root/galaxy-central/tools/metag_tools/blat_wrapper.py

リビジョン 2, 3.5 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1#!/usr/bin/env python
2
3import os, sys, tempfile
4
5assert sys.version_info[:2] >= (2.4)
6
7def stop_err( msg ):
8    sys.stderr.write( "%s\n" % msg )
9    sys.exit()
10   
11def 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
27def 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
42def __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       
104if __name__ == '__main__': __main__()
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