Mercurial > repos > drosofff > msp_sr_readmap_and_size_histograms
annotate smRtools.py @ 16:1b8108a02da3 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 16119f70b162e16eee01de1e806e180ad76149f5
author | drosofff |
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date | Wed, 20 Dec 2017 18:49:52 -0500 |
parents | be0c6b6466cc |
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ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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1 #!/usr/bin/python |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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2 # version 1 7-5-2012 unification of the SmRNAwindow class |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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3 |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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4 import sys, subprocess |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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5 from collections import defaultdict |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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6 from numpy import mean, median, std |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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7 ##Disable scipy import temporarily, as no working scipy on toolshed. |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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8 ##from scipy import stats |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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9 |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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10 def get_fasta (index="/home/galaxy/galaxy-dist/bowtie/5.37_Dmel/5.37_Dmel"): |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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11 '''This function will return a dictionary containing fasta identifiers as keys and the |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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12 sequence as values. Index must be the path to a fasta file.''' |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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13 p = subprocess.Popen(args=["bowtie-inspect","-a", "0", index], stdout=subprocess.PIPE, stderr=subprocess.STDOUT) # bowtie-inspect outputs sequences on single lines |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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14 outputlines = p.stdout.readlines() |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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15 p.wait() |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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16 item_dic = {} |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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17 for line in outputlines: |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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18 if (line[0] == ">"): |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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19 try: |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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20 item_dic[current_item] = "".join(stringlist) # to dump the sequence of the previous item - try because of the keyerror of the first item |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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21 except: pass |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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22 current_item = line[1:].rstrip().split()[0] #take the first word before space because bowtie splits headers ! |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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23 item_dic[current_item] = "" |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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24 stringlist=[] |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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25 else: |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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26 stringlist.append(line.rstrip() ) |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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27 item_dic[current_item] = "".join(stringlist) # for the last item |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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28 return item_dic |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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29 |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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30 def get_fasta_headers (index): |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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31 p = subprocess.Popen(args=["bowtie-inspect","-n", index], stdout=subprocess.PIPE, stderr=subprocess.STDOUT) # bowtie-inspect outputs sequences on single lines |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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32 outputlines = p.stdout.readlines() |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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33 p.wait() |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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34 item_dic = {} |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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35 for line in outputlines: |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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36 header = line.rstrip().split()[0] #take the first word before space because bowtie splits headers ! |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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37 item_dic[header] = 1 |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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38 return item_dic |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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39 |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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40 |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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41 def get_file_sample (file, numberoflines): |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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42 '''import random to use this function''' |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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43 F=open(file) |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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44 fullfile = F.read().splitlines() |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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45 F.close() |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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46 if len(fullfile) < numberoflines: |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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47 return "sample size exceeds file size" |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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48 return random.sample(fullfile, numberoflines) |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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49 |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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50 def get_fasta_from_history (file): |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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51 F = open (file, "r") |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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52 item_dic = {} |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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53 for line in F: |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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54 if (line[0] == ">"): |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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55 try: |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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56 item_dic[current_item] = "".join(stringlist) # to dump the sequence of the previous item - try because of the keyerror of the first item |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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57 except: pass |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
