_dict = [("tier 1.1", 0), ("tier 1.2", 0), ("tier 2.1", 0), ("tier 2.2", 0), ("tier 2.3", 0), ("tier 2.4", 0), ("tier 3.1", 0), ("tier 3.2", 0), ("tier 4.1", 0), ("tier 4.2", 0)] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
266 for k, v in values_tier_dict: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
267 tier_dict[key1][k] = v |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
268 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
269 used_keys = [] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
270 if 'ab' in mut_pos_dict[key1].keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
271 sscs_mut_ab = mut_pos_dict[key1]['ab'] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
272 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
273 sscs_mut_ab = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
274 if 'ba' in mut_pos_dict[key1].keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
275 sscs_mut_ba = mut_pos_dict[key1]['ba'] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
276 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
277 sscs_mut_ba = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
278 if 'ab' in ref_pos_dict[key1].keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
279 sscs_ref_ab = ref_pos_dict[key1]['ab'] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
280 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
281 sscs_ref_ab = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
282 if 'ba' in ref_pos_dict[key1].keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
283 sscs_ref_ba = ref_pos_dict[key1]['ba'] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
284 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
285 sscs_ref_ba = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
286 for key2, value2 in sorted(value1.items()): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
287 add_mut14 = "" |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
288 add_mut23 = "" |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
289 if (key2[:-5] in pure_tags_dict_short[key1].keys()) and (key2[:-5] not in used_keys) and (key1 in tag_dict[key2[:-5]].keys()): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
290 if key2[:-5] + '.ab.1' in mut_dict[key1].keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
291 total1 = sum(mut_dict[key1][key2[:-5] + '.ab.1'].values()) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
292 if 'na' in mut_dict[key1][key2[:-5] + '.ab.1'].keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
293 na1 = mut_dict[key1][key2[:-5] + '.ab.1']['na'] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
294 # na1f = na1/total1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
295 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
296 # na1 = na1f = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
297 na1 = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
298 if 'lowQ' in mut_dict[key1][key2[:-5] + '.ab.1'].keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
299 lowq1 = mut_dict[key1][key2[:-5] + '.ab.1']['lowQ'] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
300 # lowq1f = lowq1 / total1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
301 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
302 # lowq1 = lowq1f = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
303 lowq1 = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
304 if ref in mut_dict[key1][key2[:-5] + '.ab.1'].keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
305 ref1 = mut_dict[key1][key2[:-5] + '.ab.1'][ref] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
306 ref1f = ref1 / (total1 - na1 - lowq1) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
307 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
308 ref1 = ref1f = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
309 if alt in mut_dict[key1][key2[:-5] + '.ab.1'].keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
310 alt1 = mut_dict[key1][key2[:-5] + '.ab.1'][alt] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
311 alt1f = alt1 / (total1 - na1 - lowq1) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
312 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
313 alt1 = alt1f = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
314 total1new = total1 - na1 - lowq1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
315 if (key2[:-5] + '.ab.1') in mut_read_dict.keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
316 k1 = mut_read_dict[(key2[:-5] + '.ab.1')].keys() |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
317 add_mut1 = len(k1) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
318 if add_mut1 > 1: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
319 for k, v in mut_read_dict[(key2[:-5] + '.ab.1')].items(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
320 if k != key1: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
321 if len(add_mut14) == 0: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
322 add_mut14 = str(k) + "_" + v |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
323 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
324 add_mut14 = add_mut14 + ", " + str(k) + "_" + v |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
325 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
326 k1 = [] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
327 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
328 total1 = total1new = na1 = lowq1 = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
329 ref1 = alt1 = ref1f = alt1f = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
330 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
331 if key2[:-5] + '.ab.2' in mut_dict[key1].keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
332 total2 = sum(mut_dict[key1][key2[:-5] + '.ab.2'].values()) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
333 if 'na' in mut_dict[key1][key2[:-5] + '.ab.2'].keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
334 na2 = mut_dict[key1][key2[:-5] + '.ab.2']['na'] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
335 # na2f = na2 / total2 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
336 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
337 # na2 = na2f = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
338 na2 = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
339 if 'lowQ' in mut_dict[key1][key2[:-5] + '.ab.2'].keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
340 lowq2 = mut_dict[key1][key2[:-5] + '.ab.2']['lowQ'] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
341 # lowq2f = lowq2 / total2 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
342 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
343 # lowq2 = lowq2f = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
344 lowq2 = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
345 if ref in mut_dict[key1][key2[:-5] + '.ab.2'].keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
346 ref2 = mut_dict[key1][key2[:-5] + '.ab.2'][ref] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
347 ref2f = ref2 / (total2 - na2 - lowq2) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
348 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
349 ref2 = ref2f = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
