Mercurial > repos > drosofff > msp_sr_readmap_and_size_histograms

annotate smRtools.py @ 0:ac7d8e55bb67 draft

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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
author drosofff
date Wed, 21 Oct 2015 11:13:18 -0400
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children be0c6b6466cc
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0
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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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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])
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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75
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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76 def RNAfold (sequence_list):
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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77 thestring= "\n".join(sequence_list)
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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78 p = subprocess.Popen(args=["RNAfold","--noPS"], stdin= subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
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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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 == "sam":
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146 # F = open (self.alignmentFile, "r")
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147 # dict = {"0":"+", "16":"-"}
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148 # for line in F:
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149 # if line[0]=='@':
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150 # continue
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151 # fields = line.split()
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152 # if fields[2] == "*": continue
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153 # polarity = dict[fields[1]]
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154 # gene = fields[2]
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155 # offset = int(fields[3])
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156 # size = len (fields[9])
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157 # if self.size_inf:
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158 # if (size>=self.size_inf and size<= self.size_sup):
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159 # self.instanceDict[gene].addread (polarity, offset, size)
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160 # self.alignedReads += 1
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161 # else:
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162 # self.instanceDict[gene].addread (polarity, offset, size)
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163 # self.alignedReads += 1
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164 # F.close()
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165 elif self.alignmentFileFormat == "bam" or self.alignmentFileFormat == "sam":
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166 import pysam
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167 samfile = pysam.Samfile(self.alignmentFile)
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168 for read in samfile:
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169 if read.tid == -1:
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170 continue # filter out unaligned reads
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171 if read.is_reverse:
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172 polarity="-"
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173 else:
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174 polarity="+"
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175 gene = samfile.getrname(read.tid)
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176 offset = read.pos
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177 size = read.qlen
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178 if self.size_inf:
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179 if (size>=self.size_inf and size<= self.size_sup):
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180 self.instanceDict[gene].addread (polarity, offset+1, size) # to correct to 1-based coordinates of SmRNAwindow
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181 self.alignedReads += 1
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182 else:
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183 self.instanceDict[gene].addread (polarity, offset+1, size) # to correct to 1-based coordinates of SmRNAwindow
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184 self.alignedReads += 1
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185 return self.instanceDict
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186
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187 # def size_histogram (self):
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188 # size_dict={}
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189 # size_dict['F']= defaultdict (int)
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190 # size_dict['R']= defaultdict (int)
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191 # size_dict['both'] = defaultdict (int)
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192 # for item in self.instanceDict:
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193 # buffer_dict_F = self.instanceDict[item].size_histogram()['F']
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194 # buffer_dict_R = self.instanceDict[item].size_histogram()['R']
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195 # for size in buffer_dict_F:
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196 # size_dict['F'][size] += buffer_dict_F[size]
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197 # for size in buffer_dict_R:
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198 # size_dict['R'][size] -= buffer_dict_R[size]
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199 # allSizeKeys = list (set (size_dict['F'].keys() + size_dict['R'].keys() ) )
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200 # for size in allSizeKeys:
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201 # size_dict['both'][size] = size_dict['F'][size] + size_dict['R'][size]
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202 # return size_dict
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203 def size_histogram (self): # in HandleSmRNAwindows
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204 '''refactored on 7-9-2014 to debug size_histogram tool'''
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205 size_dict={}
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206 size_dict['F']= defaultdict (float)
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207 size_dict['R']= defaultdict (float)
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208 size_dict['both'] = defaultdict (float)
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209 for item in self.instanceDict:
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210 buffer_dict = self.instanceDict[item].size_histogram()
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211 for polarity in ["F", "R"]:
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212 for size in buffer_dict[polarity]:
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213 size_dict[polarity][size] += buffer_dict[polarity][size]
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214 for size in buffer_dict["both"]:
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215 size_dict["both"][size] += buffer_dict["F"][size] - buffer_dict["R"][size]
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216 return size_dict
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217
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218 def CountFeatures (self, GFF3="path/to/file"):
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219 featureDict = defaultdict(int)
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220 F = open (GFF3, "r")
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221 for line in F:
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222 if line[0] == "#": continue
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223 fields = line[:-1].split()
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224 chrom, feature, leftcoord, rightcoord, polarity = fields[0], fields[2], fields[3], fields[4], fields[6]
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225 featureDict[feature] += self.instanceDict[chrom].readcount(upstream_coord=int(leftcoord), downstream_coord=int(rightcoord), polarity="both", method="destructive")
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226 F.close()
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227 return featureDict
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228
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229 class SmRNAwindow:
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230
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231 def __init__(self, gene, sequence="ATGC", windowoffset=1, biosample="Undetermined", norm=1.0):
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232 self.biosample = biosample
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233 self.sequence = sequence
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234 self.gene = gene
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235 self.windowoffset = windowoffset
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236 self.size = len(sequence)
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237 self.readDict = defaultdict(list) # with a {+/-offset:[size1, size2, ...], ...}
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238 self.matchedreadsUp = 0
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239 self.matchedreadsDown = 0
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240 self.norm=norm
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241
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242 def addread (self, polarity, offset, size):
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243 '''ATTENTION ATTENTION ATTENTION'''
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244 ''' We removed the conversion from 0 to 1 based offset, as we do this now during readparsing.'''