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58 current_item = line[1:-1].split()[0] #take the first word before space because bowtie splits headers ! |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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59 item_dic[current_item] = "" |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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60 stringlist=[] |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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61 else: |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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62 stringlist.append(line[:-1]) |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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63 item_dic[current_item] = "".join(stringlist) # for the last item |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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64 return item_dic |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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65 |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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66 def antipara (sequence): |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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67 antidict = {"A":"T", "T":"A", "G":"C", "C":"G", "N":"N"} |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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68 revseq = sequence[::-1] |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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69 return "".join([antidict[i] for i in revseq]) |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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70 |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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71 def RNAtranslate (sequence): |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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72 return "".join([i if i in "AGCN" else "U" for i in sequence]) |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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73 def DNAtranslate (sequence): |
ac7d8e55bb67
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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74 return "".join([i if i in "AGCN" else "T" for i in sequence]) |
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75 |
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76 def RNAfold (sequence_list): |
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77 thestring= "\n".join(sequence_list) |
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78 p = subprocess.Popen(args=["RNAfold","--noPS"], stdin= subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) |
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79 output=p.communicate(thestring)[0] |
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80 p.wait() |
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81 output=output.split("\n") |
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82 if not output[-1]: output = output[:-1] # nasty patch to remove last empty line |
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83 buffer=[] |
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84 for line in output: |
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85 if line[0] in ["N","A","T","U","G","C"]: |
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86 buffer.append(DNAtranslate(line)) |
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87 if line[0] in ["(",".",")"]: |
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88 fields=line.split("(") |
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89 energy= fields[-1] |
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90 energy = energy[:-1] # remove the ) parenthesis |
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91 energy=float(energy) |
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92 buffer.append(str(energy)) |
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93 return dict(zip(buffer[::2], buffer[1::2])) |
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94 |
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95 def extractsubinstance (start, end, instance): |
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96 ''' Testing whether this can be an function external to the class to save memory''' |
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97 subinstance = SmRNAwindow (instance.gene, instance.sequence[start-1:end], start) |
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98 subinstance.gene = "%s %s %s" % (subinstance.gene, subinstance.windowoffset, subinstance.windowoffset + subinstance.size - 1) |
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99 upcoordinate = [i for i in range(start,end+1) if instance.readDict.has_key(i) ] |
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100 downcoordinate = [-i for i in range(start,end+1) if instance.readDict.has_key(-i) ] |
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101 for i in upcoordinate: |
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102 subinstance.readDict[i]=instance.readDict[i] |
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103 for i in downcoordinate: |
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104 subinstance.readDict[i]=instance.readDict[i] |
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105 return subinstance |
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106 |
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107 class HandleSmRNAwindows: |
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108 def __init__(self, alignmentFile="~", alignmentFileFormat="tabular", genomeRefFile="~", genomeRefFormat="bowtieIndex", biosample="undetermined", size_inf=None, size_sup=1000, norm=1.0): |
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109 self.biosample = biosample |
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110 self.alignmentFile = alignmentFile |
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111 self.alignmentFileFormat = alignmentFileFormat # can be "tabular" or "sam" |
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112 self.genomeRefFile = genomeRefFile |
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113 self.genomeRefFormat = genomeRefFormat # can be "bowtieIndex" or "fastaSource" |
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114 self.alignedReads = 0 |
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115 self.instanceDict = {} |
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116 self.size_inf=size_inf |
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117 self.size_sup=size_sup |
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118 self.norm=norm |
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119 if genomeRefFormat == "bowtieIndex": |
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120 self.itemDict = get_fasta (genomeRefFile) |
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121 elif genomeRefFormat == "fastaSource": |
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122 self.itemDict = get_fasta_from_history (genomeRefFile) |
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123 for item in self.itemDict: |
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124 self.instanceDict[item] = SmRNAwindow(item, sequence=self.itemDict[item], windowoffset=1, biosample=self.biosample, norm=self.norm) # create as many instances as there is items |
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125 self.readfile() |
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126 |
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127 def readfile (self) : |
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128 if self.alignmentFileFormat == "tabular": |
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129 F = open (self.alignmentFile, "r") |
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130 for line in F: |
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131 fields = line.split() |
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132 polarity = fields[1] |
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133 gene = fields[2] |
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134 offset = int(fields[3]) |
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135 size = len (fields[4]) |
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136 if self.size_inf: |
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137 if (size>=self.size_inf and size<= self.size_sup): |
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138 self.instanceDict[gene].addread (polarity, offset+1, size) # to correct to 1-based coordinates of SmRNAwindow |
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139 self.alignedReads += 1 |
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140 else: |
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141 self.instanceDict[gene].addread (polarity, offset+1, size) # to correct to 1-based coordinates of SmRNAwindow |
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142 self.alignedReads += 1 |
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143 F.close() |
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144 return self.instanceDict |
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145 elif self.alignmentFileFormat == "bam" or self.alignmentFileFormat == "sam": |
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146 import pysam |
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147 samfile = pysam.Samfile(self.alignmentFile) |
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148 for read in samfile: |
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149 if read.tid == -1: |
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150 continue # filter out unaligned reads |
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151 if read.is_reverse: |
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152 polarity="-" |
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153 else: |
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154 polarity="+" |
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155 gene = samfile.getrname(read.tid) |
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156 offset = read.pos |
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157 size = read.qlen |
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158 if self.size_inf: |
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159 if (size>=self.size_inf and size<= self.size_sup): |
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160 self.instanceDict[gene].addread (polarity, offset+1, size) # to correct to 1-based coordinates of SmRNAwindow |