350 if alt in mut_dict[key1][key2[:-5] + '.ab.2'].keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
351 alt2 = mut_dict[key1][key2[:-5] + '.ab.2'][alt] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
352 alt2f = alt2 / (total2 - na2 - lowq2) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
353 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
354 alt2 = alt2f = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
355 total2new = total2 - na2 - lowq2 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
356 if (key2[:-5] + '.ab.2') in mut_read_dict.keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
357 k2 = mut_read_dict[(key2[:-5] + '.ab.2')].keys() |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
358 add_mut2 = len(k2) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
359 if add_mut2 > 1: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
360 for k, v in mut_read_dict[(key2[:-5] + '.ab.2')].items(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
361 if k != key1: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
362 if len(add_mut23) == 0: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
363 add_mut23 = str(k) + "_" + v |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
364 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
365 add_mut23 = add_mut23 + ", " + str(k) + "_" + v |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
366 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
367 k2 = [] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
368 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
369 total2 = total2new = na2 = lowq2 = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
370 ref2 = alt2 = ref2f = alt2f = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
371 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
372 if key2[:-5] + '.ba.1' in mut_dict[key1].keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
373 total3 = sum(mut_dict[key1][key2[:-5] + '.ba.1'].values()) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
374 if 'na' in mut_dict[key1][key2[:-5] + '.ba.1'].keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
375 na3 = mut_dict[key1][key2[:-5] + '.ba.1']['na'] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
376 # na3f = na3 / total3 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
377 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
378 # na3 = na3f = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
379 na3 = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
380 if 'lowQ' in mut_dict[key1][key2[:-5] + '.ba.1'].keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
381 lowq3 = mut_dict[key1][key2[:-5] + '.ba.1']['lowQ'] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
382 # lowq3f = lowq3 / total3 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
383 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
384 # lowq3 = lowq3f = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
385 lowq3 = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
386 if ref in mut_dict[key1][key2[:-5] + '.ba.1'].keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
387 ref3 = mut_dict[key1][key2[:-5] + '.ba.1'][ref] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
388 ref3f = ref3 / (total3 - na3 - lowq3) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
389 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
390 ref3 = ref3f = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
391 if alt in mut_dict[key1][key2[:-5] + '.ba.1'].keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
392 alt3 = mut_dict[key1][key2[:-5] + '.ba.1'][alt] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
393 alt3f = alt3 / (total3 - na3 - lowq3) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
394 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
395 alt3 = alt3f = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
396 total3new = total3 - na3 - lowq3 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
397 if (key2[:-5] + '.ba.1') in mut_read_dict.keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
398 add_mut3 = len(mut_read_dict[(key2[:-5] + '.ba.1')].keys()) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
399 if add_mut3 > 1: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
400 for k, v in mut_read_dict[(key2[:-5] + '.ba.1')].items(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
401 if k != key1 and k not in k2: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
402 if len(add_mut23) == 0: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
403 add_mut23 = str(k) + "_" + v |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
404 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
405 add_mut23 = add_mut23 + ", " + str(k) + "_" + v |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
406 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
407 total3 = total3new = na3 = lowq3 = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
408 ref3 = alt3 = ref3f = alt3f = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
409 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
410 if key2[:-5] + '.ba.2' in mut_dict[key1].keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
411 total4 = sum(mut_dict[key1][key2[:-5] + '.ba.2'].values()) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
412 if 'na' in mut_dict[key1][key2[:-5] + '.ba.2'].keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
413 na4 = mut_dict[key1][key2[:-5] + '.ba.2']['na'] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
414 # na4f = na4 / total4 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
415 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
416 # na4 = na4f = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
417 na4 = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
418 if 'lowQ' in mut_dict[key1][key2[:-5] + '.ba.2'].keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
419 lowq4 = mut_dict[key1][key2[:-5] + '.ba.2']['lowQ'] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
420 # lowq4f = lowq4 / total4 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
421 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
422 # lowq4 = lowq4f = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
423 lowq4 = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
424 if ref in mut_dict[key1][key2[:-5] + '.ba.2'].keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
425 ref4 = mut_dict[key1][key2[:-5] + '.ba.2'][ref] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
426 ref4f = ref4 / (total4 - na4 - lowq4) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
427 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
428 ref4 = ref4f = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
429 if alt in mut_dict[key1][key2[:-5] + '.ba.2'].keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
430 alt4 = mut_dict[key1][key2[:-5] + '.ba.2'][alt] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
431 alt4f = alt4 / (total4 - na4 - lowq4) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
432 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
433 alt4 = alt4f = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
434 total4new = total4 - na4 - lowq4 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