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245 if polarity == "+":
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246 self.readDict[offset].append(size)
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247 self.matchedreadsUp += 1
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248 else:
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249 self.readDict[-(offset + size -1)].append(size)
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250 self.matchedreadsDown += 1
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251 return
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252
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253 def barycenter (self, upstream_coord=None, downstream_coord=None):
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254 '''refactored 24-12-2013 to save memory and introduce offset filtering see readcount method for further discussion on that
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255 In this version, attempt to replace the dictionary structure by a list of tupple to save memory too'''
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256 upstream_coord = upstream_coord or self.windowoffset
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257 downstream_coord = downstream_coord or self.windowoffset+self.size-1
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258 window_size = downstream_coord - upstream_coord +1
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259 def weigthAverage (TuppleList):
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260 weightSum = 0
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261 PonderWeightSum = 0
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262 for tuple in TuppleList:
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263 PonderWeightSum += tuple[0] * tuple[1]
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264 weightSum += tuple[1]
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265 if weightSum > 0:
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266 return PonderWeightSum / float(weightSum)
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267 else:
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268 return 0
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269 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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270 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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271 Fbarycenter = (weigthAverage (forwardTuppleList) - upstream_coord) / window_size
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272 Rbarycenter = (weigthAverage (reverseTuppleList) - upstream_coord) / window_size
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273 return Fbarycenter, Rbarycenter
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274
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275 def correlation_mapper (self, reference, window_size):
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276 '''to map correlation with a sliding window 26-2-2013'''
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277 from scipy import stats
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278
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279 if window_size > self.size:
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280 return []
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281 F=open(reference, "r")
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282 reference_forward = []
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283 reference_reverse = []
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284 for line in F:
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285 fields=line.split()
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286 reference_forward.append(int(float(fields[1])))
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287 reference_reverse.append(int(float(fields[2])))
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288 F.close()
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289 local_object_forward=[]
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290 local_object_reverse=[]
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291 ## Dict to list for the local object
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292 for i in range(1, self.size+1):
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293 local_object_forward.append(len(self.readDict[i]))
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294 local_object_reverse.append(len(self.readDict[-i]))
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295 ## start compiling results by slides
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296 results=[]
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297 for coordinate in range(self.size - window_size):
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298 local_forward=local_object_forward[coordinate:coordinate + window_size]
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299 local_reverse=local_object_reverse[coordinate:coordinate + window_size]
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300 if sum(local_forward) == 0 or sum(local_reverse) == 0:
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301 continue
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302 try:
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303 reference_to_local_cor_forward = stats.spearmanr(local_forward, reference_forward)
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304 reference_to_local_cor_reverse = stats.spearmanr(local_reverse, reference_reverse)
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305 if (reference_to_local_cor_forward[0] > 0.2 or reference_to_local_cor_reverse[0]>0.2):
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306 results.append([coordinate+1, reference_to_local_cor_forward[0], reference_to_local_cor_reverse[0]])
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307 except:
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308 pass
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309 return results
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310
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311 def readcount (self, size_inf=0, size_sup=1000, upstream_coord=None, downstream_coord=None, polarity="both", method="conservative"):
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312 '''refactored 24-12-2013 to save memory and introduce offset filtering
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313 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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314 the trick is to pass None and then test
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315 polarity parameter can take "both", "forward" or "reverse" as value'''
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316 upstream_coord = upstream_coord or self.windowoffset
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317 downstream_coord = downstream_coord or self.windowoffset+self.size-1
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318 if upstream_coord == 1 and downstream_coord == self.windowoffset+self.size-1 and polarity == "both":
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319 return self.matchedreadsUp + self.matchedreadsDown
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320 if upstream_coord == 1 and downstream_coord == self.windowoffset+self.size-1 and polarity == "forward":
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321 return self.matchedreadsUp
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322 if upstream_coord == 1 and downstream_coord == self.windowoffset+self.size-1 and polarity == "reverse":