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161 self.alignedReads += 1 |
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162 else: |
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163 self.instanceDict[gene].addread (polarity, offset+1, size) # to correct to 1-based coordinates of SmRNAwindow |
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164 self.alignedReads += 1 |
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165 return self.instanceDict |
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166 |
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167 def size_histogram (self): # in HandleSmRNAwindows |
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168 '''refactored on 7-9-2014 to debug size_histogram tool''' |
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169 size_dict={} |
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170 size_dict['F']= defaultdict (float) |
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171 size_dict['R']= defaultdict (float) |
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172 size_dict['both'] = defaultdict (float) |
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173 for item in self.instanceDict: |
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174 buffer_dict = self.instanceDict[item].size_histogram() |
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175 for polarity in ["F", "R"]: |
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176 for size in buffer_dict[polarity]: |
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177 size_dict[polarity][size] += buffer_dict[polarity][size] |
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178 for size in buffer_dict["both"]: |
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179 size_dict["both"][size] += buffer_dict["F"][size] - buffer_dict["R"][size] |
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180 return size_dict |
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181 |
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182 def CountFeatures (self, GFF3="path/to/file"): |
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183 featureDict = defaultdict(int) |
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184 F = open (GFF3, "r") |
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185 for line in F: |
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186 if line[0] == "#": continue |
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187 fields = line[:-1].split() |
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188 chrom, feature, leftcoord, rightcoord, polarity = fields[0], fields[2], fields[3], fields[4], fields[6] |
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189 featureDict[feature] += self.instanceDict[chrom].readcount(upstream_coord=int(leftcoord), downstream_coord=int(rightcoord), polarity="both", method="destructive") |
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190 F.close() |
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191 return featureDict |
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192 |
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193 class SmRNAwindow: |
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194 |
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195 def __init__(self, gene, sequence="ATGC", windowoffset=1, biosample="Undetermined", norm=1.0): |
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196 self.biosample = biosample |
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197 self.sequence = sequence |
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198 self.gene = gene |
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199 self.windowoffset = windowoffset |
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200 self.size = len(sequence) |
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201 self.readDict = defaultdict(list) # with a {+/-offset:[size1, size2, ...], ...} |
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202 self.matchedreadsUp = 0 |
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203 self.matchedreadsDown = 0 |
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204 self.norm=norm |
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205 |
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206 def addread (self, polarity, offset, size): |
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207 '''ATTENTION ATTENTION ATTENTION''' |
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208 ''' We removed the conversion from 0 to 1 based offset, as we do this now during readparsing.''' |
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209 if polarity == "+": |
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210 self.readDict[offset].append(size) |
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211 self.matchedreadsUp += 1 |
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212 else: |
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213 self.readDict[-(offset + size -1)].append(size) |
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214 self.matchedreadsDown += 1 |
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215 return |
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216 |
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217 def barycenter (self, upstream_coord=None, downstream_coord=None): |
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218 '''refactored 24-12-2013 to save memory and introduce offset filtering see readcount method for further discussion on that |
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219 In this version, attempt to replace the dictionary structure by a list of tupple to save memory too''' |
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220 upstream_coord = upstream_coord or self.windowoffset |
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221 downstream_coord = downstream_coord or self.windowoffset+self.size-1 |
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222 window_size = downstream_coord - upstream_coord +1 |
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223 def weigthAverage (TuppleList): |
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224 weightSum = 0 |
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225 PonderWeightSum = 0 |
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226 for tuple in TuppleList: |
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227 PonderWeightSum += tuple[0] * tuple[1] |
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228 weightSum += tuple[1] |
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229 if weightSum > 0: |
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230 return PonderWeightSum / float(weightSum) |
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231 else: |
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232 return 0 |
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233 forwardTuppleList = [(k, len(self.readDict[k])) for k in self.readDict.keys() if (k > 0 and abs(k) >= upstream_coord and abs(k) <= downstream_coord)] # both forward and in the proper offset window |
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234 reverseTuppleList = [(-k, len(self.readDict[k])) for k in self.readDict.keys() if (k < 0 and abs(k) >= upstream_coord and abs(k) <= downstream_coord)] # both reverse and in the proper offset window |
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235 Fbarycenter = (weigthAverage (forwardTuppleList) - upstream_coord) / window_size |
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236 Rbarycenter = (weigthAverage (reverseTuppleList) - upstream_coord) / window_size |
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237 return Fbarycenter, Rbarycenter |
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238 |
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239 def correlation_mapper (self, reference, window_size): |
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240 '''to map correlation with a sliding window 26-2-2013''' |
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241 from scipy import stats |
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242 |
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243 if window_size > self.size: |
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244 return [] |
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245 F=open(reference, "r") |
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246 reference_forward = [] |
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247 reference_reverse = [] |
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248 for line in F: |
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249 fields=line.split() |
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250 reference_forward.append(int(float(fields[1]))) |
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251 reference_reverse.append(int(float(fields[2]))) |
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252 F.close() |
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253 local_object_forward=[] |
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254 local_object_reverse=[] |
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255 ## Dict to list for the local object |
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256 for i in range(1, self.size+1): |
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257 local_object_forward.append(len(self.readDict[i])) |
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258 local_object_reverse.append(len(self.readDict[-i])) |
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259 ## start compiling results by slides |
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260 results=[] |
