[Bioperl-l] ClusterIO Parsing of dbSNP: Possible bug

[Allen Day]

Hi Johnny,

Yes, there were a few bugs in the parser, it's properly handling the 
NSE-FxnSet tagset now.  You'll need to use the latest CVS version to get 
the fix.

-Allen


On Sun, 10 Aug 2003, Johnny Amos wrote:

> Hello,
> 
> I seem to have run into a bug in the ClusterIO parsing of dbSNP.  The 
> functional_class() hash-element does not appear to be filled.  I suspect 
> this occurs because the corresponding XML field 
> (NSE-FxnSet_fxn-class-contig) is enumerated.  That is, it has the form:
> <NSE-FxnSet_fxn-class-contig value="intron"/>
> 
> >From my review of Bio::ClusterIO::dbsnp.pm it appears that enumerated tags 
> are not handled correctly.  The following script should return the 
> functional class for SNPs:
> 
> ### BEGIN SCRIPT
> use strict;
> use Bio::ClusterIO;
> 
> my $parser = Bio::ClusterIO->new(
> 			-file	=>	$infile,
> 			-format	=>	'dbSNP'
> 			);
> 
> while (my $record = $parser->next_cluster()) {
> 
> 	if (my $class = $record->functional_class) {
> 		$class =~ s/^\s+//;
> 		$class =~ s/\s+$//;
> 
> 		if ($class) { print "$class\n"; }
> 
> 		}
> 
> 	}
> ### END SCRIPT
> 
> I have tested this on several chromosomes, with the same results in each 
> case.  Can anyone confirm this behaviour, or see a problem with my code?
> 
> Johnny
> 
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