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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323 return self.matchedreadsDown
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324 n=0
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325 if polarity == "both":
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326 for offset in xrange(upstream_coord, downstream_coord+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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327 if self.readDict.has_key(offset):
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328 for read in self.readDict[offset]:
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329 if (read>=size_inf and read<= size_sup):
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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330 n += 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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331 if method != "conservative":
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332 del self.readDict[offset] ## Carefull ! precludes re-use on the self.readDict dictionary !!!!!! TEST
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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333 if self.readDict.has_key(-offset):
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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334 for read in self.readDict[-offset]:
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335 if (read>=size_inf and read<= size_sup):
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336 n += 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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337 if method != "conservative":
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338 del self.readDict[-offset]
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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339 return 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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340 elif polarity == "forward":
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341 for offset in xrange(upstream_coord, downstream_coord+1):
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342 if self.readDict.has_key(offset):
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343 for read in self.readDict[offset]:
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344 if (read>=size_inf and read<= size_sup):
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345 n += 1
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346 return 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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347 elif polarity == "reverse":
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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348 for offset in xrange(upstream_coord, downstream_coord+1):
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349 if self.readDict.has_key(-offset):
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350 for read in self.readDict[-offset]:
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351 if (read>=size_inf and read<= size_sup):
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352 n += 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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353 return 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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354
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355 def readsizes (self):
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356 '''return a dictionary of number of reads by size (the keys)'''
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357 dicsize = {}
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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358 for offset in self.readDict:
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359 for size in self.readDict[offset]:
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360 dicsize[size] = dicsize.get(size, 0) + 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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361 for offset in range (min(dicsize.keys()), max(dicsize.keys())+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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362 dicsize[size] = dicsize.get(size, 0) # to fill offsets with null values
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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363 return dicsize
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364
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365 # def size_histogram(self):
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366 # norm=self.norm
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367 # hist_dict={}
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368 # hist_dict['F']={}
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369 # hist_dict['R']={}
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370 # for offset in self.readDict:
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371 # for size in self.readDict[offset]:
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372 # if offset < 0:
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373 # hist_dict['R'][size] = hist_dict['R'].get(size, 0) - 1*norm
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374 # else:
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375 # hist_dict['F'][size] = hist_dict['F'].get(size, 0) + 1*norm
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376 # ## patch to avoid missing graphs when parsed by R-lattice. 27-08-2014. Test and validate !
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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377 # if not (hist_dict['F']) and (not hist_dict['R']):
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378 # hist_dict['F'][21] = 0
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379 # hist_dict['R'][21] = 0
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380 # ##
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381 # return hist_dict
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382
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383 def size_histogram(self, minquery=None, maxquery=None): # in SmRNAwindow
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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384 '''refactored on 7-9-2014 to debug size_histogram tool'''
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385 norm=self.norm
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386 size_dict={}
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387 size_dict['F']= defaultdict (float)
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388 size_dict['R']= defaultdict (float)
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389 size_dict['both']= defaultdict (float)
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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390 for offset in self.readDict:
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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391 for size in self.readDict[offset]:
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392 if offset < 0:
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393 size_dict['R'][size] = size_dict['R'][size] - 1*norm
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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394 else:
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395 size_dict['F'][size] = size_dict['F'][size] + 1*norm
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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396 ## patch to avoid missing graphs when parsed by R-lattice. 27-08-2014. Test and validate !