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261 for coordinate in range(self.size - window_size): |
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262 local_forward=local_object_forward[coordinate:coordinate + window_size] |
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263 local_reverse=local_object_reverse[coordinate:coordinate + window_size] |
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264 if sum(local_forward) == 0 or sum(local_reverse) == 0: |
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265 continue |
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266 try: |
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267 reference_to_local_cor_forward = stats.spearmanr(local_forward, reference_forward) |
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268 reference_to_local_cor_reverse = stats.spearmanr(local_reverse, reference_reverse) |
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269 if (reference_to_local_cor_forward[0] > 0.2 or reference_to_local_cor_reverse[0]>0.2): |
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270 results.append([coordinate+1, reference_to_local_cor_forward[0], reference_to_local_cor_reverse[0]]) |
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271 except: |
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272 pass |
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273 return results |
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274 |
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275 def readcount (self, size_inf=0, size_sup=1000, upstream_coord=None, downstream_coord=None, polarity="both", method="conservative"): |
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276 '''refactored 24-12-2013 to save memory and introduce offset filtering |
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277 take a look at the defaut parameters that cannot be defined relatively to the instance are they are defined before instanciation |
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278 the trick is to pass None and then test |
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279 polarity parameter can take "both", "forward" or "reverse" as value''' |
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280 upstream_coord = upstream_coord or self.windowoffset |
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281 downstream_coord = downstream_coord or self.windowoffset+self.size-1 |
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282 if upstream_coord == 1 and downstream_coord == self.windowoffset+self.size-1 and polarity == "both": |
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283 return self.matchedreadsUp + self.matchedreadsDown |
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284 if upstream_coord == 1 and downstream_coord == self.windowoffset+self.size-1 and polarity == "forward": |
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285 return self.matchedreadsUp |
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286 if upstream_coord == 1 and downstream_coord == self.windowoffset+self.size-1 and polarity == "reverse": |
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287 return self.matchedreadsDown |
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288 n=0 |
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289 if polarity == "both": |
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290 for offset in xrange(upstream_coord, downstream_coord+1): |
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291 if self.readDict.has_key(offset): |
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292 for read in self.readDict[offset]: |
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293 if (read>=size_inf and read<= size_sup): |
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294 n += 1 |
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295 if method != "conservative": |
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296 del self.readDict[offset] ## Carefull ! precludes re-use on the self.readDict dictionary !!!!!! TEST |
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297 if self.readDict.has_key(-offset): |
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298 for read in self.readDict[-offset]: |
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299 if (read>=size_inf and read<= size_sup): |
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300 n += 1 |
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301 if method != "conservative": |
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302 del self.readDict[-offset] |
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303 return n |
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304 elif polarity == "forward": |
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305 for offset in xrange(upstream_coord, downstream_coord+1): |
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306 if self.readDict.has_key(offset): |
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307 for read in self.readDict[offset]: |
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308 if (read>=size_inf and read<= size_sup): |
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309 n += 1 |
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310 return n |
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311 elif polarity == "reverse": |
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312 for offset in xrange(upstream_coord, downstream_coord+1): |
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313 if self.readDict.has_key(-offset): |
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314 for read in self.readDict[-offset]: |
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315 if (read>=size_inf and read<= size_sup): |
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316 n += 1 |
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317 return n |
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318 |
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319 def readsizes (self): |
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320 '''return a dictionary of number of reads by size (the keys)''' |
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321 dicsize = {} |
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322 for offset in self.readDict: |
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323 for size in self.readDict[offset]: |
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324 dicsize[size] = dicsize.get(size, 0) + 1 |
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325 for offset in range (min(dicsize.keys()), max(dicsize.keys())+1): |
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326 dicsize[size] = dicsize.get(size, 0) # to fill offsets with null values |
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327 return dicsize |
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328 |
0
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329 |
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330 def size_histogram(self, minquery=None, maxquery=None): # in SmRNAwindow |
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331 '''refactored on 7-9-2014 to debug size_histogram tool''' |
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332 norm=self.norm |
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333 size_dict={} |
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334 size_dict['F']= defaultdict (float) |
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335 size_dict['R']= defaultdict (float) |
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336 size_dict['both']= defaultdict (float) |
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337 for offset in self.readDict: |
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338 for size in self.readDict[offset]: |
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339 if offset < 0: |
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340 size_dict['R'][size] = size_dict['R'][size] - 1*norm |
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341 else: |
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342 size_dict['F'][size] = size_dict['F'][size] + 1*norm |
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343 ## patch to avoid missing graphs when parsed by R-lattice. 27-08-2014. Test and validate ! |
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344 if not (size_dict['F']) and (not size_dict['R']): |
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345 size_dict['F'][21] = 0 |
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346 size_dict['R'][21] = 0 |
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347 ## |
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348 allSizeKeys = list (set (size_dict['F'].keys() + size_dict['R'].keys() ) ) |
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349 for size in allSizeKeys: |
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350 size_dict['both'][size] = size_dict['F'][size] - size_dict['R'][size] |
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351 if minquery: |
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352 for polarity in size_dict.keys(): |
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353 for size in xrange(minquery, maxquery+1): |
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354 if not size in size_dict[polarity].keys(): |
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355 size_dict[polarity][size]=0 |
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356 return size_dict |
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357 |
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358 def statsizes (self, upstream_coord=None, downstream_coord=None): |
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359 ''' migration to memory saving by specifying possible subcoordinates |
