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comparison signature.py @ 0:d613dbee3ce4

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Imported from capsule None
author drosofff
date Mon, 03 Nov 2014 10:29:28 -0500
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children 2b30861d95f4
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-1:000000000000 0:d613dbee3ce4
1 #!/usr/bin/python
2 # script for computing overlap signatures from a bowtie output
3 # Christophe Antoniewski <drosofff@gmail.com>
4 # Usage signature.py <1:input> <2:format of input> <3:minsize query> <4:maxsize query> <5:minsize target> <6:maxsize target>
5 # <7:minscope> <8:maxscope> <9:output> <10:bowtie index> <11:procedure option> <12: graph (global or lattice)>
6 # <13: R code>
7 # version 2.0.0
8
9 import sys, subprocess, argparse
10 from smRtools import *
11 from collections import defaultdict # test whether it is required
12
13 def Parser():
14 the_parser = argparse.ArgumentParser()
15 the_parser.add_argument('--input', action="store", type=str, help="input alignment file")
16 the_parser.add_argument('--inputFormat', action="store", type=str, choices=["tabular", "bam", "sam"], help="format of alignment file (tabular/bam/sam)")
17 the_parser.add_argument('--minquery', type=int, help="Minimum readsize of query reads (nt) - must be an integer")
18 the_parser.add_argument('--maxquery', type=int, help="Maximum readsize of query reads (nt) - must be an integer")
19 the_parser.add_argument('--mintarget', type=int, help="Minimum readsize of target reads (nt) - must be an integer")
20 the_parser.add_argument('--maxtarget', type=int, help="Maximum readsize of target reads (nt) - must be an integer")
21 the_parser.add_argument('--minscope', type=int, help="Minimum overlap analyzed (nt) - must be an integer")
22 the_parser.add_argument('--maxscope', type=int, help="Maximum overlap analyzed (nt) - must be an integer")
23 the_parser.add_argument('--outputOverlapDataframe', action="store", type=str, help="Overlap dataframe")
24 the_parser.add_argument('--referenceGenome', action='store', help="path to the bowtie-indexed or fasta reference")
25 the_parser.add_argument('--extract_index', action='store_true', help="specify if the reference is an indexed Bowtie reference")
26 the_parser.add_argument('--graph', action='store', choices=["global", "lattice"], help="small RNA signature is computed either globally or by item (global-lattice)")
27 the_parser.add_argument('--rcode', type=str, help="R code to be passed to the python script")
28 args = the_parser.parse_args()
29 return args
30
31 args = Parser()
32
33 if args.extract_index:
34 GenomeFormat = "bowtieIndex"
35 else:
36 GenomeFormat = "fastaSource"
37
38 if args.inputFormat == "tabular":
39 Genome = HandleSmRNAwindows (args.input, args.inputFormat, args.referenceGenome, GenomeFormat)
40 elif args.inputFormat == "sam":
41 Genome = HandleSmRNAwindows (args.input, args.inputFormat, args.referenceGenome, GenomeFormat)
42 else:
43 Genome = HandleSmRNAwindows (args.input, args.inputFormat, args.referenceGenome, GenomeFormat)
44
45 # replace objDic by Genome.instanceDict or... objDic = Genome.instanceDict
46 objDic = Genome.instanceDict
47
48 args.maxscope += 1
49
50 general_frequency_table = dict ([(i,0) for i in range(args.minscope, args.maxscope)])
51 general_percent_table = dict ([(i,0) for i in range(args.minscope, args.maxscope)])
52 OUT = open (args.outputOverlapDataframe, "w")
53
54 if args.graph == "global":
55 ###### for normalized summing of local_percent_table(s)
56 readcount_dic = {}
57 Total_read_in_objDic = 0
58 for item in objDic:
59 readcount_dic[item] = objDic[item].readcount(args.minquery, args.maxquery)
60 Total_read_in_objDic += readcount_dic[item]
61 ######
62 for x in (objDic):
63 local_frequency_table = objDic[x].signature( args.minquery, args.maxquery, args.mintarget, args.maxtarget, range(args.minscope, args.maxscope) )
64 local_percent_table = objDic[x].hannon_signature( args.minquery, args.maxquery, args.mintarget, args.maxtarget, range(args.minscope, args.maxscope) )
65 try:
66 for overlap in local_frequency_table.keys():
67 general_frequency_table[overlap] = general_frequency_table.get(overlap, 0) + local_frequency_table[overlap]
68 except:
69 pass
70 try:
71 for overlap in local_percent_table.keys():
72 general_percent_table[overlap] = general_percent_table.get(overlap, 0) + (1./Total_read_in_objDic*readcount_dic[x]*local_percent_table[overlap])
73 except:
74 pass
75 print >> OUT, "overlap\tnum of pairs\tprobability"
76 for classe in sorted(general_frequency_table):
77 print >> OUT, "%i\t%i\t%f" % (classe, general_frequency_table[classe], general_percent_table[classe])
78
79 else:
80 print >> OUT, "overlap\tnum of pairs\tprobability\titem"
81 for x in (objDic):
82 local_frequency_table = objDic[x].signature( args.minquery, args.maxquery, args.mintarget, args.maxtarget, range(args.minscope, args.maxscope) )
83 local_percent_table = objDic[x].hannon_signature( args.minquery, args.maxquery, args.mintarget, args.maxtarget, range(args.minscope, args.maxscope) )
84 for classe in range(args.minscope, args.maxscope):
85 print >> OUT, "%i\t%i\t%f\t%s" % (classe, local_frequency_table[classe], local_percent_table[classe], x)
86
87 OUT.close()
88
89 ## Run the R script that is defined in the xml using the Rscript binary provided with R.
90 R_command="Rscript "+ args.rcode
91 process = subprocess.Popen(R_command.split())