| Subject: | ACCESSION section reported as invalid |
Hello Ken,
thanks for developing Bio::GenBankParser, it seems to be exactly what I
was looking for. However, I have run into a problem. When I run the
following script (attached example gbk file is expected to be in the
local directory):
#!/usr/bin/perl
use strict;
use warnings;
use Bio::GenBankParser;
my $parser = Bio::GenBankParser->new(file => 'error_test.gbk');
my $seq = $parser->next_seq;
then I get the following error:
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 origin, or comment, or
record delimiter
ERROR (line 5): Invalid startrule: Was expecting eofile but
found
"M14239-M14245 M14253-M14259 M14591-M14598 V01323"
instead
The reported line is a bit strange, at least in the original file which
I narrowed down to the attached one, the reported line seemed
completely unrelated to the error (is it a line of your code?), but the
found string was helpful to locate the problem. If I remove the
"ACCESSION" entry (lines 4 and 5) then the error is gone.
I don't know if this is a problem in Bio::GenBankParser or in the gbk
file. However, it is (part of) a "real world" gbk file, so it would be
very helpful if Bio::GenBankParser would digest it.
Thanks a lot and best wishes,
Lutz
| Subject: | error_test.gbk |
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