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annotate signature.py @ 5:837e4350661f draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 2588072aa6ffd90f0c8b63c61222bd817af7c76a
author drosofff
date Thu, 21 Dec 2017 08:54:03 -0500
parents 6218b518cd16
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1 #!/usr/bin/python
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2 # script for computing overlap signatures from a bowtie output
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3 # Christophe Antoniewski <drosofff@gmail.com>
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4 # Usage signature.py <1:input> <2:format of input> <3:minsize query> <4:maxsize query> <5:minsize target> <6:maxsize target>
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5 # <7:minscope> <8:maxscope> <9:output> <10:bowtie index> <11:procedure option> <12: graph (global or lattice)>
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6 # <13: R code>
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7 # version 2.0.0
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9 import subprocess
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10 import argparse
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11 from smRtools import HandleSmRNAwindows
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14 def Parser():
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15 the_parser = argparse.ArgumentParser()
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16 the_parser.add_argument(
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17 '--input', action="store", type=str, help="input alignment file")
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18 the_parser.add_argument('--inputFormat', action="store", type=str, choices=[
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19 "tabular", "bam", "sam"], help="format of alignment file (tabular/bam/sam)")
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20 the_parser.add_argument(
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21 '--minquery', type=int, help="Minimum readsize of query reads (nt) - must be an integer")
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22 the_parser.add_argument(
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23 '--maxquery', type=int, help="Maximum readsize of query reads (nt) - must be an integer")
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24 the_parser.add_argument(
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25 '--mintarget', type=int, help="Minimum readsize of target reads (nt) - must be an integer")
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26 the_parser.add_argument(
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27 '--maxtarget', type=int, help="Maximum readsize of target reads (nt) - must be an integer")
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28 the_parser.add_argument(
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29 '--minscope', type=int, help="Minimum overlap analyzed (nt) - must be an integer")
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30 the_parser.add_argument(
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31 '--maxscope', type=int, help="Maximum overlap analyzed (nt) - must be an integer")
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32 the_parser.add_argument(
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33 '--outputOverlapDataframe', action="store", type=str, help="Overlap dataframe")
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34 the_parser.add_argument('--referenceGenome', action='store',
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35 help="path to the bowtie-indexed or fasta reference")
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36 the_parser.add_argument('--extract_index', action='store_true',
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37 help="specify if the reference is an indexed Bowtie reference")
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38 the_parser.add_argument('--graph', action='store', choices=[
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39 "global", "lattice"], help="small RNA signature is computed either globally or by item (global-lattice)")
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40 the_parser.add_argument(
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41 '--rcode', type=str, help="R code to be passed to the python script")
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42 args = the_parser.parse_args()
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43 return args
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44
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45 args = Parser()
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46
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47 if args.extract_index:
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48 GenomeFormat = "bowtieIndex"
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49 else:
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50 GenomeFormat = "fastaSource"
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51
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52 if args.inputFormat == "tabular":
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53 Genome = HandleSmRNAwindows(
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54 args.input, args.inputFormat, args.referenceGenome, GenomeFormat)
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55 elif args.inputFormat == "sam":
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56 Genome = HandleSmRNAwindows(
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57 args.input, args.inputFormat, args.referenceGenome, GenomeFormat)
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58 else:
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59 Genome = HandleSmRNAwindows(
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60 args.input, args.inputFormat, args.referenceGenome, GenomeFormat)
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61
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62 # replace objDic by Genome.instanceDict or... objDic = Genome.instanceDict
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63 objDic = Genome.instanceDict
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64
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65 args.maxscope += 1
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66
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67 general_frequency_table = dict(
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68 [(i, 0) for i in range(args.minscope, args.maxscope)])
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69 general_percent_table = dict(
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70 [(i, 0) for i in range(args.minscope, args.maxscope)])
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71 OUT = open(args.outputOverlapDataframe, "w")
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72
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73 if args.graph == "global":
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74 # for normalized summing of local_percent_table(s)
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75 readcount_dic = {}
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76 Total_read_in_objDic = 0
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77 for item in objDic:
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78 readcount_dic[item] = objDic[item].readcount(
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79 args.minquery, args.maxquery)
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80 Total_read_in_objDic += readcount_dic[item]
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81 ######
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82 for x in (objDic):
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83 local_frequency_table = objDic[x].signature(
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84 args.minquery, args.maxquery, args.mintarget, args.maxtarget, range(args.minscope, args.maxscope))
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85 local_percent_table = objDic[x].hannon_signature(
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86 args.minquery, args.maxquery, args.mintarget, args.maxtarget, range(args.minscope, args.maxscope))
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87 try:
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88 for overlap in local_frequency_table.keys():
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89 general_frequency_table[overlap] = general_frequency_table.get(
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90 overlap, 0) + local_frequency_table[overlap]
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91 except:
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92 pass
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93 try:
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94 for overlap in local_percent_table.keys():
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95 general_percent_table[overlap] = general_percent_table.get(
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96 overlap, 0) + (1. / Total_read_in_objDic * readcount_dic[x] * local_percent_table[overlap])
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97 except:
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98 pass
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99 print >> OUT, "overlap\tnum of pairs\tprobability"
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100 for classe in sorted(general_frequency_table):
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101 print >> OUT, "%i\t%i\t%f" % (
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102 classe, general_frequency_table[classe], general_percent_table[classe])
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103
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104 else:
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105 print >> OUT, "overlap\tnum of pairs\tprobability\titem"
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106 for x in (objDic):
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107 local_frequency_table = objDic[x].signature(
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108 args.minquery, args.maxquery, args.mintarget, args.maxtarget, range(args.minscope, args.maxscope))
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109 local_percent_table = objDic[x].hannon_signature(
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110 args.minquery, args.maxquery, args.mintarget, args.maxtarget, range(args.minscope, args.maxscope))
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111 for classe in range(args.minscope, args.maxscope):
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112 print >> OUT, "%i\t%i\t%f\t%s" % (
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113 classe, local_frequency_table[classe], local_percent_table[classe], x)
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114
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115 OUT.close()
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116
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117 # Run the R script that is defined in the xml using the Rscript binary
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118 # provided with R.
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119 R_command = "Rscript " + args.rcode
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120 process = subprocess.Popen(R_command.split())