comparison delly.py @ 2:aac59860a454 draft

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author jeremie
date Tue, 17 Jun 2014 07:34:44 -0400
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1:6fda22b6c486 2:aac59860a454
1 #!/usr/bin/python
2
3 import argparse, os, shutil, subprocess, sys, tempfile, shlex, vcf
4
5 parser = argparse.ArgumentParser(description='')
6 parser.add_argument ( '-b', dest='bam', help='the bam file', required=True )
7 parser.add_argument ( '-t', dest='types', help='SV analysis type (DEL, DUP, INV, TRA)', nargs='+', required=True )
8 parser.add_argument ( '-q', dest='map_qual', help='min. paired-end mapping quality', default='0' )
9 parser.add_argument ( '-s', dest='mad_cutoff', help='insert size cutoff, median+s*MAD (deletions only)', default=5 )
10 parser.add_argument ( '-g', dest='genome', help='genome fasta file' )
11 parser.add_argument ( '-m', dest='min_flank', help='minimum flanking sequence size', default=13 )
12 parser.add_argument ( '-e', dest='epsilon', help='allowed epsilon deviation of PE vs. SR deletion', default=0.1 )
13 parser.add_argument ( '-o', dest='output', help='output file' )
14
15
16 def execute( cmd, output="" ):
17 tmp_dir = tempfile.mkdtemp()
18 try:
19 err = open(tmp_dir+"/errorLog", 'a')
20 if output != "":
21 out = open(output, 'w')
22 else:
23 out = subprocess.PIPE
24 process = subprocess.Popen( args=shlex.split(cmd), stdout=out, stderr=err )
25 process.wait()
26 err.close()
27 if out != subprocess.PIPE:
28 out.close()
29 except Exception, e:
30 sys.stderr.write("problem doing : %s\n" %(cmd))
31 sys.stderr.write( '%s\n\n' % str(e) )
32
33
34 def delly(args, tempDir):
35 tempOutputs=[];
36 for typ in args.types:
37 output=str(tempDir)+"/"+str(typ)
38 tempOutputs.append(output)
39 cmd = "delly %s -t %s -o %s -q %s -s %s -m %s -e %s " % (args.bam, typ, output, args.map_qual, args.mad_cutoff, args.min_flank, args.epsilon)
40 if (args.genome!="" and args.genome!=None):
41 cmd += "-g %s" % (args.genome)
42 # print ("commande = "+cmd)
43 execute( cmd )
44 return tempOutputs
45
46
47 def merge(outputs, outputFile):
48 template = vcf.Reader(filename=outputs[0])
49 vcfWriter = vcf.Writer(open(outputFile, 'w'), template)
50 for output in outputs:
51 vcfReader = vcf.Reader(filename=output)
52 for record in vcfReader:
53 vcfWriter.write_record(record)
54 return 0
55
56
57 def getVersion(program):
58 try:
59 tmp = tempfile.NamedTemporaryFile().name
60 tmp_stdout = open( tmp, 'wb' )
61 proc = subprocess.Popen( args=program, shell=True, stdout=tmp_stdout )
62 tmp_stdout.close()
63 returncode = proc.wait()
64 stdout = None
65 for line in open( tmp_stdout.name, 'rb' ):
66 if line.lower().find( 'version' ) >= 0:
67 stdout = line.strip()
68 break
69 if stdout:
70 sys.stdout.write( '%s\n' % stdout )
71 except:
72 sys.stdout.write( 'Could not determine %s version\n' % (program) )
73
74
75 def __main__():
76
77 args = parser.parse_args()
78
79 tempDir = tempfile.mkdtemp();
80 getVersion("delly")
81
82 try:
83 execute("samtools index " + args.bam)
84 except Exception, e:
85 print("problem while indexing bam file " + str(e))
86
87 try:
88 tempOutputs = delly(args, tempDir)
89 except Exception, e:
90 sys.stdout.write("problem while runing delly " + str(e))
91
92 try:
93 if args.output:
94 outputs=[]
95 for output in tempOutputs:
96 if os.path.exists(output):
97 if os.path.getsize(output)>0:
98 outputs.append(output)
99 if len(outputs)>0:
100 merge(outputs, args.output)
101 except Exception, e:
102 sys.stdout.write("problem while merging files " + str(e))
103
104 finally:
105 try:
106 if os.path.exists(tempDir):
107 shutil.rmtree(tempDir)
108 os.system("rm "+str(args.bam)+".bai")
109 except:
110 pass
111
112 if __name__=="__main__":
113 __main__()