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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397 if not (size_dict['F']) and (not size_dict['R']):
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398 size_dict['F'][21] = 0
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399 size_dict['R'][21] = 0
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400 ##
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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401 allSizeKeys = list (set (size_dict['F'].keys() + size_dict['R'].keys() ) )
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402 for size in allSizeKeys:
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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diff changeset
403 size_dict['both'][size] = size_dict['F'][size] - size_dict['R'][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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diff changeset
404 if minquery:
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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diff changeset
405 for polarity in size_dict.keys():
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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diff changeset
406 for size in xrange(minquery, maxquery+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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diff changeset
407 if not size in size_dict[polarity].keys():
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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diff changeset
408 size_dict[polarity][size]=0
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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diff changeset
409 return size_dict
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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diff changeset
410
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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diff changeset
411 def statsizes (self, upstream_coord=None, downstream_coord=None):
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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diff changeset
412 ''' migration to memory saving by specifying possible subcoordinates
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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diff changeset
413 see the readcount method for further discussion'''
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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diff changeset
414 upstream_coord = upstream_coord or self.windowoffset
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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diff changeset
415 downstream_coord = downstream_coord or self.windowoffset+self.size-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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diff changeset
416 L = []
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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diff changeset
417 for offset in self.readDict:
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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418 if (abs(offset) < upstream_coord or abs(offset) > downstream_coord): continue
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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diff changeset
419 for size in self.readDict[offset]:
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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420 L.append(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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421 meansize = mean(L)
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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diff changeset
422 stdv = std(L)
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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423 mediansize = median(L)
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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424 return meansize, mediansize, stdv
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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diff changeset
425
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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diff changeset
426 def foldEnergy (self, upstream_coord=None, downstream_coord=None):
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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diff changeset
427 ''' migration to memory saving by specifying possible subcoordinates
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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diff changeset
428 see the readcount method for further discussion'''
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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diff changeset
429 upstream_coord = upstream_coord or self.windowoffset
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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430 downstream_coord = downstream_coord or self.windowoffset+self.size-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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431 Energy = RNAfold ([self.sequence[upstream_coord-1:downstream_coord] ])
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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432 return float(Energy[self.sequence[upstream_coord-1:downstream_coord]])
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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diff changeset
433
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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434 def Ufreq (self, size_scope, upstream_coord=None, downstream_coord=None):
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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diff changeset
435 ''' migration to memory saving by specifying possible subcoordinates
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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diff changeset
436 see the readcount method for further discussion. size_scope must be an interable'''
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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diff changeset
437 upstream_coord = upstream_coord or self.windowoffset
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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diff changeset
438 downstream_coord = downstream_coord or self.windowoffset+self.size-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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diff changeset
439 freqDic = {"A":0,"T":0,"G":0,"C":0, "N":0}
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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440 convertDic = {"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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diff changeset
441 for offset in self.readDict:
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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442 if (abs(offset) < upstream_coord or abs(offset) > downstream_coord): continue
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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diff changeset
443 for size in self.readDict[offset]:
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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diff changeset
444 if size in size_scope:
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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diff changeset
445 startbase = self.sequence[abs(offset)-self.windowoffset]
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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diff changeset
446 if offset < 0:
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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diff changeset
447 startbase = convertDic[startbase]
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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diff changeset
448 freqDic[startbase] += 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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diff changeset
449 base_sum = float ( sum( freqDic.values()) )
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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diff changeset
450 if base_sum == 0:
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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diff changeset
451 return "."
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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diff changeset
452 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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453 return freqDic["T"] / base_sum * 100
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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diff changeset
454
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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diff changeset
455 def Ufreq_stranded (self, size_scope, upstream_coord=None, downstream_coord=None):
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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diff changeset
456 ''' migration to memory saving by specifying possible subcoordinates
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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diff changeset
457 see the readcount method for further discussion. size_scope must be an interable
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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diff changeset
458 This method is similar to the Ufreq method but take strandness into account'''
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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diff changeset
459 upstream_coord = upstream_coord or self.windowoffset
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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diff changeset
460 downstream_coord = downstream_coord or self.windowoffset+self.size-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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diff changeset
461 freqDic = {"Afor":0,"Tfor":0,"Gfor":0,"Cfor":0, "Nfor":0,"Arev":0,"Trev":0,"Grev":0,"Crev":0, "Nrev":0}
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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diff changeset
462 convertDic = {"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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diff changeset
463 for offset in self.readDict:
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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diff changeset
464 if (abs(offset) < upstream_coord or abs(offset) > downstream_coord): continue
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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diff changeset
465 for size in self.readDict[offset]:
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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diff changeset
466 if size in size_scope:
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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diff changeset
467 startbase = self.sequence[abs(offset)-self.windowoffset]
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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diff changeset
468 if offset < 0:
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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diff changeset
469 startbase = convertDic[startbase]
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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diff changeset
470 freqDic[startbase+"rev"] += 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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diff changeset
471 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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diff changeset
472 freqDic[startbase+"for"] += 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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diff changeset
473 forward_sum = float ( freqDic["Afor"]+freqDic["Tfor"]+freqDic["Gfor"]+freqDic["Cfor"]+freqDic["Nfor"])
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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diff changeset
474 reverse_sum = float ( freqDic["Arev"]+freqDic["Trev"]+freqDic["Grev"]+freqDic["Crev"]+freqDic["Nrev"])
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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diff changeset
475 if forward_sum == 0 and reverse_sum == 0:
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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diff changeset
476 return ". | ."
