Mercurial > repos > cmonjeau > kissplice

comparison kisspliceGWrapper.py @ 0:131c36a303ee

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Imported from capsule None
author cmonjeau
date Fri, 05 Jun 2015 11:40:36 -0400
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-1:000000000000 0:131c36a303ee
1 import subprocess, os, sys, shutil, tempfile, os.path
2 from os.path import basename, splitext
3
4 ## inputs
5 kmer_value = sys.argv[7]
6 smallc_value = sys.argv[8]
7 bigc_value = sys.argv[9]
8 output_contex_value = sys.argv[10]
9 counts_value = sys.argv[11]
10 input_dat = sys.argv[12:len(sys.argv):2] # contains filename1... filenameq
11 input_ext = sys.argv[13:len(sys.argv):2] # contains extension1... extensionq
12
13 ## tmp directory
14 tmp_dir = tempfile.mkdtemp(prefix='kissplice-galaxy.')
15
16 ## command line (init)
17 command_line = []
18 command_line.append("kissplice")
19
20 ## symlink for .fasta/q (extension required)
21 ## command line built with -r option
22 identifier = ""
23 for i in range(0,len(input_dat)):
24 tmp_input_fasta = os.path.join(tmp_dir, 'input'+str(i)+'.'+input_ext[i])
25 identifier += 'input'+str(i)+'_'
26 os.symlink(input_dat[i], tmp_input_fasta)
27 command_line.append("-r")
28 command_line.append(tmp_input_fasta)
29
30 ## command line (end)
31 opath=tmp_dir+"/results"
32 nocontext = ""
33 nosnp = ""
34 if output_contex_value == "yes":
35 command_line.extend(["-k", kmer_value,
36 "-c", smallc_value, "-C", bigc_value,
37 "--counts", counts_value, "--output-context",
38 "-o", opath, "-s"])
39 else:
40 command_line.extend(["-k", kmer_value,
41 "-c", smallc_value, "-C", bigc_value,
42 "--counts", counts_value,
43 "-o", opath, "-s"])
44
45 ## running kissplice
46 p=subprocess.Popen(command_line,
47 stdout=subprocess.PIPE,stderr=subprocess.PIPE)
48 stdoutput = p.communicate()
49
50 ## outputs
51 output_f1=sys.argv[1]
52 out1=open(output_f1, 'w' )
53 out1.write(stdoutput[0])
54 out1.close()
55
56 output_type0=sys.argv[2]
57 output_type1=sys.argv[3]
58 output_type2=sys.argv[4]
59 output_type3=sys.argv[5]
60 output_type4=sys.argv[6]
61
62 result_type0 = opath+"/"+"results_"+identifier+"k"+kmer_value+"_coherents_type_0.fa"
63 result_type1 = opath+"/"+"results_"+identifier+"k"+kmer_value+"_coherents_type_1.fa"
64 result_type2 = opath+"/"+"results_"+identifier+"k"+kmer_value+"_coherents_type_2.fa"
65 result_type3 = opath+"/"+"results_"+identifier+"k"+kmer_value+"_coherents_type_3.fa"
66 result_type4 = opath+"/"+"results_"+identifier+"k"+kmer_value+"_coherents_type_4.fa"
67
68 shutil.move(result_type0, output_type0)
69 shutil.move(result_type1, output_type1)
70 shutil.move(result_type2, output_type2)
71 shutil.move(result_type3, output_type3)
72 shutil.move(result_type4, output_type4)
73
74 ## cleaning
75 shutil.rmtree(tmp_dir)