435 if (key2[:-5] + '.ba.2') in mut_read_dict.keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
436 add_mut4 = len(mut_read_dict[(key2[:-5] + '.ba.2')].keys()) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
437 if add_mut4 > 1: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
438 for k, v in mut_read_dict[(key2[:-5] + '.ba.2')].items(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
439 if k != key1 and k not in k1: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
440 if len(add_mut14) == 0: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
441 add_mut14 = str(k) + "_" + v |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
442 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
443 add_mut14 = add_mut14 + ", " + str(k) + "_" + v |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
444 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
445 total4 = total4new = na4 = lowq4 = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
446 ref4 = alt4 = ref4f = alt4f = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
447 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
448 read_pos1 = read_pos2 = read_pos3 = read_pos4 = -1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
449 read_len_median1 = read_len_median2 = read_len_median3 = read_len_median4 = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
450 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
451 if key2[:-5] + '.ab.1' in mut_read_pos_dict[key1].keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
452 read_pos1 = np.median(mut_read_pos_dict[key1][key2[:-5] + '.ab.1']) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
453 read_len_median1 = np.median(reads_dict[key1][key2[:-5] + '.ab.1']) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
454 if key2[:-5] + '.ab.2' in mut_read_pos_dict[key1].keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
455 read_pos2 = np.median(mut_read_pos_dict[key1][key2[:-5] + '.ab.2']) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
456 read_len_median2 = np.median(reads_dict[key1][key2[:-5] + '.ab.2']) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
457 if key2[:-5] + '.ba.1' in mut_read_pos_dict[key1].keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
458 read_pos3 = np.median(mut_read_pos_dict[key1][key2[:-5] + '.ba.1']) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
459 read_len_median3 = np.median(reads_dict[key1][key2[:-5] + '.ba.1']) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
460 if key2[:-5] + '.ba.2' in mut_read_pos_dict[key1].keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
461 read_pos4 = np.median(mut_read_pos_dict[key1][key2[:-5] + '.ba.2']) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
462 read_len_median4 = np.median(reads_dict[key1][key2[:-5] + '.ba.2']) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
463 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
464 used_keys.append(key2[:-5]) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
465 counts_mut += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
466 if (alt1f + alt2f + alt3f + alt4f) > 0.5: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
467 if total1new == 0: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
468 ref1f = alt1f = None |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
469 alt1ff = -1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
470 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
471 alt1ff = alt1f |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
472 if total2new == 0: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
473 ref2f = alt2f = None |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
474 alt2ff = -1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
475 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
476 alt2ff = alt2f |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
477 if total3new == 0: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
478 ref3f = alt3f = None |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
479 alt3ff = -1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
480 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
481 alt3ff = alt3f |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
482 if total4new == 0: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
483 ref4f = alt4f = None |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
484 alt4ff = -1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
485 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
486 alt4ff = alt4f |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
487 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
488 details1 = (total1, total4, total1new, total4new, ref1, ref4, alt1, alt4, ref1f, ref4f, alt1f, alt4f, na1, na4, lowq1, lowq4) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
489 details2 = (total2, total3, total2new, total3new, ref2, ref3, alt2, alt3, ref2f, ref3f, alt2f, alt3f, na2, na3, lowq2, lowq3) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
490 trimmed = False |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
491 if ((read_pos1 >= 0) and ((read_pos1 <= trim) | (abs(read_len_median1 - read_pos1) <= trim))): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
492 total1new = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
493 alt1ff = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
494 trimmed = True |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
495 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
496 if ((read_pos4 >= 0) and ((read_pos4 <= trim) | (abs(read_len_median4 - read_pos4) <= trim))): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
497 total4new = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
498 alt4ff = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
499 trimmed = True |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
500 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
501 if ((read_pos2 >= 0) and ((read_pos2 <= trim) | (abs(read_len_median2 - read_pos2) <= trim))): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
502 total2new = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
503 alt2ff = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
504 trimmed = True |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
505 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
506 if ((read_pos3 >= 0) and ((read_pos3 <= trim) | (abs(read_len_median3 - read_pos3) <= trim))): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
507 total3new = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
508 alt3ff = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
509 trimmed = True |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
510 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
511 chrom, pos = re.split(r'\#', key1) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
512 # assign tiers |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
513 if ((all(int(ij) >= 3 for ij in [total1new, total4new]) & |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
514 all(float(ij) >= 0.75 for ij in [alt1ff, alt4ff])) | |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
515 (all(int(ij) >= 3 for ij in [total2new, total3new]) & |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