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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diff changeset
477 elif reverse_sum == 0:
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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diff changeset
478 return "%s | ." % (freqDic["Tfor"] / forward_sum * 100)
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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diff changeset
479 elif forward_sum == 0:
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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diff changeset
480 return ". | %s" % (freqDic["Trev"] / reverse_sum * 100)
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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diff changeset
481 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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diff changeset
482 return "%s | %s" % (freqDic["Tfor"] / forward_sum * 100, freqDic["Trev"] / reverse_sum * 100)
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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diff changeset
483
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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diff changeset
484
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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485 def readplot (self):
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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486 norm=self.norm
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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487 readmap = {}
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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488 for offset in self.readDict.keys():
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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489 readmap[abs(offset)] = ( len(self.readDict.get(-abs(offset),[]))*norm , len(self.readDict.get(abs(offset),[]))*norm )
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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490 mylist = []
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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491 for offset in sorted(readmap):
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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492 if readmap[offset][1] != 0:
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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493 mylist.append("%s\t%s\t%s\t%s" % (self.gene, offset, readmap[offset][1], "F") )
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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494 if readmap[offset][0] != 0:
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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495 mylist.append("%s\t%s\t%s\t%s" % (self.gene, offset, -readmap[offset][0], "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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496 ## patch to avoid missing graphs when parsed by R-lattice. 27-08-2014. Test and validate !
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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497 if not mylist:
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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498 mylist.append("%s\t%s\t%s\t%s" % (self.gene, 1, 0, "F") )
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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499 ###
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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500 return mylist
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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501
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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502 def readcoverage (self, upstream_coord=None, downstream_coord=None, windowName=None):
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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503 '''Use by MirParser tool'''
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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504 upstream_coord = upstream_coord or 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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505 downstream_coord = downstream_coord or self.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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506 windowName = windowName or "%s_%s_%s" % (self.gene, upstream_coord, downstream_coord)
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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507 forORrev_coverage = dict ([(i,0) for i in xrange(1, downstream_coord-upstream_coord+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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508 totalforward = self.readcount(upstream_coord=upstream_coord, downstream_coord=downstream_coord, polarity="forward")
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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509 totalreverse = self.readcount(upstream_coord=upstream_coord, downstream_coord=downstream_coord, polarity="reverse")
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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510 if totalforward > totalreverse:
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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511 majorcoverage = "forward"
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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512 for offset in self.readDict.keys():
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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513 if (offset > 0) and ((offset-upstream_coord+1) in forORrev_coverage.keys() ):
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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514 for read in self.readDict[offset]:
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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515 for i in xrange(read):
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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516 try:
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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517 forORrev_coverage[offset-upstream_coord+1+i] += 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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518 except KeyError:
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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519 continue # a sense read may span over the downstream limit
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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520 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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521 majorcoverage = "reverse"
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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522 for offset in self.readDict.keys():
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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523 if (offset < 0) and (-offset-upstream_coord+1 in forORrev_coverage.keys() ):
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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524 for read in self.readDict[offset]:
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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525 for i in xrange(read):
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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526 try:
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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527 forORrev_coverage[-offset-upstream_coord-i] += 1 ## positive coordinates in the instance, with + for forward coverage and - for reverse coverage
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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528 except KeyError:
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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529 continue # an antisense read may span over the upstream limit
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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diff changeset
530 output_list = []
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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531 maximum = max (forORrev_coverage.values()) or 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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532 for n in sorted (forORrev_coverage):
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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533 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))
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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534 return "\n".join(output_list)
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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535
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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536
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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537 def signature (self, minquery, maxquery, mintarget, maxtarget, scope, zscore="no", upstream_coord=None, downstream_coord=None):
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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diff changeset
538 ''' migration to memory saving by specifying possible subcoordinates
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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diff changeset
539 see the readcount method for further discussion
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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diff changeset
540 scope must be a python iterable; scope define the *relative* offset range to be computed'''
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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diff changeset
541 upstream_coord = upstream_coord or self.windowoffset
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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diff changeset
542 downstream_coord = downstream_coord or self.windowoffset+self.size-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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543 query_range = range (minquery, maxquery+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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544 target_range = range (mintarget, maxtarget+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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diff changeset
