Mercurial > repos > drosofff > msp_sr_readmap_and_size_histograms

annotate readmap.py @ 4:4efe210c91f3 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 9237338d798251fb2667280d597746e852f3ffcc-dirty
author mvdbeek
date Wed, 03 Feb 2016 11:35:00 -0500
parents 9b62e6b0d219
children bcc0c7093e7a
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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">
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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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12
ac7d8e55bb67 planemo 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 the_parser.add_argument('--rcode', type=str, help="R script")
ac7d8e55bb67 planemo 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 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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28 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
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30 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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31 if args.reference_fasta:
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32 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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33 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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34 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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35 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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36 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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37 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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38 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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39 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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40 maxquery=args.maxquery
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41 Rcode = args.rcode
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42 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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43 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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44 fileLabel=args.label
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45 normalization_factor=args.normalization_factor
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46
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47 MasterListOfGenomes = OrderedDict()
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48
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49 def 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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50 for i, filePath in enumerate(filePath):
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51 norm=normalization_factor[i]
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52 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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53 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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54 biosample=fileLabel[i], size_inf=minquery, size_sup=maxquery, norm=norm)
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55 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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56
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57 def dataframe_sanityzer (listofdatalines):
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58 Dict = defaultdict(float)
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59 for line in listofdatalines:
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60 fields= line.split("\t")
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61 Dict[fields[0]] += float (fields[2])
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62 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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63 for line in listofdatalines:
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64 fields= line.split("\t")
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65 if Dict[fields[0]] != 0:
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66 filtered_list.append(line)
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67 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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68
2
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69
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70 def listify_plottable_item(item):
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71 """
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72 plottable is a list of strings:
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73 '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
mvdbeek
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74 split on tab and return gene, coordinate, count and orientation
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75 """
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76 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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77 return gene, coordinate, count, orientation
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78
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79 def lookup_gene_length(gene, readDict):
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80 return readDict[readDict.keys()[0]].instanceDict.values()[0].size
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81
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82 def handle_start_stop_coordinates(plottable, readDict):
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83 """
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84 To ensure that the plot area always includes the correct start and end coordinates,
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85 we add an entry at start [coordinate 0] and end [last coordinate] of count 0, if these do not exist.
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86 """
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87 first_line = plottable[0]
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88 last_line = plottable[-1]
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89 gene, coordinate, count, orientation = listify_plottable_item(first_line)
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90 if not coordinate == "0":
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91 new_line = "\t".join([gene, "0", "0", "F"])
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92 plottable = [new_line] + plottable
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93 gene_length = str(lookup_gene_length(gene, readDict))
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94 gene, coordinate, count, orientation = listify_plottable_item(last_line)
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95 if not coordinate == gene_length:
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96 last_line = "\t".join([gene, gene_length, "0", "F"])
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97 plottable = plottable + [last_line]
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98 return plottable
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99
0
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100 def write_readplot_dataframe(readDict, readmap_file):
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101 listoflines = []
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102 with open(readmap_file, 'w') as readmap:
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103 print >>readmap, "gene\tcoord\tcount\tpolarity\tsample"
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104 for sample in readDict.keys():
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105 if args.gff:
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106 dict=readDict[sample]
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107 else:
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108 dict=readDict[sample].instanceDict
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109 for gene in dict.keys():
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110 plottable = dict[gene].readplot()
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111 plottable = handle_start_stop_coordinates(plottable, readDict)
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112 for line in plottable:
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113 #print >>readmap, "%s\t%s" % (line, sample)
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114 listoflines.append ("%s\t%s" % (line, sample))
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115 listoflines = dataframe_sanityzer(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=args.minquery, maxquery=args.maxquery)
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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 in xrange(args.minquery, args.maxquery):
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134 # if not size in histogram[polarity].keys():
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135 # histogram[size]=0
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136 for size, count in histogram[polarity].iteritems():
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137 #print >>size_distrib, "%s\t%s\t%s\t%s\t%s" % (gene, size, count, polarity, sample) # test, changed the order accordingly
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138 listoflines.append ("%s\t%s\t%s\t%s\t%s" % (gene, size, count, polarity, sample) )
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139 listoflines = dataframe_sanityzer(listoflines)
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140 for line in listoflines:
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141 print >>size_distrib, line
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142
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143 def gff_item_subinstances(readDict, gff3):
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144 GFFinstanceDict=OrderedDict()
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145 for sample in readDict.keys():
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146 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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147 with open(gff3) as gff:
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148 for line in gff:
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149 if line[0] == "#": continue
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150 gff_fields = line[:-1].split("\t")
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151 chrom = gff_fields[0]
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152 gff_name = gff_fields[-1].split("Name=")[-1].split(";")[0] # to isolate the GFF Name
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153 item_upstream_coordinate = int(gff_fields[3])
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154 item_downstream_coordinate = int(gff_fields[4])
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155 item_polarity = gff_fields[6]
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156 for sample in readDict.keys():
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157 ## this is not required anymore but test
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158 # if not GFFinstanceDict.has_key(sample):
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159 # GFFinstanceDict[sample]={}
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160 ####
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161 subinstance=extractsubinstance(item_upstream_coordinate, item_downstream_coordinate, readDict[sample].instanceDict[chrom])
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162 if item_polarity == '-':
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163 subinstance.readDict={key*-1:value for key, value in subinstance.readDict.iteritems()}
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164 subinstance.gene=gff_name
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165 GFFinstanceDict[sample][gff_name]=subinstance
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166 return GFFinstanceDict
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167
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168 MasterListOfGenomes=process_samples(filePath)
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169
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170 if args.gff:
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171 MasterListOfGenomes=gff_item_subinstances(MasterListOfGenomes, args.gff)
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172
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173 write_readplot_dataframe(MasterListOfGenomes, readmap_file)
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174 write_size_distribution_dataframe(MasterListOfGenomes, size_distribution_file)
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175
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176 R_command="Rscript "+ Rcode
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177 process = subprocess.Popen(R_command.split())
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178 process.wait()
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179