root/galaxy-central/tools/extract/extract_genomic_dna.py

リビジョン 2, 7.2 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1#!/usr/bin/env python
2"""
3usage: %prog $input $out_file1
4    -1, --cols=N,N,N,N: Columns for start, end, strand in input file
5    -d, --dbkey=N: Genome build of input file
6    -o, --output_format=N: the data type of the output file
7    -g, --GALAXY_DATA_INDEX_DIR=N: the directory containing alignseq.loc
8    -G, --gff: input and output file, when it is interval, coordinates are treated as GFF format (1-based, half-open) rather than 'traditional' 0-based, closed format.
9"""
10from galaxy import eggs
11import pkg_resources
12pkg_resources.require( "bx-python" )
13import sys, string, os, re
14from bx.cookbook import doc_optparse
15import bx.seq.nib
16import bx.seq.twobit
17from galaxy.tools.util.galaxyops import *
18from galaxy.tools.util.gff_util import *
19
20assert sys.version_info[:2] >= ( 2, 4 )
21   
22def stop_err( msg ):
23    sys.stderr.write( msg )
24    sys.exit()
25
26def reverse_complement( s ):
27    complement_dna = {"A":"T", "T":"A", "C":"G", "G":"C", "a":"t", "t":"a", "c":"g", "g":"c", "N":"N", "n":"n" }
28    reversed_s = []
29    for i in s:
30        reversed_s.append( complement_dna[i] )
31    reversed_s.reverse()
32    return "".join( reversed_s )
33
34def check_seq_file( dbkey, GALAXY_DATA_INDEX_DIR ):
35    seq_file = "%s/alignseq.loc" % GALAXY_DATA_INDEX_DIR
36    seq_path = ''
37    for line in open( seq_file ):
38        line = line.rstrip( '\r\n' )
39        if line and not line.startswith( "#" ) and line.startswith( 'seq' ):
40            fields = line.split( '\t' )
41            if len( fields ) < 3:
42                continue
43            if fields[1] == dbkey:
44                seq_path = fields[2].strip()
45                break
46    return seq_path
47
48       
49def __main__():
50    options, args = doc_optparse.parse( __doc__ )
51    try:
52        chrom_col, start_col, end_col, strand_col = parse_cols_arg( options.cols )
53        dbkey = options.dbkey
54        output_format = options.output_format
55        gff_format = options.gff
56        GALAXY_DATA_INDEX_DIR = options.GALAXY_DATA_INDEX_DIR
57        input_filename, output_filename = args
58    except:
59        doc_optparse.exception()
60
61    includes_strand_col = strand_col >= 0
62    strand = None
63    nibs = {}
64    twobits = {}
65    seq_path = check_seq_file( dbkey, GALAXY_DATA_INDEX_DIR )
66    if not os.path.exists( seq_path ):
67        # If this occurs, we need to fix the metadata validator.
68        stop_err( "No sequences are available for '%s', request them by reporting this error." % dbkey )
69
70    skipped_lines = 0
71    first_invalid_line = 0
72    invalid_line = ''
73    fout = open( output_filename, "w" )
74    warnings = []
75    warning = ''
76    twobitfile = None
77     
78    for i, line in enumerate( open( input_filename ) ):
79        line = line.rstrip( '\r\n' )
80        if line and not line.startswith( "#" ):
81            fields = line.split( '\t' )
82            try:
83                chrom = fields[chrom_col]
84                start = int( fields[start_col] )
85                end = int( fields[end_col] )
86                if gff_format:
87                    start, end = convert_gff_coords_to_bed( [start, end] )
88                if includes_strand_col:
89                    strand = fields[strand_col]
90            except:
91                warning = "Invalid chrom, start or end column values. "
92                warnings.append( warning )
93                skipped_lines += 1
94                if not invalid_line:
95                    first_invalid_line = i + 1
96                    invalid_line = line
97                continue
98            if start > end:
99                warning = "Invalid interval, start '%d' > end '%d'.  " % ( start, end )
100                warnings.append( warning )
101                skipped_lines += 1
102                if not invalid_line:
103                    first_invalid_line = i + 1
104                    invalid_line = line
105                continue
106
107            if strand not in ['+', '-']:
108                strand = '+'
109            sequence = ''
110
111            if seq_path and os.path.exists( "%s/%s.nib" % ( seq_path, chrom ) ):
112                if chrom in nibs:
113                    nib = nibs[chrom]
114                else:
115                    nibs[chrom] = nib = bx.seq.nib.NibFile( file( "%s/%s.nib" % ( seq_path, chrom ) ) )
116                try:
117                    sequence = nib.get( start, end-start )
118                except:
119                    warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " %( start, end-start, dbkey )
120                    warnings.append( warning )
121                    skipped_lines += 1
122                    if not invalid_line:
123                        first_invalid_line = i + 1
124                        invalid_line = line
125                    continue
126            elif seq_path and os.path.isfile( seq_path ):
127                if not(twobitfile):
128                    twobitfile = bx.seq.twobit.TwoBitFile( file( seq_path ) )
129                try:
130                    sequence = twobitfile[chrom][start:end]
131                except:
132                    warning = "Unable to fetch the sequence from '%d' to '%d' for build '%s'. " %( start, end-start, dbkey )
133                    warnings.append( warning )
134                    skipped_lines += 1
135                    if not invalid_line:
136                        first_invalid_line = i + 1
137                        invalid_line = line
138                    continue
139            else:
140                warning = "Chromosome by name '%s' was not found for build '%s'. " % ( chrom, dbkey )
141                warnings.append( warning )
142                skipped_lines += 1
143                if not invalid_line:
144                    first_invalid_line = i + 1
145                    invalid_line = line
146                continue
147            if sequence == '':
148                warning = "Chrom: '%s', start: '%s', end: '%s' is either invalid or not present in build '%s'. " %( chrom, start, end, dbkey )
149                warnings.append( warning )
150                skipped_lines += 1
151                if not invalid_line:
152                    first_invalid_line = i + 1
153                    invalid_line = line
154                continue
155            if includes_strand_col and strand == "-":
156                sequence = reverse_complement( sequence )
157
158            if output_format == "fasta" :
159                l = len( sequence )       
160                c = 0
161                if gff_format:
162                    start, end = convert_bed_coords_to_gff( [ start, end ] )
163                fields = [dbkey, str( chrom ), str( start ), str( end ), strand]
164                meta_data = "_".join( fields )
165                fout.write( ">%s\n" % meta_data )
166                while c < l:
167                    b = min( c + 50, l )
168                    fout.write( "%s\n" % str( sequence[c:b] ) )
169                    c = b
170            else: # output_format == "interval"
171                meta_data = "\t".join( fields )
172                if gff_format:
173                    format_str = "%s seq \"%s\";\n"
174                else:
175                    format_str = "%s\t%s\n"
176                fout.write( format_str % ( meta_data, str( sequence ) ) )
177
178    fout.close()
179
180    if warnings:
181        warn_msg = "%d warnings, 1st is: " % len( warnings )
182        warn_msg += warnings[0]
183        print warn_msg
184    if skipped_lines:
185        print 'Skipped %d invalid lines, 1st is #%d, "%s"' % ( skipped_lines, first_invalid_line, invalid_line )
186
187if __name__ == "__main__": __main__()
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