[Bioperl-l] SeqIO and large GenBank files

Roy rchu at coh.org
Mon Feb 25 16:33:10 EST 2008


Hi everyone,

I want to parse some of the .gbk RefSeq files from ncbi, more specifically,
ref_chr*.gbk.  My script seems to open the sequence stream okay, but when I try
to get the next sequence in the stream, my script spits out a lot of warnings of
subroutine redefinitions.  Is this file incompatible with SeqIO genbank reader?
 Any insight is appreciated, thanks.

Roy

test file: 

ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_01

===start_code===
#!/usr/bin/perl -w
use strict;
use warnings;
use Bio::Perl;
use Bio::SeqIO;
my $USAGE = "usage: $0 <filename>\n\n";
unless (@ARGV) {
	print $USAGE;
	exit;
}
my $stream = Bio::SeqIO->new(-file => $ARGV[0], -format => "genbank");
my $seq_obj = $stream->next_seq;
exit;
===end_code===

===start warnings===
Subroutine new redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 80,
<GEN0> line 36.
Subroutine start redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 102,
<GEN0> line 36.
Subroutine end redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 128,
<GEN0> line 36.
Subroutine length redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 165,
<GEN0> line 36.
Subroutine location_type redefined at C:/Perl/site/lib/Bio\Location\Simple.pm
line 256, <GEN0> line 36.
Subroutine to_FTstring redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line
303, <GEN0> line 36.
Subroutine trunc redefined at C:/Perl/site/lib/Bio\Location\Simple.pm line 334,
<GEN0> line 36.
Subroutine new redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 91,
<GEN0> line 49.
Subroutine each_Location redefined at C:/Perl/site/lib/Bio\Location\Split.pm
line 123, <GEN0> line 49.
Subroutine sub_Location redefined at C:/Perl/site/lib/Bio\Location\Split.pm line
152, <GEN0> line 49.
Subroutine add_sub_Location redefined at C:/Perl/site/lib/Bio\Location\Split.pm
line 221, <GEN0> line 49.
Subroutine splittype redefined at C:/Perl/site/lib/Bio\Location\Split.pm line
245, <GEN0> line 49.
Subroutine is_single_sequence redefined at
C:/Perl/site/lib/Bio\Location\Split.pm line 273, <GEN0> line 49.
Subroutine guide_strand redefined at C:/Perl/site/lib/Bio\Location\Split.pm line
298, <GEN0> line 49.
Subroutine strand redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 326,
<GEN0> line 49.
Subroutine flip_strand redefined at C:/Perl/site/lib/Bio\Location\Split.pm line
367, <GEN0> line 49.
Subroutine start redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 388,
<GEN0> line 49.
Subroutine end redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 407,
<GEN0> line 49.
Subroutine min_start redefined at C:/Perl/site/lib/Bio\Location\Split.pm line
426, <GEN0> line 49.
Subroutine max_start redefined at C:/Perl/site/lib/Bio\Location\Split.pm line
448, <GEN0> line 49.
Subroutine start_pos_type redefined at C:/Perl/site/lib/Bio\Location\Split.pm
line 471, <GEN0> line 49.
Subroutine min_end redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 492,
<GEN0> line 49.
Subroutine max_end redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 515,
<GEN0> line 49.
Subroutine end_pos_type redefined at C:/Perl/site/lib/Bio\Location\Split.pm line
539, <GEN0> line 49.
Subroutine seq_id redefined at C:/Perl/site/lib/Bio\Location\Split.pm line 565,
<GEN0> line 49.
Subroutine to_FTstring redefined at C:/Perl/site/lib/Bio\Location\Split.pm line
611, <GEN0> line 49.
Subroutine new redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 134,
<GEN0> line 747.
Subroutine location_type redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm
line 161, <GEN0> line 747.
Subroutine start redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 223,
<GEN0> line 747.
Subroutine end redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 250,
<GEN0> line 747.
Subroutine min_start redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line
277, <GEN0> line 747.
Subroutine max_start redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line
296, <GEN0> line 747.
Subroutine start_pos_type redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm
line 316, <GEN0> line 747.
Subroutine min_end redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 346,
<GEN0> line 747.
Subroutine max_end redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line 365,
<GEN0> line 747.
Subroutine end_pos_type redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line
385, <GEN0> line 747.
Subroutine to_FTstring redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm line
456, <GEN0> line 747.
Subroutine _fuzzypointdecode redefined at C:/Perl/site/lib/Bio\Location\Fuzzy.pm
line 557, <GEN0> line 747.
==end warnings==



More information about the Bioperl-l mailing list