Mercurial > repos > xuebing > sharplabtool
comparison tools/metag_tools/blat_wrapper.py @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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-1:000000000000 | 0:9071e359b9a3 |
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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 sys.stderr.write( "%s\n" % msg ) | |
9 sys.exit() | |
10 | |
11 def check_nib_file( dbkey, GALAXY_DATA_INDEX_DIR ): | |
12 nib_file = "%s/alignseq.loc" % GALAXY_DATA_INDEX_DIR | |
13 nib_path = '' | |
14 nibs = {} | |
15 for i, line in enumerate( file( nib_file ) ): | |
16 line = line.rstrip( '\r\n' ) | |
17 if line and not line.startswith( "#" ): | |
18 fields = line.split( '\t' ) | |
19 if len( fields ) < 3: | |
20 continue | |
21 if fields[0] == 'seq': | |
22 nibs[( fields[1] )] = fields[2] | |
23 if nibs.has_key( dbkey ): | |
24 nib_path = nibs[( dbkey )] | |
25 return nib_path | |
26 | |
27 def check_twobit_file( dbkey, GALAXY_DATA_INDEX_DIR ): | |
28 twobit_file = "%s/twobit.loc" % GALAXY_DATA_INDEX_DIR | |
29 twobit_path = '' | |
30 twobits = {} | |
31 for i, line in enumerate( file( twobit_file ) ): | |
32 line = line.rstrip( '\r\n' ) | |
33 if line and not line.startswith( "#" ): | |
34 fields = line.split( '\t' ) | |
35 if len( fields ) < 2: | |
36 continue | |
37 twobits[( fields[0] )] = fields[1] | |
38 if twobits.has_key( dbkey ): | |
39 twobit_path = twobits[( dbkey )] | |
40 return twobit_path | |
41 | |
42 def __main__(): | |
43 # I/O | |
44 source_format = sys.argv[1] # 0: dbkey; 1: upload file | |
45 target_file = sys.argv[2] | |
46 query_file = sys.argv[3] | |
47 output_file = sys.argv[4] | |
48 min_iden = sys.argv[5] | |
49 tile_size = sys.argv[6] | |
50 one_off = sys.argv[7] | |
51 | |
52 try: | |
53 float(min_iden) | |
54 except: | |
55 stop_err('Invalid value for minimal identity.') | |
56 | |
57 try: | |
58 test = int(tile_size) | |
59 assert test >= 6 and test <= 18 | |
60 except: | |
61 stop_err('Invalid value for tile size. DNA word size must be between 6 and 18.') | |
62 | |
63 try: | |
64 test = int(one_off) | |
65 assert test >= 0 and test <= int(tile_size) | |
66 except: | |
67 stop_err('Invalid value for mismatch numbers in the word') | |
68 | |
69 GALAXY_DATA_INDEX_DIR = sys.argv[8] | |
70 | |
71 all_files = [] | |
72 if source_format == '0': | |
73 # check target genome | |
74 dbkey = target_file | |
75 nib_path = check_nib_file( dbkey, GALAXY_DATA_INDEX_DIR ) | |
76 twobit_path = check_twobit_file( dbkey, GALAXY_DATA_INDEX_DIR ) | |
77 if not os.path.exists( nib_path ) and not os.path.exists( twobit_path ): | |
78 stop_err("No sequences are available for %s, request them by reporting this error." % dbkey) | |
79 | |
80 # check the query file, see whether all of them are legitimate sequence | |
81 if nib_path and os.path.isdir( nib_path ): | |
82 compress_files = os.listdir(nib_path) | |
83 target_path = nib_path | |
84 elif twobit_path: | |
85 compress_files = [twobit_path] | |
86 target_path = "" | |
87 else: | |
88 stop_err("Requested genome build has no available sequence.") | |
89 | |
90 for file in compress_files: | |
91 file = "%s/%s" % ( target_path, file ) | |
92 file = os.path.normpath(file) | |
93 all_files.append(file) | |
94 else: | |
95 all_files = [target_file] | |
96 | |
97 for detail_file_path in all_files: | |
98 output_tempfile = tempfile.NamedTemporaryFile().name | |
99 command = "blat %s %s %s -oneOff=%s -tileSize=%s -minIdentity=%s -mask=lower -noHead -out=pslx 2>&1" % ( detail_file_path, query_file, output_tempfile, one_off, tile_size, min_iden ) | |
100 os.system( command ) | |
101 os.system( 'cat %s >> %s' % ( output_tempfile, output_file ) ) | |
102 os.remove( output_tempfile ) | |
103 | |
104 if __name__ == '__main__': __main__() |