545 Query_table = {}
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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diff changeset
546 Target_table = {}
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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547 frequency_table = dict ([(i, 0) for i in scope])
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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diff changeset
548 for offset in self.readDict:
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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549 if (abs(offset) < upstream_coord or abs(offset) > downstream_coord): continue
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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550 for size in self.readDict[offset]:
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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diff changeset
551 if size in query_range:
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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diff changeset
552 Query_table[offset] = Query_table.get(offset, 0) + 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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diff changeset
553 if size in target_range:
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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diff changeset
554 Target_table[offset] = Target_table.get(offset, 0) + 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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diff changeset
555 for offset in Query_table:
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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diff changeset
556 for i in scope:
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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diff changeset
557 frequency_table[i] += min(Query_table[offset], Target_table.get(-offset -i +1, 0))
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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diff changeset
558 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
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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diff changeset
559 frequency_table = dict([(i,frequency_table[i]/2) for i in frequency_table])
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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diff changeset
560 if zscore == "yes":
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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parents:
diff changeset
561 z_mean = mean(frequency_table.values() )
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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parents:
diff changeset
562 z_std = std(frequency_table.values() )
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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parents:
diff changeset
563 if z_std == 0:
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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parents:
diff changeset
564 frequency_table = dict([(i,0) for i in frequency_table] )
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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parents:
diff changeset
565 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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parents:
diff changeset
566 frequency_table = dict([(i, (frequency_table[i]- z_mean)/z_std) for i in frequency_table] )
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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parents:
diff changeset
567 return frequency_table
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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parents:
diff changeset
568
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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parents:
diff changeset
569 def hannon_signature (self, minquery, maxquery, mintarget, maxtarget, scope, upstream_coord=None, downstream_coord=None):
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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parents:
diff changeset
570 ''' migration to memory saving by specifying possible subcoordinates see the readcount method for further discussion
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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parents:
diff changeset
571 note that scope must be an iterable (a list or a tuple), which specifies the relative offsets that will be computed'''
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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parents:
diff changeset
572 upstream_coord = upstream_coord or self.windowoffset
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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parents:
diff changeset
573 downstream_coord = downstream_coord or self.windowoffset+self.size-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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parents:
diff changeset
574 query_range = range (minquery, maxquery+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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parents:
diff changeset
575 target_range = range (mintarget, maxtarget+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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parents:
diff changeset
576 Query_table = {}
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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parents:
diff changeset
577 Target_table = {}
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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parents:
diff changeset
578 Total_Query_Numb = 0
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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parents:
diff changeset
579 general_frequency_table = dict ([(i,0) for i in scope])
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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parents:
diff changeset
580 ## filtering the appropriate reads for the study
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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parents:
diff changeset
581 for offset in self.readDict:
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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parents:
diff changeset
582 if (abs(offset) < upstream_coord or abs(offset) > downstream_coord): continue
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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parents:
diff changeset
583 for size in self.readDict[offset]:
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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parents:
diff changeset
584 if size in query_range:
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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parents:
diff changeset
585 Query_table[offset] = Query_table.get(offset, 0) + 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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parents:
diff changeset
586 Total_Query_Numb += 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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parents:
diff changeset
587 if size in target_range:
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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parents:
diff changeset
588 Target_table[offset] = Target_table.get(offset, 0) + 1
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
589 for offset in Query_table:
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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parents:
diff changeset
590 frequency_table = dict ([(i,0) for i in scope])
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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parents:
diff changeset
591 number_of_targets = 0
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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parents:
diff changeset
592 for i in scope:
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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parents:
diff changeset
593 frequency_table[i] += Query_table[offset] * Target_table.get(-offset -i +1, 0)
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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parents:
diff changeset
594 number_of_targets += Target_table.get(-offset -i +1, 0)
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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parents:
diff changeset
595 for i in scope:
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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parents:
diff changeset
596 try:
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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parents:
diff changeset
597 general_frequency_table[i] += (1. / number_of_targets / Total_Query_Numb) * frequency_table[i]
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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parents:
diff changeset
598 except ZeroDivisionError :
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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parents:
diff changeset
599 continue
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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parents:
diff changeset
600 return general_frequency_table
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
601
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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parents:
diff changeset
602 def phasing (self, size_range, scope):
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
603 ''' to calculate autocorelation like signal - scope must be an python iterable'''
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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parents:
diff changeset
604 read_table = {}
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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parents:
diff changeset
605 total_read_number = 0
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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parents:
diff changeset
606 general_frequency_table = dict ([(i, 0) for i in scope])
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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parents:
diff changeset
607 ## read input filtering
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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parents:
diff changeset
608 for offset in self.readDict:
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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parents:
diff changeset
609 for size in self.readDict[offset]:
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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parents:
diff changeset
610 if size in size_range:
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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parents:
diff changeset
611 read_table[offset] = read_table.get(offset, 0) + 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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parents:
diff changeset
612 total_read_number += 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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parents:
diff changeset
613 ## per offset read phasing computing
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
614 for offset in read_table:
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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parents:
diff changeset
615 frequency_table = dict ([(i, 0) for i in scope]) # local frequency table
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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parents:
diff changeset
616 number_of_targets = 0
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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parents:
diff changeset
617 for i in scope:
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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parents:
diff changeset
618 if offset > 0:
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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parents:
diff changeset
619 frequency_table[i] += read_table[offset] * read_table.get(offset + i, 0)
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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parents:
diff changeset
620 number_of_targets += read_table.get(offset + i, 0)
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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parents:
diff changeset
621 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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parents:
diff changeset
622 frequency_table[i] += read_table[offset] * read_table.get(offset - i, 0)
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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parents:
diff changeset
623 number_of_targets += read_table.get(offset - i, 0)
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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parents:
diff changeset
624 ## inclusion of local frequency table in the general frequency table (all offsets average)
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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parents:
diff changeset
625 for i in scope:
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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parents:
diff changeset
626 try:
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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parents:
diff changeset
627 general_frequency_table[i] += (1. / number_of_targets / total_read_number) * frequency_table[i]
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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parents:
diff changeset
628 except ZeroDivisionError :
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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parents:
diff changeset
629 continue
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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parents:
diff changeset
630 return general_frequency_table
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
631
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
632
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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parents:
diff changeset
633
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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parents:
diff changeset
634 def z_signature (self, minquery, maxquery, mintarget, maxtarget, scope):
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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parents:
diff changeset
635 '''Must do: from numpy import mean, std, to use this method; scope must be a python iterable and defines the relative offsets to compute'''
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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parents:
diff changeset
636 frequency_table = self.signature (minquery, maxquery, mintarget, maxtarget, scope)
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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parents:
diff changeset
637 z_table = {}
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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parents:
diff changeset
638 frequency_list = [frequency_table[i] for i in sorted (frequency_table)]
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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parents:
diff changeset
639 if std(frequency_list):
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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parents:
diff changeset
640 meanlist = mean(frequency_list)
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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parents:
diff changeset
641 stdlist = std(frequency_list)
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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642 z_list = [(i-meanlist)/stdlist for i in frequency_list]
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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643 return dict (zip (sorted(frequency_table), z_list) )
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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diff changeset
644 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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645 return dict (zip (sorted(frequency_table), [0 for i in frequency_table]) )
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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diff changeset
646
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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647 def percent_signature (self, minquery, maxquery, mintarget, maxtarget, scope):
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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648 frequency_table = self.signature (minquery, maxquery, mintarget, maxtarget, scope)
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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649 total = float(sum ([self.readsizes().get(i,0) for i in set(range(minquery,maxquery)+range(mintarget,maxtarget))]) )
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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650 if total == 0:
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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651 return dict( [(i,0) for i in scope])
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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652 return dict( [(i, frequency_table[i]/total*100) for i in scope])
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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diff changeset
653
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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654 def pairer (self, overlap, minquery, maxquery, mintarget, maxtarget):
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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655 queryhash = defaultdict(list)
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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656 targethash = defaultdict(list)
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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657 query_range = range (int(minquery), int(maxquery)+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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658 target_range = range (int(mintarget), int(maxtarget)+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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659 paired_sequences = []
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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660 for offset in self.readDict: # selection of data
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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661 for size in self.readDict[offset]:
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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662 if size in query_range:
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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663 queryhash[offset].append(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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diff changeset
664 if size in target_range:
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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diff changeset
665 targethash[offset].append(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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666 for offset in queryhash:
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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667 if offset >= 0: matched_offset = -offset - overlap + 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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668 else: matched_offset = -offset - overlap + 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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diff changeset
669 if targethash[matched_offset]:
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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670 paired = min ( len(queryhash[offset]), len(targethash[matched_offset]) )
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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diff changeset
671 if offset >= 0:
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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672 for i in range (paired):
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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673 paired_sequences.append("+%s" % RNAtranslate ( self.sequence[offset:offset+queryhash[offset][i]]) )
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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674 paired_sequences.append("-%s" % RNAtranslate (antipara (self.sequence[-matched_offset-targethash[matched_offset][i]+1:-matched_offset+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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diff changeset
