Mercurial > repos > drosofff > msp_sr_readmap_and_size_histograms

annotate readmap.py @ 13:7234d438f495 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 eec44c6edc352050a20a9170932be1c3cfaba7bf
author drosofff
date Wed, 20 Dec 2017 10:51:22 -0500
parents be0c6b6466cc
children
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ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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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 # python parser module for for readmaps and size distributions, guided by GFF3
ac7d8e55bb67 planemo 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 # version 0.9.1 (1-6-2014)
ac7d8e55bb67 planemo 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 # Usage readmap.py <1:index source> <2:extraction directive> <3:output pre-mir> <4: output mature miRs> <5:mirbase GFF3>
ac7d8e55bb67 planemo 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 # <6:pathToLatticeDataframe or "dummy_dataframe_path"> <7:Rcode or "dummy_plotCode"> <8:latticePDF or "dummy_latticePDF">
ac7d8e55bb67 planemo 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 # <9:10:11 filePath:FileExt:FileLabel> <.. ad lib>
ac7d8e55bb67 planemo 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
ac7d8e55bb67 planemo 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 import sys, subprocess, argparse
ac7d8e55bb67 planemo 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 from smRtools import *
ac7d8e55bb67 planemo 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 from collections import OrderedDict, 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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11 import os
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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13 def Parser():
ac7d8e55bb67 planemo 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 the_parser = argparse.ArgumentParser()
ac7d8e55bb67 planemo 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 the_parser.add_argument('--output_readmap', action="store", type=str, help="readmap dataframe")
ac7d8e55bb67 planemo 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 the_parser.add_argument('--output_size_distribution', action="store", type=str, help="size distribution dataframe")
ac7d8e55bb67 planemo 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 the_parser.add_argument('--reference_fasta', action="store", type=str, help="output 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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18 the_parser.add_argument('--reference_bowtie_index',action='store', help="paths to indexed or fasta references")
ac7d8e55bb67 planemo 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 the_parser.add_argument('--input',nargs='+', help="paths to multiple input files")
ac7d8e55bb67 planemo 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 the_parser.add_argument('--ext',nargs='+', help="input file type")
ac7d8e55bb67 planemo 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 the_parser.add_argument('--label',nargs='+', help="labels of multiple input files")
ac7d8e55bb67 planemo 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 the_parser.add_argument('--normalization_factor',nargs='+', type=float, help="Normalization factor for input 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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23 the_parser.add_argument('--gff', type=str, help="GFF containing regions of interest")
ac7d8e55bb67 planemo 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 the_parser.add_argument('--minquery', type=int, help="Minimum readsize")
ac7d8e55bb67 planemo 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 the_parser.add_argument('--maxquery', type=int, help="Maximum readsize")
ac7d8e55bb67 planemo 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 args = the_parser.parse_args()
ac7d8e55bb67 planemo 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 return args
ac7d8e55bb67 planemo 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 args=Parser()
ac7d8e55bb67 planemo 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 if args.reference_fasta:
ac7d8e55bb67 planemo 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 genomeRefFormat = "fastaSource"
ac7d8e55bb67 planemo 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 genomeRefFile = args.reference_fasta
ac7d8e55bb67 planemo 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 if args.reference_bowtie_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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34 genomeRefFormat = "bowtieIndex"
ac7d8e55bb67 planemo 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 genomeRefFile = args.reference_bowtie_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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36 readmap_file=args.output_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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37 size_distribution_file=args.output_size_distribution
ac7d8e55bb67 planemo 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 minquery=args.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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39 maxquery=args.maxquery
ac7d8e55bb67 planemo 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 filePath=args.input
ac7d8e55bb67 planemo 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 fileExt=args.ext
ac7d8e55bb67 planemo 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 fileLabel=args.label
ac7d8e55bb67 planemo 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 normalization_factor=args.normalization_factor
ac7d8e55bb67 planemo 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
ac7d8e55bb67 planemo 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 MasterListOfGenomes = OrderedDict()
ac7d8e55bb67 planemo 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
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47 def process_samples(filePath):
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48 for i, filePath in enumerate(filePath):
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49 norm=normalization_factor[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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50 print fileLabel[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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51 MasterListOfGenomes[fileLabel[i]] = HandleSmRNAwindows (alignmentFile=filePath, alignmentFileFormat=fileExt[i], genomeRefFile=genomeRefFile, genomeRefFormat=genomeRefFormat,\
ac7d8e55bb67 planemo 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 biosample=fileLabel[i], size_inf=minquery, size_sup=maxquery, norm=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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53 return MasterListOfGenomes
ac7d8e55bb67 planemo 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
8
be0c6b6466cc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
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55 def remove_null_entries(listofdatalines):
be0c6b6466cc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
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56 """
be0c6b6466cc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
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57 This function removes genes that have no reads aligned.
