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More friendly error reporting for mutate SNP codon tool.

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This commit is contained in:
Daniel Blankenberg
2009-09-22 11:37:41 -04:00
parent a21cd9b298
commit 97297d4e3a
1 changed files with 47 additions and 8 deletions
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tools/evolution/mutate_snp_codon.py
+47 -8
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@@ -34,32 +34,66 @@ def main():
DNA_COMP = string.maketrans( "ACGTacgt", "TGCAtgca" )
skipped_lines = 0
for line in open( input_file ):
errors = {}
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' ) ]:
errors[ name ] = { 'count':0, 'message':message }
line_count = 0
for line_count, line in enumerate( open( input_file ) ):
line = line.rstrip( '\n\r' )
if line and not line.startswith( '#' ):
fields = line.split( '\t' )
if max_field_index >= len( fields ):
skipped_lines += 1
errors[ 'max_field_index' ]['count'] += 1
continue
#read codon info
codon_chrom = fields[codon_chrom_col]
codon_start = int( fields[codon_start_col] )
codon_end = int( fields[codon_end_col] )
if codon_end - codon_start != 3:
#codons must be length 3
skipped_lines += 1
errors[ 'codon_len' ]['count'] += 1
continue
codon_strand = strandify( fields, codon_strand_col )
codon_seq = fields[codon_seq_col].upper()
if len( codon_seq ) != 3:
#codon sequence must have length 3
skipped_lines += 1
errors[ 'codon_seq' ]['count'] += 1
continue
#read snp info
snp_chrom = fields[snp_chrom_col]
snp_start = int( fields[snp_start_col] )
snp_end = int( fields[snp_end_col] )
if snp_end - snp_start != 1:
#snps must be length 1
skipped_lines += 1
errors[ 'snp_len' ]['count'] += 1
continue
snp_strand = strandify( fields, snp_strand_col )
snp_observed = fields[snp_observed_col].split( '/' )
snp_observed = [ observed for observed in snp_observed if len( observed ) == 1 ]
if not snp_observed:
#sequence replacements must be length 1
skipped_lines += 1
errors[ 'snp_observed' ]['count'] += 1
continue
#Determine index of replacement for observed values into codon
offset = snp_start - codon_start
#Extract DNA on neg strand codons will have positions reversed relative to interval positions; i.e. position 0 == position 2
if codon_strand == '-':
offset = 2 - offset
if offset < 0 and offset > 2: #assert offset >= 0 and offset <= 2, ValueError( 'Impossible offset determined: %s' % offset )
#codon and snp do not overlap
skipped_lines += 1
errors[ 'no_overlap' ]['count'] += 1
continue
for observed in snp_observed:
#Extract DNA on neg strand codons will have positions reversed relative to interval positions; i.e. position 0 == position 2
offset = snp_start - codon_start
if codon_strand == '-':
offset = 2 - offset
assert offset >= 0 and offset <= 2, ValueError( 'Impossible offset determined: %s' % offset )
if codon_strand != snp_strand:
#if our SNP is on a different strand than our codon, take complement of provided observed SNP base
observed = observed.translate( DNA_COMP )
@@ -69,5 +103,10 @@ def main():
if codon_seq != snp_codon: #only output when we actually have a different codon
out.write( "%s\t%s\n" % ( line, snp_codon ) )
else:
skipped_lines += 1
errors[ 'empty_comment' ]['count'] += 1
if skipped_lines:
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'] ] ) )
if __name__ == "__main__": main()