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360 see the readcount method for further discussion''' |
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361 upstream_coord = upstream_coord or self.windowoffset |
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362 downstream_coord = downstream_coord or self.windowoffset+self.size-1 |
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363 L = [] |
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364 for offset in self.readDict: |
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365 if (abs(offset) < upstream_coord or abs(offset) > downstream_coord): continue |
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366 for size in self.readDict[offset]: |
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367 L.append(size) |
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368 meansize = mean(L) |
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369 stdv = std(L) |
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370 mediansize = median(L) |
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371 return meansize, mediansize, stdv |
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372 |
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373 def foldEnergy (self, upstream_coord=None, downstream_coord=None): |
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374 ''' migration to memory saving by specifying possible subcoordinates |
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375 see the readcount method for further discussion''' |
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376 upstream_coord = upstream_coord or self.windowoffset |
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377 downstream_coord = downstream_coord or self.windowoffset+self.size-1 |
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378 Energy = RNAfold ([self.sequence[upstream_coord-1:downstream_coord] ]) |
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379 return float(Energy[self.sequence[upstream_coord-1:downstream_coord]]) |
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380 |
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381 def Ufreq (self, size_scope, upstream_coord=None, downstream_coord=None): |
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382 ''' migration to memory saving by specifying possible subcoordinates |
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383 see the readcount method for further discussion. size_scope must be an interable''' |
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384 upstream_coord = upstream_coord or self.windowoffset |
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385 downstream_coord = downstream_coord or self.windowoffset+self.size-1 |
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386 freqDic = {"A":0,"T":0,"G":0,"C":0, "N":0} |
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387 convertDic = {"A":"T","T":"A","G":"C","C":"G","N":"N"} |
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388 for offset in self.readDict: |
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389 if (abs(offset) < upstream_coord or abs(offset) > downstream_coord): continue |
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390 for size in self.readDict[offset]: |
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391 if size in size_scope: |
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392 startbase = self.sequence[abs(offset)-self.windowoffset] |
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393 if offset < 0: |
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394 startbase = convertDic[startbase] |
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395 freqDic[startbase] += 1 |
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396 base_sum = float ( sum( freqDic.values()) ) |
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397 if base_sum == 0: |
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398 return "." |
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399 else: |
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400 return freqDic["T"] / base_sum * 100 |
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401 |
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402 def Ufreq_stranded (self, size_scope, upstream_coord=None, downstream_coord=None): |
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403 ''' migration to memory saving by specifying possible subcoordinates |
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404 see the readcount method for further discussion. size_scope must be an interable |
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405 This method is similar to the Ufreq method but take strandness into account''' |
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406 upstream_coord = upstream_coord or self.windowoffset |
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407 downstream_coord = downstream_coord or self.windowoffset+self.size-1 |
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408 freqDic = {"Afor":0,"Tfor":0,"Gfor":0,"Cfor":0, "Nfor":0,"Arev":0,"Trev":0,"Grev":0,"Crev":0, "Nrev":0} |
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409 convertDic = {"A":"T","T":"A","G":"C","C":"G","N":"N"} |
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410 for offset in self.readDict: |
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411 if (abs(offset) < upstream_coord or abs(offset) > downstream_coord): continue |
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412 for size in self.readDict[offset]: |
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413 if size in size_scope: |
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414 startbase = self.sequence[abs(offset)-self.windowoffset] |
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415 if offset < 0: |
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416 startbase = convertDic[startbase] |
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417 freqDic[startbase+"rev"] += 1 |
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418 else: |
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419 freqDic[startbase+"for"] += 1 |
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420 forward_sum = float ( freqDic["Afor"]+freqDic["Tfor"]+freqDic["Gfor"]+freqDic["Cfor"]+freqDic["Nfor"]) |
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421 reverse_sum = float ( freqDic["Arev"]+freqDic["Trev"]+freqDic["Grev"]+freqDic["Crev"]+freqDic["Nrev"]) |
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422 if forward_sum == 0 and reverse_sum == 0: |
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423 return ". | ." |
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424 elif reverse_sum == 0: |
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425 return "%s | ." % (freqDic["Tfor"] / forward_sum * 100) |
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426 elif forward_sum == 0: |
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427 return ". | %s" % (freqDic["Trev"] / reverse_sum * 100) |
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428 else: |
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429 return "%s | %s" % (freqDic["Tfor"] / forward_sum * 100, freqDic["Trev"] / reverse_sum * 100) |
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430 |
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431 def readplot (self): |
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432 norm=self.norm |
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433 readmap = {} |
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434 for offset in self.readDict.keys(): |
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435 readmap[abs(offset)] = ( len(self.readDict.get(-abs(offset),[]))*norm , len(self.readDict.get(abs(offset),[]))*norm ) |
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436 mylist = [] |
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437 for offset in sorted(readmap): |
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438 if readmap[offset][1] != 0: |
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439 mylist.append("%s\t%s\t%s\t%s" % (self.gene, offset, readmap[offset][1], "F") ) |
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440 if readmap[offset][0] != 0: |
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441 mylist.append("%s\t%s\t%s\t%s" % (self.gene, offset, -readmap[offset][0], "R") ) |
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442 ## patch to avoid missing graphs when parsed by R-lattice. 27-08-2014. Test and validate ! |
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443 if not mylist: |
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444 mylist.append("%s\t%s\t%s\t%s" % (self.gene, 1, 0, "F") ) |
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445 ### |
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446 return mylist |
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447 |
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448 def readcoverage (self, upstream_coord=None, downstream_coord=None, windowName=None): |
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449 '''Use by MirParser tool''' |
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450 upstream_coord = upstream_coord or 1 |
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451 downstream_coord = downstream_coord or self.size |
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452 windowName = windowName or "%s_%s_%s" % (self.gene, upstream_coord, downstream_coord) |
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453 forORrev_coverage = dict ([(i,0) for i in xrange(1, downstream_coord-upstream_coord+1)]) |