516 all(float(ij) >= 0.75 for ij in [alt2ff, alt3ff]))): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
517 tier = "1.1" |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
518 counter_tier11 += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
519 tier_dict[key1]["tier 1.1"] += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
520 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
521 elif (all(int(ij) >= 1 for ij in [total1new, total2new, total3new, total4new]) & |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
522 any(int(ij) >= 3 for ij in [total1new, total4new]) & |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
523 any(int(ij) >= 3 for ij in [total2new, total3new]) & |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
524 all(float(ij) >= 0.75 for ij in [alt1ff, alt2ff, alt3ff, alt4ff])): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
525 tier = "1.2" |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
526 counter_tier12 += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
527 tier_dict[key1]["tier 1.2"] += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
528 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
529 elif ((all(int(ij) >= 1 for ij in [total1new, total4new]) & |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
530 any(int(ij) >= 3 for ij in [total1new, total4new]) & |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
531 all(float(ij) >= 0.75 for ij in [alt1ff, alt4ff])) | |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
532 (all(int(ij) >= 1 for ij in [total2new, total3new]) & |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
533 any(int(ij) >= 3 for ij in [total2new, total3new]) & |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
534 all(float(ij) >= 0.75 for ij in [alt2ff, alt3ff]))): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
535 tier = "2.1" |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
536 counter_tier21 += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
537 tier_dict[key1]["tier 2.1"] += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
538 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
539 elif (all(int(ij) >= 1 for ij in [total1new, total2new, total3new, total4new]) & |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
540 all(float(ij) >= 0.75 for ij in [alt1ff, alt2ff, alt3ff, alt4ff])): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
541 tier = "2.2" |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
542 counter_tier22 += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
543 tier_dict[key1]["tier 2.2"] += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
544 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
545 elif ((all(int(ij) >= 1 for ij in [total1new, total4new]) & |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
546 any(int(ij) >= 3 for ij in [total2new, total3new]) & |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
547 all(float(ij) >= 0.75 for ij in [alt1ff, alt4ff]) & |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
548 any(float(ij) >= 0.75 for ij in [alt2ff, alt3ff])) | |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
549 (all(int(ij) >= 1 for ij in [total2new, total3new]) & |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
550 any(int(ij) >= 3 for ij in [total1new, total4new]) & |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
551 all(float(ij) >= 0.75 for ij in [alt2ff, alt3ff]) & |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
552 any(float(ij) >= 0.75 for ij in [alt1ff, alt4ff]))): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
553 tier = "2.3" |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
554 counter_tier23 += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
555 tier_dict[key1]["tier 2.3"] += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
556 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
557 elif ((all(int(ij) >= 1 for ij in [total1new, total4new]) & |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
558 all(float(ij) >= 0.75 for ij in [alt1ff, alt4ff])) | |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
559 (all(int(ij) >= 1 for ij in [total2new, total3new]) & |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
560 all(float(ij) >= 0.75 for ij in [alt2ff, alt3ff]))): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
561 tier = "2.4" |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
562 counter_tier24 += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
563 tier_dict[key1]["tier 2.4"] += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
564 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
565 elif ((len(pure_tags_dict_short[key1]) > 1) & |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
566 (all(float(ij) >= 0.5 for ij in [alt1ff, alt4ff]) | |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
567 all(float(ij) >= 0.5 for ij in [alt2ff, alt3ff]))): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
568 tier = "3.1" |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
569 counter_tier31 += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
570 tier_dict[key1]["tier 3.1"] += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
571 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
572 elif ((all(int(ij) >= 1 for ij in [total1new, total4new]) & |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
573 all(float(ij) >= 0.5 for ij in [alt1ff, alt4ff])) | |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
574 (all(int(ij) >= 1 for ij in [total2new, total3new]) & |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
575 all(float(ij) >= 0.5 for ij in [alt2ff, alt3ff]))): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
576 tier = "3.2" |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
577 counter_tier32 += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
578 tier_dict[key1]["tier 3.2"] += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
579 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
580 elif (trimmed): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
581 tier = "4.1" |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
582 counter_tier41 += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
583 tier_dict[key1]["tier 4.1"] += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
584 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
585 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
586 tier = "4.2" |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
587 counter_tier42 += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
588 tier_dict[key1]["tier 4.2"] += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
589 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
590 var_id = '-'.join([chrom, pos, ref, alt]) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
591 sample_tag = key2[:-5] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
592 array2 = np.unique(whole_array) # remove duplicate sequences to decrease running time |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
593 # exclude identical tag from array2, to prevent comparison to itself |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
594 same_tag = np.where(array2 == sample_tag) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
595 index_array2 = np.arange(0, len(array2), 1) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
