[Bioperl-l] SeqIO and large GenBank files

Chris Fields cjfields at uiuc.edu
Mon Feb 25 17:17:49 EST 2008


The perl executable is overly paranoid on Windows for some reason when  
the '-w' flag is set on the shebang line ('#!/usr/bin/perl -w'); it  
doesn't like method overloading for some reason.  Remove it and the  
warnings should go away (note: you should still leave 'use strict' and  
'use warnings').

chris

On Feb 25, 2008, at 3:33 PM, Roy wrote:

> 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==
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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