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454 totalforward = self.readcount(upstream_coord=upstream_coord, downstream_coord=downstream_coord, polarity="forward") |
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455 totalreverse = self.readcount(upstream_coord=upstream_coord, downstream_coord=downstream_coord, polarity="reverse") |
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456 if totalforward > totalreverse: |
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457 majorcoverage = "forward" |
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458 for offset in self.readDict.keys(): |
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459 if (offset > 0) and ((offset-upstream_coord+1) in forORrev_coverage.keys() ): |
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460 for read in self.readDict[offset]: |
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461 for i in xrange(read): |
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462 try: |
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463 forORrev_coverage[offset-upstream_coord+1+i] += 1 |
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464 except KeyError: |
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465 continue # a sense read may span over the downstream limit |
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466 else: |
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467 majorcoverage = "reverse" |
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468 for offset in self.readDict.keys(): |
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469 if (offset < 0) and (-offset-upstream_coord+1 in forORrev_coverage.keys() ): |
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470 for read in self.readDict[offset]: |
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471 for i in xrange(read): |
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472 try: |
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473 forORrev_coverage[-offset-upstream_coord-i] += 1 ## positive coordinates in the instance, with + for forward coverage and - for reverse coverage |
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474 except KeyError: |
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475 continue # an antisense read may span over the upstream limit |
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476 output_list = [] |
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477 maximum = max (forORrev_coverage.values()) or 1 |
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478 for n in sorted (forORrev_coverage): |
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479 output_list.append("%s\t%s\t%s\t%s\t%s\t%s\t%s" % (self.biosample, windowName, n, float(n)/(downstream_coord-upstream_coord+1), forORrev_coverage[n], float(forORrev_coverage[n])/maximum, majorcoverage)) |
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480 return "\n".join(output_list) |
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481 |
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482 |
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483 def signature (self, minquery, maxquery, mintarget, maxtarget, scope, zscore="no", upstream_coord=None, downstream_coord=None): |
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484 ''' migration to memory saving by specifying possible subcoordinates |
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485 see the readcount method for further discussion |
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486 scope must be a python iterable; scope define the *relative* offset range to be computed''' |
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487 upstream_coord = upstream_coord or self.windowoffset |
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488 downstream_coord = downstream_coord or self.windowoffset+self.size-1 |
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489 query_range = range (minquery, maxquery+1) |
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490 target_range = range (mintarget, maxtarget+1) |
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491 Query_table = {} |
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492 Target_table = {} |
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493 frequency_table = dict ([(i, 0) for i in scope]) |
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494 for offset in self.readDict: |
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495 if (abs(offset) < upstream_coord or abs(offset) > downstream_coord): continue |
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496 for size in self.readDict[offset]: |
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497 if size in query_range: |
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498 Query_table[offset] = Query_table.get(offset, 0) + 1 |
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499 if size in target_range: |
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500 Target_table[offset] = Target_table.get(offset, 0) + 1 |
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501 for offset in Query_table: |
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502 for i in scope: |
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503 frequency_table[i] += min(Query_table[offset], Target_table.get(-offset -i +1, 0)) |
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504 if minquery==mintarget and maxquery==maxtarget: ## added to incorporate the division by 2 in the method (26/11/2013), see signature_options.py and lattice_signature.py |
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505 frequency_table = dict([(i,frequency_table[i]/2) for i in frequency_table]) |
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506 if zscore == "yes": |
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507 z_mean = mean(frequency_table.values() ) |
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508 z_std = std(frequency_table.values() ) |
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509 if z_std == 0: |
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510 frequency_table = dict([(i,0) for i in frequency_table] ) |
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511 else: |
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512 frequency_table = dict([(i, (frequency_table[i]- z_mean)/z_std) for i in frequency_table] ) |
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513 return frequency_table |
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514 |
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515 def hannon_signature (self, minquery, maxquery, mintarget, maxtarget, scope, upstream_coord=None, downstream_coord=None): |
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516 ''' migration to memory saving by specifying possible subcoordinates see the readcount method for further discussion |
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517 note that scope must be an iterable (a list or a tuple), which specifies the relative offsets that will be computed''' |
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518 upstream_coord = upstream_coord or self.windowoffset |
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519 downstream_coord = downstream_coord or self.windowoffset+self.size-1 |
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520 query_range = range (minquery, maxquery+1) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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521 target_range = range (mintarget, maxtarget+1) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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522 Query_table = {} |
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523 Target_table = {} |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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524 Total_Query_Numb = 0 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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525 general_frequency_table = dict ([(i,0) for i in scope]) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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526 ## filtering the appropriate reads for the study |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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527 for offset in self.readDict: |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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528 if (abs(offset) < upstream_coord or abs(offset) > downstream_coord): continue |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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529 for size in self.readDict[offset]: |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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530 if size in query_range: |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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531 Query_table[offset] = Query_table.get(offset, 0) + 1 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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532 Total_Query_Numb += 1 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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533 if size in target_range: |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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534 Target_table[offset] = Target_table.get(offset, 0) + 1 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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535 for offset in Query_table: |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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536 frequency_table = dict ([(i,0) for i in scope]) |
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537 number_of_targets = 0 |
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538 for i in scope: |