596 index_withoutSame = np.delete(index_array2, same_tag) # delete identical tag from the data |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
597 array2 = array2[index_withoutSame] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
598 if len(array2) != 0: # only perform chimera analysis if there is more than 1 variant |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
599 array1_half = sample_tag[0:int(len(sample_tag) / 2)] # mate1 part1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
600 array1_half2 = sample_tag[int(len(sample_tag) / 2):int(len(sample_tag))] # mate1 part 2 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
601 array2_half = np.array([ii[0:int(len(ii) / 2)] for ii in array2]) # mate2 part1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
602 array2_half2 = np.array([ii[int(len(ii) / 2):int(len(ii))] for ii in array2]) # mate2 part2 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
603 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
604 min_tags_list_zeros = [] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
605 chimera_tags = [] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
606 for mate_b in [False, True]: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
607 i = 0 # counter, only used to see how many HDs of tags were already calculated |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
608 if mate_b is False: # HD calculation for all a's |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
609 half1_mate1 = array1_half |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
610 half2_mate1 = array1_half2 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
611 half1_mate2 = array2_half |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
612 half2_mate2 = array2_half2 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
613 elif mate_b is True: # HD calculation for all b's |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
614 half1_mate1 = array1_half2 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
615 half2_mate1 = array1_half |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
616 half1_mate2 = array2_half2 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
617 half2_mate2 = array2_half |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
618 # calculate HD of "a" in the tag to all "a's" or "b" in the tag to all "b's" |
1
3556001ff2db
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 60dc8db809909edf44d662683b1f392b9d5964bf"
iuc
parents:
0
diff
changeset
|
619 dist = np.array([sum(map(operator.ne, half1_mate1, c)) for c in half1_mate2]) |
0
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
620 min_index = np.where(dist == dist.min()) # get index of min HD |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
621 # get all "b's" of the tag or all "a's" of the tag with minimum HD |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
622 min_tag_half2 = half2_mate2[min_index] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
623 min_tag_array2 = array2[min_index] # get whole tag with min HD |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
624 min_value = dist.min() |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
625 # calculate HD of "b" to all "b's" or "a" to all "a's" |
1
3556001ff2db
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 60dc8db809909edf44d662683b1f392b9d5964bf"
iuc
parents:
0
diff
changeset
|
626 dist_second_half = np.array([sum(map(operator.ne, half2_mate1, e)) |
0
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
627 for e in min_tag_half2]) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
628 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
629 dist2 = dist_second_half.max() |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
630 max_index = np.where(dist_second_half == dist_second_half.max())[0] # get index of max HD |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
631 max_tag = min_tag_array2[max_index] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
632 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
633 # tags which have identical parts: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
634 if min_value == 0 or dist2 == 0: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
635 min_tags_list_zeros.append(tag) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
636 chimera_tags.append(max_tag) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
637 # chimeric = True |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
638 # else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
639 # chimeric = False |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
640 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
641 # if mate_b is False: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
642 # text = "pos {}: sample tag: {}; HD a = {}; HD b' = {}; similar tag(s): {}; chimeric = {}".format(pos, sample_tag, min_value, dist2, list(max_tag), chimeric) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
643 # else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
644 # text = "pos {}: sample tag: {}; HD a' = {}; HD b = {}; similar tag(s): {}; chimeric = {}".format(pos, sample_tag, dist2, min_value, list(max_tag), chimeric) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
645 i += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
646 chimera_tags = [x for x in chimera_tags if x != []] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
647 chimera_tags_new = [] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
648 for i in chimera_tags: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
649 if len(i) > 1: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
650 for t in i: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
651 chimera_tags_new.append(t) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
652 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
653 chimera_tags_new.extend(i) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
654 chimera_tags_new = np.asarray(chimera_tags_new) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
655 chimera = ", ".join(chimera_tags_new) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
656 else: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
657 chimera = "" |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
658 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
659 if (read_pos1 == -1): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
660 read_pos1 = read_len_median1 = None |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
661 if (read_pos4 == -1): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
662 read_pos4 = read_len_median4 = None |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
663 if (read_pos2 == -1): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
664 read_pos2 = read_len_median2 = None |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
665 if (read_pos3 == -1): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
666 read_pos3 = read_len_median3 = None |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
667 line = (var_id, tier, key2[:-5], 'ab1.ba2', read_pos1, read_pos4, read_len_median1, read_len_median4, dcs_median) + details1 + (sscs_mut_ab, sscs_mut_ba, sscs_ref_ab, sscs_ref_ba, add_mut14, chimera) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
