| Subject: | NCBI.pm match string wrong |
| Date: | Tue, 1 Feb 2011 14:10:40 +0100 |
| To: | bug-Boulder [...] rt.cpan.org |
| From: | david.bauer [...] bayer.com |
Hi,
I was happy to find this light weighted module to quickly parse BLAST
results.
But the absolute extraction of the match string (which is already in the
code marked as UGLY ;-)) did not work reliably. Most the times it starts
at position 12 but, depending on the length of the start and end position
numbers, it can also be 11 or 13. So I added some lines to get the start
position from the start position of the Query sequence string.
Here is the diff:
###########################################
diff NCBI.pm NCBI.pm.ori
148d147
< my $offset;
247,254d245
< # get absolute position of query sequence to grab match string
< my $test = $_;
< $test =~ s/Query: //;
< my @test = split(//,$test);
< $offset=7;
< foreach my $test (@test) {
< if (($test =~ /\d/) || ($test =~ /\s/)) {$offset++} else
{last}
< }
269,270c260
< # This did not work. Modified to get offset from Query line. DB
01.01.2011
< $match .= substr($_,$offset,60) if $query;
---
Show quoted text
> $match .= substr($_,12,60) if $query;
##############################################
Kind regards,
David.
Freundliche Grüße / Best Regards
David Bauer
Show quoted text_________________________________________
Bayer Schering Pharma Aktiengesellschaft
BSP-GDD-CP-TS-BMB
Berlin, S110, 02, 707
Phone: +49 30 468 12657
Fax: +49 30 468 92657
E-mail: david.bauer@bayer.com
Web: http://www.bayerscheringpharma.de
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