| Subject: | Fwd: Possible bug or my mistake |
| Date: | Thu, 27 Feb 2014 17:54:44 +0100 |
| To: | bug-Bio-GenBankParser [...] rt.cpan.org |
| From: | Bernardo Bello <popnard [...] gmail.com> |
Sorry, this is the error, forget the one I sent before.
' ERROR (line 5): Invalid section: Was expecting commented line, or
header, or locus, or dbsource, or definition, or accession line, or project
line, or version line, or keywords, or source line, or organism, or
reference, or features, or base count, or contig, or origin, or comment, or
record delimiter ERROR (line 5): Invalid startrule: Was expecting eofile
but found "DBLINK Project: 59273" instead'
Show quoted text
---------- Forwarded message ----------
From: Bernardo Bello <popnard@gmail.com>
Date: 2014-02-27 17:52 GMT+01:00
Subject: Possible bug or my mistake
To: bug-Bio-GenBankParser@rt.cpan.org
Module is installed, but I have this error message: 'syntax error at
/Users/bernardo/Documents/BioLinux/A0_scripts/parse_gbk_2.pl line 13,
near "say join" Execution of
/Users/bernardo/Documents/BioLinux/A0_scripts/parse_gbk_2.pl aborted
due to compilation errors.'
Thanks. Here is the code I used. Seems to be happening with any GenBank file
use strict;use warnings;use feature 'say';use Bio::GenBankParser;
my $file = shift;my $parser = Bio::GenBankParser->new( file => $file
);while ( my $seq = $parser->next_seq ) {
my $feat = $seq->{'FEATURES'};
for my $f (@$feat) {
my $tag = $f->{'feature'}{'locus_tag'};
my $prod = $f->{'feature'}{'product'};
if (defined $tag and defined $prod) {
say join "\t", $tag, $prod;
}
}}
--
*Bernardo Bello Ortí*
PhD student
CReSA-IRTA
Campus de Bellaterra-Universitat Autònoma de Barcelona
Edifici CReSA
08193 Bellaterra (Barcelona, Spain)
Tel.: 647 42 52 63 *www.cresa.es <http://www.cresa.es> *
--
*Bernardo Bello Ortí*
PhD student
CReSA-IRTA
Campus de Bellaterra-Universitat Autònoma de Barcelona
Edifici CReSA
08193 Bellaterra (Barcelona, Spain)
Tel.: 647 42 52 63 *www.cresa.es <http://www.cresa.es> *
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