668 ws1.write_row(row, 0, line) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
669 line = ("", "", key2[:-5], 'ab2.ba1', read_pos2, read_pos3, read_len_median2, read_len_median3, dcs_median) + details2 + (sscs_mut_ab, sscs_mut_ba, sscs_ref_ab, sscs_ref_ba, add_mut23, chimera) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
670 ws1.write_row(row + 1, 0, line) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
671 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
672 ws1.conditional_format('L{}:M{}'.format(row + 1, row + 2), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
673 {'type': 'formula', |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
674 'criteria': '=OR($B${}="1.1", $B${}="1.2")'.format(row + 1, row + 1), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
675 'format': format1, |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
676 'multi_range': 'L{}:M{} T{}:U{} B{}'.format(row + 1, row + 2, row + 1, row + 2, row + 1, row + 2)}) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
677 ws1.conditional_format('L{}:M{}'.format(row + 1, row + 2), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
678 {'type': 'formula', |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
679 'criteria': '=OR($B${}="2.1", $B${}="2.2", $B${}="2.3", $B${}="2.4")'.format(row + 1, row + 1, row + 1, row + 1), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
680 'format': format3, |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
681 'multi_range': 'L{}:M{} T{}:U{} B{}'.format(row + 1, row + 2, row + 1, row + 2, row + 1, row + 2)}) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
682 ws1.conditional_format('L{}:M{}'.format(row + 1, row + 2), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
683 {'type': 'formula', |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
684 'criteria': '=$B${}>="3"'.format(row + 1), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
685 'format': format2, |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
686 'multi_range': 'L{}:M{} T{}:U{} B{}'.format(row + 1, row + 2, row + 1, row + 2, row + 1, row + 2)}) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
687 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
688 row += 3 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
689 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
690 # sheet 2 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
691 header_line2 = ('variant ID', 'cvrg', 'AC alt (all tiers)', 'AF (all tiers)', 'cvrg (tiers 1.1-2.4)', 'AC alt (tiers 1.1-2.4)', 'AF (tiers 1.1-2.4)', 'AC alt (Du Novo)', 'AF (Du Novo)', |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
692 'tier 1.1', 'tier 1.2', 'tier 2.1', 'tier 2.2', 'tier 2.3', 'tier 2.4', |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
693 'tier 3.1', 'tier 3.2', 'tier 4.1', 'tier 4.2', 'AF 1.1-1.2', 'AF 1.1-2.1', 'AF 1.1-2.2', |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
694 'AF 1.1-2.3', 'AF 1.1-2.4', 'AF 1.1-3.1', 'AF 1.1-3.2', 'AF 1.1-4.1', 'AF 1.1-4.2') |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
695 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
696 ws2.write_row(0, 0, header_line2) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
697 row = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
698 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
699 for key1, value1 in sorted(tier_dict.items()): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
700 if key1 in pure_tags_dict_short.keys(): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
701 i = np.where(np.array(['#'.join(str(i) for i in z) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
702 for z in zip(mut_array[:, 1], mut_array[:, 2])]) == key1)[0][0] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
703 ref = mut_array[i, 9] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
704 alt = mut_array[i, 10] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
705 chrom, pos = re.split(r'\#', key1) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
706 ref_count = cvrg_dict[key1][0] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
707 alt_count = cvrg_dict[key1][1] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
708 cvrg = ref_count + alt_count |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
709 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
710 var_id = '-'.join([chrom, pos, ref, alt]) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
711 lst = [var_id, cvrg] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
712 used_tiers = [] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
713 cum_af = [] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
714 for key2, value2 in sorted(value1.items()): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
715 # calculate cummulative AF |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
716 used_tiers.append(value2) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
717 if len(used_tiers) > 1: |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
718 cum = safe_div(sum(used_tiers), cvrg) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
719 cum_af.append(cum) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
720 lst.extend([sum(used_tiers), safe_div(sum(used_tiers), cvrg), (cvrg - sum(used_tiers[-4:])), sum(used_tiers[0:6]), safe_div(sum(used_tiers[0:6]), (cvrg - sum(used_tiers[-4:]))), alt_count, safe_div(alt_count, cvrg)]) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
721 lst.extend(used_tiers) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
722 lst.extend(cum_af) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
723 lst = tuple(lst) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
724 ws2.write_row(row + 1, 0, lst) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
725 ws2.conditional_format('J{}:K{}'.format(row + 2, row + 2), {'type': 'formula', 'criteria': '=$J$1="tier 1.1"', 'format': format1, 'multi_range': 'J{}:K{} J1:K1'.format(row + 2, row + 2)}) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
726 ws2.conditional_format('L{}:O{}'.format(row + 2, row + 2), {'type': 'formula', 'criteria': '=$L$1="tier 2.1"', 'format': format3, 'multi_range': 'L{}:O{} L1:O1'.format(row + 2, row + 2)}) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
727 ws2.conditional_format('P{}:S{}'.format(row + 2, row + 2), {'type': 'formula', 'criteria': '=$P$1="tier 3.1"', 'format': format2, 'multi_range': 'P{}:S{} P1:S1'.format(row + 2, row + 2)}) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
728 row += 1 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
729 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
730 # sheet 3 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
731 sheet3 = [("tier 1.1", counter_tier11), ("tier 1.2", counter_tier12), ("tier 2.1", counter_tier21), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
732 ("tier 2.2", counter_tier22), ("tier 2.3", counter_tier23), ("tier 2.4", counter_tier24), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
733 ("tier 3.1", counter_tier31), ("tier 3.2", counter_tier32), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
734 ("tier 4.1", counter_tier41), ("tier 4.2", counter_tier42)] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
