comparison rmapq_wrapper.py @ 0:f6e5bb5aa2f5 draft

Imported from capsule None
author devteam
date Mon, 19 May 2014 12:34:22 -0400
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-1:000000000000 0:f6e5bb5aa2f5
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 scorefile = sys.argv[3]
19 high_score = sys.argv[4] # -q
20 high_len = sys.argv[5] # -M
21 read_len = sys.argv[6] # -w
22 align_len = sys.argv[7] # -h
23 mismatch = sys.argv[8] # -m
24 output_file = sys.argv[9]
25
26 try:
27 float(high_score)
28 except:
29 stop_err('Invalid value for minimal quality score.')
30
31 try:
32 int(high_len)
33 except:
34 stop_err('Invalid value for minimal high quality bases.')
35
36 # first guess the read length
37 guess_read_len = 0
38 seq = ''
39 for i, line in enumerate(open(infile)):
40 line = line.rstrip('\r\n')
41 if line.startswith('>'):
42 if seq:
43 guess_read_len = len(seq)
44 break
45 else:
46 seq += line
47
48 try:
49 test = int(read_len)
50 if test == 0:
51 read_len = str(guess_read_len)
52 else:
53 assert test >= 20 and test <= 64
54 except:
55 stop_err('Invalid value for read length. Must be between 20 and 64.')
56
57
58 try:
59 int(align_len)
60 except:
61 stop_err('Invalid value for minimal length of a hit.')
62
63 try:
64 int(mismatch)
65 except:
66 stop_err('Invalid value for mismatch numbers in an alignment.')
67
68 all_files = []
69 if os.path.isdir(target_path):
70 # check target genome
71 fa_files = os.listdir(target_path)
72
73 for file in fa_files:
74 file = "%s/%s" % ( target_path, file )
75 file = os.path.normpath(file)
76 all_files.append(file)
77 else:
78 stop_err("No sequences for %s are available for search, please report this error." %(target_path))
79
80 for detail_file_path in all_files:
81 output_tempfile = tempfile.NamedTemporaryFile().name
82 command = "rmapq -q %s -M %s -h %s -w %s -m %s -Q %s -c %s %s -o %s 2>&1" % ( high_score, high_len, align_len, read_len, mismatch, scorefile, detail_file_path, infile, output_tempfile )
83 #print command
84 try:
85 os.system( command )
86 except Exception, e:
87 stop_err( str( e ) )
88
89 try:
90 assert os.system( 'cat %s >> %s' % ( output_tempfile, output_file ) ) == 0
91 except Exception, e:
92 stop_err( str( e ) )
93
94 try:
95 os.remove( output_tempfile )
96 except:
97 pass
98
99
100 if __name__ == '__main__': __main__()