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comparison MirParser.py @ 0:035df35a257e draft

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author drosofff
date Mon, 29 Jun 2015 05:50:44 -0400
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children 101fec3cba04
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-1:000000000000 0:035df35a257e
1 #!/usr/bin/env python
2 # python parser module for pre-mir and mature miRNAs, guided by mirbase.org GFF3
3 # version 0.0.9 (1-6-2014)
4 # Usage MirParser.py <1:index source> <2:extraction directive> <3:output pre-mir> <4: output mature miRs> <5:mirbase GFF3>
5 # <6:pathToLatticeDataframe or "dummy_dataframe_path"> <7:Rcode or "dummy_plotCode"> <8:latticePDF or "dummy_latticePDF">
6 # <9:10:11 filePath:FileExt:FileLabel> <.. ad lib>
7
8 import sys, subprocess
9 from smRtools import *
10
11 IndexSource = sys.argv[1]
12 ExtractionDirective = sys.argv[2]
13 if ExtractionDirective == "--do_not_extract_index":
14 genomeRefFormat = "fastaSource"
15 elif ExtractionDirective == "--extract_index":
16 genomeRefFormat = "bowtieIndex"
17 OutputPre_mirs = sys.argv[3]
18 OutputMature_Mirs = sys.argv[4]
19 GFF3_file = sys.argv[5]
20 lattice = sys.argv[6]
21 Rcode = sys.argv[7]
22 latticePDF = sys.argv[8]
23 Triplets = [sys.argv[9:][i:i+3] for i in xrange(0, len(sys.argv[9:]), 3)]
24 MasterListOfGenomes = {}
25
26 for [filePath, FileExt, FileLabel] in Triplets:
27 print FileLabel
28 MasterListOfGenomes[FileLabel] = HandleSmRNAwindows (alignmentFile=filePath, alignmentFileFormat=FileExt, genomeRefFile=IndexSource, genomeRefFormat=genomeRefFormat, biosample=FileLabel)
29
30 header = ["gene"]
31 for [filePath, FileExt, FileLabel] in Triplets:
32 header.append(FileLabel)
33
34 hit_table = ["\t".join(header)] # table header: gene, sample1, sample2, sample3, etc. separated by tabulation
35
36 ## read GFF3 to subinstantiate
37 gff3 = open (GFF3_file, "r")
38 lattice_dataframe = []
39 for line in gff3:
40 if line[0] == "#": continue
41 gff_fields = line[:-1].split("\t")
42 chrom = gff_fields[0]
43 gff_name = gff_fields[-1].split("Name=")[-1].split(";")[0] # to isolate the GFF Name
44 item_upstream_coordinate = int(gff_fields[3])
45 item_downstream_coordinate = int(gff_fields[4])
46 if gff_fields[6] == "+":
47 item_polarity = "forward"
48 else:
49 item_polarity = "reverse"
50 item_line = [gff_name]
51 for sample in header[1:]:
52 count = MasterListOfGenomes[sample].instanceDict[chrom].readcount(upstream_coord=item_upstream_coordinate, downstream_coord=item_downstream_coordinate, polarity=item_polarity)
53 item_line.append(str(count))
54 ## subtreatement for lattice
55 if lattice != "dummy_dataframe_path":
56 if ("5p" not in gff_name) and ("3p" not in gff_name):
57 lattice_dataframe.append(MasterListOfGenomes[sample].instanceDict[chrom].readcoverage(upstream_coord=item_upstream_coordinate, downstream_coord=item_downstream_coordinate, windowName=gff_name+"_"+sample) )
58 ## end of subtreatement for lattice
59 hit_table.append("\t".join(item_line) )
60 gff3.close()
61
62 Fpremirs = open (OutputPre_mirs, "w")
63 print >> Fpremirs, hit_table[0]
64 finalPreList = [ i for i in sorted(hit_table[1:]) if ("5p" not in i) and ("3p" not in i)]
65 print >> Fpremirs, "\n".join(finalPreList )
66 Fpremirs.close()
67
68 Fmaturemires = open (OutputMature_Mirs, "w")
69 print >> Fmaturemires, hit_table[0]
70 finalMatureList = [ i for i in sorted(hit_table[1:]) if ("5p" in i) or ("3p" in i)]
71 print >> Fmaturemires, "\n".join(finalMatureList )
72 Fmaturemires.close()
73
74 if lattice != "dummy_dataframe_path":
75 Flattice = open(lattice, "w")
76 print >> Flattice, "%s\t%s\t%s\t%s\t%s\t%s\t%s" % ("sample", "mir", "offset", "offsetNorm", "counts","countsNorm", "polarity")
77 print >> Flattice, "\n".join(lattice_dataframe)
78 Flattice.close()
79 R_command="Rscript "+ Rcode
80 process = subprocess.Popen(R_command.split())
81 process.wait()