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539 frequency_table[i] += Query_table[offset] * Target_table.get(-offset -i +1, 0) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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540 number_of_targets += Target_table.get(-offset -i +1, 0) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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541 for i in scope: |
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542 try: |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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543 general_frequency_table[i] += (1. / number_of_targets / Total_Query_Numb) * frequency_table[i] |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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544 except ZeroDivisionError : |
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545 continue |
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546 return general_frequency_table |
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547 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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548 def phasing (self, size_range, scope): |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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549 ''' to calculate autocorelation like signal - scope must be an python iterable''' |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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550 read_table = {} |
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551 total_read_number = 0 |
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552 general_frequency_table = dict ([(i, 0) for i in scope]) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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553 ## read input filtering |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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554 for offset in self.readDict: |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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555 for size in self.readDict[offset]: |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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556 if size in size_range: |
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557 read_table[offset] = read_table.get(offset, 0) + 1 |
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558 total_read_number += 1 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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559 ## per offset read phasing computing |
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560 for offset in read_table: |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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561 frequency_table = dict ([(i, 0) for i in scope]) # local frequency table |
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562 number_of_targets = 0 |
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563 for i in scope: |
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564 if offset > 0: |
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565 frequency_table[i] += read_table[offset] * read_table.get(offset + i, 0) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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566 number_of_targets += read_table.get(offset + i, 0) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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567 else: |
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568 frequency_table[i] += read_table[offset] * read_table.get(offset - i, 0) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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569 number_of_targets += read_table.get(offset - i, 0) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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570 ## inclusion of local frequency table in the general frequency table (all offsets average) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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571 for i in scope: |
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572 try: |
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573 general_frequency_table[i] += (1. / number_of_targets / total_read_number) * frequency_table[i] |
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574 except ZeroDivisionError : |
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575 continue |
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576 return general_frequency_table |
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577 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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578 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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579 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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580 def z_signature (self, minquery, maxquery, mintarget, maxtarget, scope): |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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581 '''Must do: from numpy import mean, std, to use this method; scope must be a python iterable and defines the relative offsets to compute''' |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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582 frequency_table = self.signature (minquery, maxquery, mintarget, maxtarget, scope) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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583 z_table = {} |
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584 frequency_list = [frequency_table[i] for i in sorted (frequency_table)] |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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585 if std(frequency_list): |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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586 meanlist = mean(frequency_list) |
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587 stdlist = std(frequency_list) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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588 z_list = [(i-meanlist)/stdlist for i in frequency_list] |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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589 return dict (zip (sorted(frequency_table), z_list) ) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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590 else: |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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591 return dict (zip (sorted(frequency_table), [0 for i in frequency_table]) ) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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592 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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593 def percent_signature (self, minquery, maxquery, mintarget, maxtarget, scope): |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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594 frequency_table = self.signature (minquery, maxquery, mintarget, maxtarget, scope) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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595 total = float(sum ([self.readsizes().get(i,0) for i in set(range(minquery,maxquery)+range(mintarget,maxtarget))]) ) |
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596 if total == 0: |
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597 return dict( [(i,0) for i in scope]) |
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598 return dict( [(i, frequency_table[i]/total*100) for i in scope]) |
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599 |
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600 def pairer (self, overlap, minquery, maxquery, mintarget, maxtarget): |
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601 queryhash = defaultdict(list) |
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602 targethash = defaultdict(list) |
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603 query_range = range (int(minquery), int(maxquery)+1) |
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604 target_range = range (int(mintarget), int(maxtarget)+1) |
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605 paired_sequences = [] |
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606 for offset in self.readDict: # selection of data |
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607 for size in self.readDict[offset]: |
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608 if size in query_range: |
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609 queryhash[offset].append(size) |
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610 if size in target_range: |
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611 targethash[offset].append(size) |
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612 for offset in queryhash: |
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613 if offset >= 0: matched_offset = -offset - overlap + 1 |
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614 else: matched_offset = -offset - overlap + 1 |
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615 if targethash[matched_offset]: |
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616 paired = min ( len(queryhash[offset]), len(targethash[matched_offset]) ) |
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617 if offset >= 0: |
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618 for i in range (paired): |
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619 paired_sequences.append("+%s" % RNAtranslate ( self.sequence[offset:offset+queryhash[offset][i]]) ) |