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58 """
be0c6b6466cc planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454
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59 Dict = defaultdict(float)
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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60 for line in listofdatalines:
ac7d8e55bb67 planemo 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 fields= line.split("\t")
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62 Dict[fields[0]] += abs(float(fields[2]))
0
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63 filtered_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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64 for line in listofdatalines:
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65 fields= line.split("\t")
ac7d8e55bb67 planemo 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 if Dict[fields[0]] != 0:
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67 filtered_list.append(line)
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68 return filtered_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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69
2
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70
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71 def listify_plottable_item(item):
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72 """
ebfc73c72652 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit c9ca5272028c778ad137601e75ddbea3459d9a05-dirty
mvdbeek
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73 plottable is a list of strings:
ebfc73c72652 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit c9ca5272028c778ad137601e75ddbea3459d9a05-dirty
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74 'FBti0020401\t78\t-1.0\tR'
ebfc73c72652 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit c9ca5272028c778ad137601e75ddbea3459d9a05-dirty
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75 split on tab and return gene, coordinate, count and orientation
ebfc73c72652 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit c9ca5272028c778ad137601e75ddbea3459d9a05-dirty
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76 """
ebfc73c72652 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit c9ca5272028c778ad137601e75ddbea3459d9a05-dirty
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77 gene, coordinate, count, orientation = item.split("\t")
ebfc73c72652 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit c9ca5272028c778ad137601e75ddbea3459d9a05-dirty
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78 return gene, coordinate, count, orientation
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79
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80 def lookup_gene_length(gene, readDict):
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81 return readDict[readDict.keys()[0]].instanceDict[gene].size
2
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82
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83 def handle_start_stop_coordinates(plottable, readDict):
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84 """
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85 To ensure that the plot area always includes the correct start and end coordinates,
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86 we add an entry at start [coordinate 0] and end [last coordinate] of count 0, if these do not exist.
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87 """
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88 first_line = plottable[0]
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89 last_line = plottable[-1]
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90 gene, coordinate, count, orientation = listify_plottable_item(first_line)
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91 if not coordinate == "0":
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92 new_line = "\t".join([gene, "0", "0", "F"])
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93 plottable = [new_line] + plottable
2
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94 gene_length = str(lookup_gene_length(gene, readDict))
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95 gene, coordinate, count, orientation = listify_plottable_item(last_line)
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96 if not coordinate == gene_length:
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97 last_line = "\t".join([gene, gene_length, "0", "F"])
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98 plottable = plottable + [last_line]
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99 return plottable
2
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100
0
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101 def write_readplot_dataframe(readDict, readmap_file):
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102 listoflines = []
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103 with open(readmap_file, 'w') as readmap:
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104 print >>readmap, "gene\tcoord\tcount\tpolarity\tsample"
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105 for sample in readDict.keys():
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106 if args.gff:
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107 dict=readDict[sample]
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108 else:
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109 dict=readDict[sample].instanceDict
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110 for gene in dict.keys():
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111 plottable = dict[gene].readplot()
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112 plottable = handle_start_stop_coordinates(plottable, readDict)
0
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113 for line in plottable:
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114 listoflines.append ("%s\t%s" % (line, sample))
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115 listoflines = remove_null_entries(listoflines)
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116 for line in listoflines:
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117 print >>readmap, line
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118
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119 def write_size_distribution_dataframe(readDict, size_distribution_file):
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120 listoflines = []
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121 with open(size_distribution_file, 'w') as size_distrib:
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122 print >>size_distrib, "gene\tsize\tcount\tpolarity\tsample" # test before was "gene\tpolarity\tsize\tcount\tsample"
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123 for sample in readDict.keys():
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124 if args.gff:
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125 dict=readDict[sample]
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126 else:
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127 dict=readDict[sample].instanceDict
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128 for gene in dict.keys():
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129 histogram = dict[gene].size_histogram(minquery=minquery, maxquery=maxquery)
0
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130 for polarity in histogram.keys():
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131 if polarity=='both':
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132 continue
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133 for size, count in histogram[polarity].iteritems():
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134 listoflines.append ("%s\t%s\t%s\t%s\t%s" % (gene, size, count, polarity, sample) )
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135 listoflines = remove_null_entries(listoflines)
0
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136 for line in listoflines:
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137 print >>size_distrib, line
0
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138
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139 def gff_item_subinstances(readDict, gff3):
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140 GFFinstanceDict=OrderedDict()
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141 for sample in readDict.keys():
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142 GFFinstanceDict[sample]={} # to implement the 2nd level of directionary in an OrderedDict Class object (would not be required with defaultdict Class)
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143 with open(gff3) as gff:
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144 for line in gff:
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145 if line[0] == "#": continue
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146 gff_fields = line[:-1].split("\t")
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147 chrom = gff_fields[0]
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148 gff_name = gff_fields[-1].split("Name=")[-1].split(";")[0] # to isolate the GFF Name
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149 item_upstream_coordinate = int(gff_fields[3])
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150 item_downstream_coordinate = int(gff_fields[4])
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151 item_polarity = gff_fields[6]
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152 for sample in readDict.keys():
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153 subinstance=extractsubinstance(item_upstream_coordinate, item_downstream_coordinate, readDict[sample].instanceDict[chrom])
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154 if item_polarity == '-':
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155 subinstance.readDict={key*-1:value for key, value in subinstance.readDict.iteritems()}
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156 subinstance.gene=gff_name
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157 GFFinstanceDict[sample][gff_name]=subinstance
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158 return GFFinstanceDict
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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160 MasterListOfGenomes=process_samples(filePath)
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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162 if args.gff:
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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163 MasterListOfGenomes=gff_item_subinstances(MasterListOfGenomes, args.gff)
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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164
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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165 write_readplot_dataframe(MasterListOfGenomes, readmap_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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166 write_size_distribution_dataframe(MasterListOfGenomes, size_distribution_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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167