root/galaxy-central/tools/evolution/mutate_snp_codon.py

リビジョン 2, 5.0 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1#!/usr/bin/env python
2"""
3Script to mutate SNP codons.
4Dan Blankenberg
5"""
6
7import sys, string
8
9def strandify( fields, column ):
10    strand = '+'
11    if column >= 0 and column < len( fields ):
12        strand = fields[ column ]
13        if strand not in [ '+', '-' ]:
14            strand = '+'
15    return strand
16
17def main():
18    # parse command line
19    input_file = sys.argv[1]
20    out = open( sys.argv[2], 'wb+' )
21    codon_chrom_col = int( sys.argv[3] ) - 1
22    codon_start_col = int( sys.argv[4] ) - 1
23    codon_end_col = int( sys.argv[5] ) - 1
24    codon_strand_col = int( sys.argv[6] ) - 1
25    codon_seq_col = int( sys.argv[7] ) - 1
26   
27    snp_chrom_col = int( sys.argv[8] ) - 1
28    snp_start_col = int( sys.argv[9] ) - 1
29    snp_end_col = int( sys.argv[10] ) - 1
30    snp_strand_col = int( sys.argv[11] ) - 1
31    snp_observed_col = int( sys.argv[12] ) - 1
32   
33    max_field_index = max( codon_chrom_col, codon_start_col, codon_end_col, codon_strand_col, codon_seq_col, snp_chrom_col, snp_start_col, snp_end_col, snp_strand_col, snp_observed_col )
34   
35    DNA_COMP = string.maketrans( "ACGTacgt", "TGCAtgca" )
36    skipped_lines = 0
37    errors = {}
38    for name, message in [ ('max_field_index','not enough fields'), ( 'codon_len', 'codon length must be 3' ), ( 'codon_seq', 'codon sequence must have length 3' ), ( 'snp_len', 'SNP length must be 3' ), ( 'snp_observed', 'SNP observed values must have length 3' ), ( 'empty_comment', 'empty or comment'), ( 'no_overlap', 'codon and SNP do not overlap' ) ]:
39        errors[ name ] = { 'count':0, 'message':message }
40    line_count = 0
41    for line_count, line in enumerate( open( input_file ) ):
42        line = line.rstrip( '\n\r' )
43        if line and not line.startswith( '#' ):
44            fields = line.split( '\t' )
45            if max_field_index >= len( fields ):
46                skipped_lines += 1
47                errors[ 'max_field_index' ]['count'] += 1
48                continue
49           
50            #read codon info
51            codon_chrom = fields[codon_chrom_col]
52            codon_start = int( fields[codon_start_col] )
53            codon_end = int( fields[codon_end_col] )
54            if codon_end - codon_start != 3:
55                #codons must be length 3
56                skipped_lines += 1
57                errors[ 'codon_len' ]['count'] += 1
58                continue
59            codon_strand = strandify( fields, codon_strand_col )
60            codon_seq = fields[codon_seq_col].upper()
61            if len( codon_seq ) != 3:
62                #codon sequence must have length 3
63                skipped_lines += 1
64                errors[ 'codon_seq' ]['count'] += 1
65                continue
66           
67            #read snp info
68            snp_chrom = fields[snp_chrom_col]
69            snp_start = int( fields[snp_start_col] )
70            snp_end = int( fields[snp_end_col] )
71            if snp_end - snp_start != 1:
72                #snps must be length 1
73                skipped_lines += 1
74                errors[ 'snp_len' ]['count'] += 1
75                continue
76            snp_strand = strandify( fields, snp_strand_col )
77            snp_observed = fields[snp_observed_col].split( '/' )
78            snp_observed = [ observed for observed in snp_observed if len( observed ) == 1 ]
79            if not snp_observed:
80                #sequence replacements must be length 1
81                skipped_lines += 1
82                errors[ 'snp_observed' ]['count'] += 1
83                continue
84           
85            #Determine index of replacement for observed values into codon
86            offset = snp_start - codon_start
87            #Extract DNA on neg strand codons will have positions reversed relative to interval positions; i.e. position 0 == position 2
88            if codon_strand == '-':
89                offset = 2 - offset
90            if offset < 0 or offset > 2: #assert offset >= 0 and offset <= 2, ValueError( 'Impossible offset determined: %s' % offset )
91                #codon and snp do not overlap
92                skipped_lines += 1
93                errors[ 'no_overlap' ]['count'] += 1
94                continue
95           
96            for observed in snp_observed:
97                if codon_strand != snp_strand:
98                    #if our SNP is on a different strand than our codon, take complement of provided observed SNP base
99                    observed = observed.translate( DNA_COMP )
100                snp_codon = [ char for char in codon_seq ]
101                snp_codon[offset] = observed.upper()
102                snp_codon = ''.join( snp_codon )
103               
104                if codon_seq != snp_codon: #only output when we actually have a different codon
105                    out.write( "%s\t%s\n" % ( line, snp_codon )  )
106        else:
107            skipped_lines += 1
108            errors[ 'empty_comment' ]['count'] += 1
109    if skipped_lines:
110        print "Skipped %i (%4.2f%%) of %i lines; reasons: %s" % ( skipped_lines, ( float( skipped_lines )/float( line_count ) ) * 100, line_count, ', '.join( [ "%s (%i)" % ( error['message'], error['count'] ) for error in errors.itervalues() if error['count'] ] ) )
111   
112if __name__ == "__main__": main()
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