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620 paired_sequences.append("-%s" % RNAtranslate (antipara (self.sequence[-matched_offset-targethash[matched_offset][i]+1:-matched_offset+1]) ) ) |
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621 if offset < 0: |
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622 for i in range (paired): |
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623 paired_sequences.append("-%s" % RNAtranslate (antipara (self.sequence[-offset-queryhash[offset][i]+1:-offset+1]) ) ) |
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624 paired_sequences.append("+%s" % RNAtranslate (self.sequence[matched_offset:matched_offset+targethash[matched_offset][i]] ) ) |
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625 return paired_sequences |
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626 |
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627 def pairable (self, overlap, minquery, maxquery, mintarget, maxtarget): |
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628 queryhash = defaultdict(list) |
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629 targethash = defaultdict(list) |
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630 query_range = range (int(minquery), int(maxquery)+1) |
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631 target_range = range (int(mintarget), int(maxtarget)+1) |
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632 paired_sequences = [] |
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633 |
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634 for offset in self.readDict: # selection of data |
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635 for size in self.readDict[offset]: |
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636 if size in query_range: |
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637 queryhash[offset].append(size) |
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638 if size in target_range: |
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639 targethash[offset].append(size) |
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640 |
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641 for offset in queryhash: |
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642 matched_offset = -offset - overlap + 1 |
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643 if targethash[matched_offset]: |
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644 if offset >= 0: |
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645 for i in queryhash[offset]: |
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646 paired_sequences.append("+%s" % RNAtranslate (self.sequence[offset:offset+i]) ) |
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647 for i in targethash[matched_offset]: |
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648 paired_sequences.append( "-%s" % RNAtranslate (antipara (self.sequence[-matched_offset-i+1:-matched_offset+1]) ) ) |
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649 if offset < 0: |
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650 for i in queryhash[offset]: |
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651 paired_sequences.append("-%s" % RNAtranslate (antipara (self.sequence[-offset-i+1:-offset+1]) ) ) |
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652 for i in targethash[matched_offset]: |
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653 paired_sequences.append("+%s" % RNAtranslate (self.sequence[matched_offset:matched_offset+i] ) ) |
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654 return paired_sequences |
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655 |
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656 def newpairable_bowtie (self, overlap, minquery, maxquery, mintarget, maxtarget): |
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657 ''' revision of pairable on 3-12-2012, with focus on the offset shift problem (bowtie is 1-based cooordinates whereas python strings are 0-based coordinates''' |
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658 queryhash = defaultdict(list) |
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659 targethash = defaultdict(list) |
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660 query_range = range (int(minquery), int(maxquery)+1) |
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661 target_range = range (int(mintarget), int(maxtarget)+1) |
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662 bowtie_output = [] |
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663 |
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664 for offset in self.readDict: # selection of data |
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665 for size in self.readDict[offset]: |
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666 if size in query_range: |
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667 queryhash[offset].append(size) |
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668 if size in target_range: |
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669 targethash[offset].append(size) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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670 counter = 0 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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671 for offset in queryhash: |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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672 matched_offset = -offset - overlap + 1 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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673 if targethash[matched_offset]: |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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674 if offset >= 0: |
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675 for i in queryhash[offset]: |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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676 counter += 1 |
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677 bowtie_output.append("%s\t%s\t%s\t%s\t%s" % (counter, "+", self.gene, offset-1, self.sequence[offset-1:offset-1+i]) ) # attention a la base 1-0 de l'offset |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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678 if offset < 0: |
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679 for i in queryhash[offset]: |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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680 counter += 1 |
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681 bowtie_output.append("%s\t%s\t%s\t%s\t%s" % (counter, "-", self.gene, -offset-i, self.sequence[-offset-i:-offset])) # attention a la base 1-0 de l'offset |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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682 return bowtie_output |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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683 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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684 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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685 def __main__(bowtie_index_path, bowtie_output_path): |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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686 sequenceDic = get_fasta (bowtie_index_path) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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687 objDic = {} |
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688 F = open (bowtie_output_path, "r") # F is the bowtie output taken as input |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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689 for line in F: |
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690 fields = line.split() |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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691 polarity = fields[1] |
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692 gene = fields[2] |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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693 offset = int(fields[3]) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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694 size = len (fields[4]) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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695 try: |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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696 objDic[gene].addread (polarity, offset, size) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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697 except KeyError: |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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698 objDic[gene] = SmRNAwindow(gene, sequenceDic[gene]) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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699 objDic[gene].addread (polarity, offset, size) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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700 F.close() |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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701 for gene in objDic: |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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702 print gene, objDic[gene].pairer(19,19,23,19,23) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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703 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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704 if __name__ == "__main__" : __main__(sys.argv[1], sys.argv[2]) |