735 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
736 header = ("tier", "count") |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
737 ws3.write_row(0, 0, header) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
738 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
739 for i in range(len(sheet3)): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
740 ws3.write_row(i + 1, 0, sheet3[i]) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
741 ws3.conditional_format('A{}:B{}'.format(i + 2, i + 2), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
742 {'type': 'formula', |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
743 'criteria': '=OR($A${}="tier 1.1", $A${}="tier 1.2")'.format(i + 2, i + 2), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
744 'format': format1}) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
745 ws3.conditional_format('A{}:B{}'.format(i + 2, i + 2), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
746 {'type': 'formula', |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
747 'criteria': '=OR($A${}="tier 2.1", $A${}="tier 2.2", $A${}="tier 2.3", $A${}="tier 2.4")'.format(i + 2, i + 2, i + 2, i + 2), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
748 'format': format3}) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
749 ws3.conditional_format('A{}:B{}'.format(i + 2, i + 2), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
750 {'type': 'formula', |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
751 'criteria': '=OR($A${}="tier 3.1", $A${}="tier 3.2", $A${}="tier 4.1", $A${}="tier 4.2")'.format(i + 2, i + 2, i + 2, i + 2), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
752 'format': format2}) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
753 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
754 description_tiers = [("Tier 1.1", "both ab and ba SSCS present (>75% of the sites with alternative base) and minimal FS>=3 for both SSCS in at least one mate"), ("", ""), ("Tier 1.2", "both ab and ba SSCS present (>75% of the sites with alt. base) and mate pair validation (min. FS=1) and minimal FS>=3 for at least one of the SSCS"), ("Tier 2.1", "both ab and ba SSCS present (>75% of the sites with alt. base) and minimal FS>=3 for at least one of the SSCS in at least one mate"), ("Tier 2.2", "both ab and ba SSCS present (>75% of the sites with alt. base) and mate pair validation (min. FS=1)"), ("Tier 2.3", "both ab and ba SSCS present (>75% of the sites with alt. base) and minimal FS=1 for both SSCS in one mate and minimal FS>=3 for at least one of the SSCS in the other mate"), ("Tier 2.4", "both ab and ba SSCS present (>75% of the sites with alt. base) and minimal FS=1 for both SSCS in at least one mate"), ("Tier 3.1", "both ab and ba SSCS present (>50% of the sites with alt. base) and recurring mutation on this position"), ("Tier 3.2", "both ab and ba SSCS present (>50% of the sites with alt. base) and minimal FS>=1 for both SSCS in at least one mate"), ("Tier 4.1", "variants at the start or end of the reads"), ("Tier 4.2", "remaining variants")] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
755 examples_tiers = [[("Chr5:5-20000-11068-C-G", "1.1", "AAAAAGATGCCGACTACCTT", "ab1.ba2", "254", "228", "287", "288", "289", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
756 "3", "6", "3", "6", "0", "0", "3", "6", "0", "0", "1", "1", "0", "0", "0", "0", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
757 "4081", "4098", "5", "10", "", ""), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
758 ("", "", "AAAAAGATGCCGACTACCTT", "ab2.ba1", None, None, None, None, |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
759 "289", "0", "0", "0", "0", "0", "0", "3", "6", None, None, None, None, |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
760 "0", "0", "0", "0", "4081", "4098", "5", "10", "", "")], |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
761 [("Chr5:5-20000-11068-C-G", "1.1", "AAAAATGCGTAGAAATATGC", "ab1.ba2", "254", "228", "287", "288", "289", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
762 "33", "43", "33", "43", "0", "0", "33", "43", "0", "0", "1", "1", "0", "0", "0", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
763 "0", "4081", "4098", "5", "10", "", ""), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
764 ("", "", "AAAAATGCGTAGAAATATGC", "ab2.ba1", "11068", "268", "268", "270", "288", "289", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
765 "11", "34", "10", "27", "0", "0", "10", "27", "0", "0", "1", "1", "0", "0", "1", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
766 "7", "4081", "4098", "5", "10", "", "")], |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
767 [("Chr5:5-20000-10776-G-T", "1.2", "CTATGACCCGTGAGCCCATG", "ab1.ba2", "132", "132", "287", "288", "290", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
768 "4", "1", "4", "1", "0", "0", "4", "1", "0", "0", "1", "1", "0", "0", "0", "0", "1", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
769 "6", "47170", "41149", "", ""), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
770 ("", "", "CTATGACCCGTGAGCCCATG", "ab2.ba1", "77", "132", "233", "200", "290", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
771 "4", "1", "4", "1", "0", "0", "4", "1", "0", "0", "1", "1", "0", "0", "0", "0", "1", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
772 "6", "47170", "41149", "", "")], |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
773 [("Chr5:5-20000-11068-C-G", "2.1", "AAAAAAACATCATACACCCA", "ab1.ba2", "246", "244", "287", "288", "289", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
774 "2", "8", "2", "8", "0", "0", "2", "8", "0", "0", "1", "1", "0", "0", "0", "0", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
775 "4081", "4098", "5", "10", "", ""), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
776 ("", "", "AAAAAAACATCATACACCCA", "ab2.ba1", None, None, None, None, |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
777 "289", "0", "0", "0", "0", "0", "0", "0", "0", "0", "0", None, None, "0", "0", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
778 "0", "0", "4081", "4098", "5", "10", "", "")], |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
779 [("Chr5:5-20000-11068-C-G", "2.2", "ATCAGCCATGGCTATTATTG", "ab1.ba2", "72", "72", "217", "288", "289", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
780 "1", "1", "1", "1", "0", "0", "1", "1", "0", "0", "1", "1", "0", "0", "0", "0", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
781 "4081", "4098", "5", "10", "", ""), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
782 ("", "", "ATCAGCCATGGCTATTATTG", "ab2.ba1", "153", "164", "217", "260", "289", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
783 "1", "1", "1", "1", "0", "0", "1", "1", "0", "0", "1", "1", "0", "0", "0", "0", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
784 "4081", "4098", "5", "10", "", "")], |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
785 [("Chr5:5-20000-11068-C-G", "2.3", "ATCAATATGGCCTCGCCACG", "ab1.ba2", None, None, None, None, |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
786 "289", "0", "5", "0", "5", "0", "0", "0", "5", None, None, None, "1", "0", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
