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comparison rmap_wrapper.py @ 0:a0c8173dbdc9 draft

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Imported from capsule None
author devteam
date Mon, 19 May 2014 10:59:29 -0400
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-1:000000000000 0:a0c8173dbdc9
1 #!/usr/bin/env python
2
3 import os, sys, tempfile
4
5 assert sys.version_info[:2] >= (2.4)
6
7 def stop_err( msg ):
8
9 sys.stderr.write( "%s\n" % msg )
10 sys.exit()
11
12
13 def __main__():
14
15 # I/O
16 target_path = sys.argv[1]
17 infile = sys.argv[2]
18 read_len = sys.argv[3] # -w
19 align_len = sys.argv[4] # -h
20 mismatch = sys.argv[5] # -m
21 output_file = sys.argv[6]
22
23 # first guess the read length
24 guess_read_len = 0
25 seq = ''
26 for i, line in enumerate(open(infile)):
27 line = line.rstrip('\r\n')
28 if line.startswith('>'):
29 if seq:
30 guess_read_len = len(seq)
31 break
32 else:
33 seq += line
34
35 try:
36 test = int(read_len)
37 if test == 0:
38 read_len = str(guess_read_len)
39 else:
40 assert test >= 20 and test <= 64
41 except:
42 stop_err('Invalid value for read length. Must be between 20 and 64.')
43
44 try:
45 int(align_len)
46 except:
47 stop_err('Invalid value for minimal length of a hit.')
48
49 try:
50 int(mismatch)
51 #assert test >= 0 and test <= int(0.1*int(read_len))
52 except:
53 stop_err('Invalid value for mismatch numbers in an alignment.')
54
55 all_files = []
56 if os.path.isdir(target_path):
57
58 # check target genome
59 fa_files = os.listdir(target_path)
60
61 for file in fa_files:
62 file = "%s/%s" % ( target_path, file )
63 file = os.path.normpath(file)
64 all_files.append(file)
65 else:
66 stop_err("No sequences for %s are available for search, please report this error." %(target_path))
67
68 for detail_file_path in all_files:
69 output_tempfile = tempfile.NamedTemporaryFile().name
70 command = "rmap -h %s -w %s -m %s -c %s %s -o %s 2>&1" % ( align_len, read_len, mismatch, detail_file_path, infile, output_tempfile )
71 #print command
72 try:
73 os.system( command )
74 except Exception, e:
75 stop_err( str( e ) )
76
77 try:
78 os.system( 'cat %s >> %s' % ( output_tempfile, output_file ) )
79 except Exception, e:
80 stop_err( str( e ) )
81
82 try:
83 os.remove( output_tempfile )
84 except:
85 pass
86
87
88 if __name__ == '__main__': __main__()