675 if offset < 0:
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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676 for i in range (paired):
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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677 paired_sequences.append("-%s" % RNAtranslate (antipara (self.sequence[-offset-queryhash[offset][i]+1:-offset+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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diff changeset
678 paired_sequences.append("+%s" % RNAtranslate (self.sequence[matched_offset:matched_offset+targethash[matched_offset][i]] ) )
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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679 return paired_sequences
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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diff changeset
680
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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diff changeset
681 def pairable (self, overlap, minquery, maxquery, mintarget, maxtarget):
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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682 queryhash = defaultdict(list)
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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683 targethash = defaultdict(list)
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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diff changeset
684 query_range = range (int(minquery), int(maxquery)+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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diff changeset
685 target_range = range (int(mintarget), int(maxtarget)+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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diff changeset
686 paired_sequences = []
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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687
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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688 for offset in self.readDict: # selection of data
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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689 for size in self.readDict[offset]:
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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diff changeset
690 if size in query_range:
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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691 queryhash[offset].append(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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diff changeset
692 if size in target_range:
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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diff changeset
693 targethash[offset].append(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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diff changeset
694
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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diff changeset
695 for offset in queryhash:
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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696 matched_offset = -offset - overlap + 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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diff changeset
697 if targethash[matched_offset]:
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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diff changeset
698 if offset >= 0:
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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diff changeset
699 for i in queryhash[offset]:
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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diff changeset
700 paired_sequences.append("+%s" % RNAtranslate (self.sequence[offset:offset+i]) )
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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diff changeset
701 for i in targethash[matched_offset]:
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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diff changeset
702 paired_sequences.append( "-%s" % RNAtranslate (antipara (self.sequence[-matched_offset-i+1:-matched_offset+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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diff changeset
703 if offset < 0:
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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diff changeset
704 for i in queryhash[offset]:
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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diff changeset
705 paired_sequences.append("-%s" % RNAtranslate (antipara (self.sequence[-offset-i+1:-offset+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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diff changeset
706 for i in targethash[matched_offset]:
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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diff changeset
707 paired_sequences.append("+%s" % RNAtranslate (self.sequence[matched_offset:matched_offset+i] ) )
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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diff changeset
708 return paired_sequences
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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diff changeset
709
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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diff changeset
710 def newpairable_bowtie (self, overlap, minquery, maxquery, mintarget, maxtarget):
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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diff changeset
711 ''' 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'''
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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diff changeset
712 queryhash = defaultdict(list)
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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diff changeset
713 targethash = defaultdict(list)
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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diff changeset
714 query_range = range (int(minquery), int(maxquery)+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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diff changeset
715 target_range = range (int(mintarget), int(maxtarget)+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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diff changeset
716 bowtie_output = []
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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diff changeset
717
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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diff changeset
718 for offset in self.readDict: # selection of data
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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diff changeset
719 for size in self.readDict[offset]:
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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diff changeset
720 if size in query_range:
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
721 queryhash[offset].append(size)
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
722 if size in target_range:
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
723 targethash[offset].append(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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parents:
diff changeset
724 counter = 0
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
725 for offset in queryhash:
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
726 matched_offset = -offset - overlap + 1
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
727 if targethash[matched_offset]:
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
728 if offset >= 0:
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
729 for i in queryhash[offset]:
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
730 counter += 1
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
731 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
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
732 if offset < 0:
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
733 for i in queryhash[offset]:
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
734 counter += 1
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
735 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
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
736 return bowtie_output
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
737
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
738
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
739 def __main__(bowtie_index_path, bowtie_output_path):
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
740 sequenceDic = get_fasta (bowtie_index_path)
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
741 objDic = {}
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
742 F = open (bowtie_output_path, "r") # F is the bowtie output taken as input
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
743 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
parents:
diff changeset
744 fields = line.split()
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
745 polarity = fields[1]
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
746 gene = fields[2]
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
747 offset = int(fields[3])
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
748 size = len (fields[4])
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
749 try:
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
750 objDic[gene].addread (polarity, offset, size)
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
751 except KeyError:
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
752 objDic[gene] = SmRNAwindow(gene, sequenceDic[gene])
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
753 objDic[gene].addread (polarity, offset, size)
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
754 F.close()
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
755 for gene in objDic:
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
756 print gene, objDic[gene].pairer(19,19,23,19,23)
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
757
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
drosofff
parents:
diff changeset
758 if __name__ == "__main__" : __main__(sys.argv[1], sys.argv[2])