787 "0", "0", "0", "4081", "4098", "5", "10", "", ""), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
788 ("", "", "ATCAATATGGCCTCGCCACG", "ab2.ba1", "202", "255", "277", "290", "289", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
789 "1", "3", "1", "3", "0", "0", "1", "3", "0", "0", "1", "1", "0", "0", "1", "7", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
790 "4081", "4098", "5", "10", "", "")], |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
791 [("Chr5:5-20000-11068-C-G", "2.4", "ATCAGCCATGGCTATTTTTT", "ab1.ba2", "72", "72", "217", "288", "289", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
792 "1", "1", "1", "1", "0", "0", "1", "1", "0", "0", "1", "1", "0", "0", "0", "0", "4081", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
793 "4098", "5", "10", "", ""), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
794 ("", "", "ATCAGCCATGGCTATTTTTT", "ab2.ba1", "153", "164", "217", "260", "289", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
795 "1", "1", "0", "0", "0", "0", "1", "1", "0", "0", "0", "0", "0", "0", "0", "0", "4081", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
796 "4098", "5", "10", "", "")], |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
797 [("Chr5:5-20000-10776-G-T", "3.1", "ATGCCTACCTCATTTGTCGT", "ab1.ba2", "46", "15", "287", "288", "290", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
798 "3", "3", "3", "2", "3", "1", "0", "1", "1", "0.5", "0", "0.5", "0", "0", "0", "1", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
799 "3", "3", "47170", "41149", "", ""), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
800 ("", "", "ATGCCTACCTCATTTGTCGT", "ab2.ba1", None, "274", None, |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
801 "288", "290", "0", "3", "0", "2", "0", "1", "0", "1", None, "0.5", None, "0.5", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
802 "0", "0", "0", "1", "3", "3", "47170", "41149", "", "")], |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
803 [("Chr5:5-20000-11315-C-T", "3.2", "ACAACATCACGTATTCAGGT", "ab1.ba2", "197", "197", "240", "255", "271", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
804 "2", "3", "2", "3", "0", "1", "2", "2", "0", "0.333333333333333", "1", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
805 "0.666666666666667", "0", "0", "0", "0", "1", "1", "6584", "6482", "", ""), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
806 ("", "", "ACAACATCACGTATTCAGGT", "ab2.ba1", "35", "35", "240", "258", "271", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
807 "2", "3", "2", "3", "0", "1", "2", "2", "0", "0.333333333333333", "1", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
808 "0.666666666666667", "0", "0", "0", "0", "1", "1", "6584", "6482", "", "")], |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
809 [("Chr5:5-20000-13983-G-C", "4.1", "AAAAAAAGAATAACCCACAC", "ab1.ba2", "0", "0", "255", "276", "269", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
810 "5", "6", "5", "6", "0", "0", "5", "6", "0", "0", "1", "1", "0", "0", "0", "0", "1", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
811 "1", "5348", "5350", "", ""), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
812 ("", "", "AAAAAAAGAATAACCCACAC", "ab2.ba1", None, None, None, None, |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
813 "269", "0", "0", "0", "0", "0", "0", "0", "0", None, None, None, None, "0", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
814 "0", "0", "0", "1", "1", "5348", "5350", "", "")], |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
815 [("Chr5:5-20000-13983-G-C", "4.2", "ATGTTGTGAATAACCCACAC", "ab1.ba2", "209", "186", "255", "276", "269", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
816 "0", "6", "0", "6", "0", "0", "0", "6", "0", "0", "0", "1", "0", "0", "0", "0", "1", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
817 "1", "5348", "5350", "", ""), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
818 ("", "", "ATGTTGTGAATAACCCACAC", "ab2.ba1", None, None, None, None, |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
819 "269", "0", "0", "0", "0", "0", "0", "0", "0", None, None, None, None, "0", |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
820 "0", "0", "0", "1", "1", "5348", "5350", "", "")]] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
821 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
822 ws3.write(11, 0, "Description of tiers with examples") |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
823 ws3.write_row(12, 0, header_line) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
824 row = 0 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
825 for i in range(len(description_tiers)): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
826 ws3.write_row(13 + row + i + 1, 0, description_tiers[i]) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
827 ex = examples_tiers[i] |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
828 for k in range(len(ex)): |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
829 ws3.write_row(13 + row + i + k + 2, 0, ex[k]) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
830 ws3.conditional_format('L{}:M{}'.format(13 + row + i + k + 2, 13 + row + i + k + 3), {'type': 'formula', 'criteria': '=OR($B${}="1.1", $B${}="1.2")'.format(13 + row + i + k + 2, 13 + row + i + k + 2), 'format': format1, 'multi_range': 'L{}:M{} T{}:U{} B{}'.format(13 + row + i + k + 2, 13 + row + i + k + 3, 13 + row + i + k + 2, 13 + row + i + k + 3, 13 + row + i + k + 2, 13 + row + i + k + 3)}) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
831 ws3.conditional_format('L{}:M{}'.format(13 + row + i + k + 2, 13 + row + i + k + 3), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
832 {'type': 'formula', 'criteria': '=OR($B${}="2.1",$B${}="2.2", $B${}="2.3", $B${}="2.4")'.format(13 + row + i + k + 2, 13 + row + i + k + 2, 13 + row + i + k + 2, 13 + row + i + k + 2), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
833 'format': format3, |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
834 'multi_range': 'L{}:M{} T{}:U{} B{}'.format(13 + row + i + k + 2, 13 + row + i + k + 3, 13 + row + i + k + 2, 13 + row + i + k + 3, 13 + row + i + k + 2, 13 + row + i + k + 3)}) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
835 ws3.conditional_format('L{}:M{}'.format(13 + row + i + k + 2, 13 + row + i + k + 3), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
836 {'type': 'formula', |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
837 'criteria': '=$B${}>="3"'.format(13 + row + i + k + 2), |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
838 'format': format2, |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
839 'multi_range': 'L{}:M{} T{}:U{} B{}'.format(13 + row + i + k + 2, 13 + row + i + k + 3, 13 + row + i + k + 2, 13 + row + i + k + 3, 13 + row + i + k + 2, 13 + row + i + k + 3)}) |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
840 row += 3 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
841 workbook.close() |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
842 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
843 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
844 if __name__ == '__main__': |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
parents:
diff
changeset
|
845 sys.exit(read2mut(sys.argv)) |