[Bioperl-l] BioPerl 1.6 and parsing multiple EMBL records

[Chris Fields]

Just saw that mark responded, so if possible submit a bug.  We may be doing a mini-hackathon this Wednesday, so we can probably tackle it in the process (possibly along with a few other pressing issues).

chris

On Jan 11, 2010, at 8:16 AM, Peter wrote:

> Hi,
> 
> I'm running bioperl-live from SVN, just updated to revision 16648.
> 
> $ perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'
> 1.0069
> 
> I am trying to get Bio::SeqIO to convert a multiple record EMBL
> file into GenBank format, piping the data via stdin/stdout using
> the following trivial Perl script:
> 
> #!/usr/bin/env perl
> use Bio::SeqIO;
> my $in  = Bio::SeqIO->new(-fh => \*STDIN, -format => 'embl');
> my $out = Bio::SeqIO->new(-format => 'genbank');
> while (my $seq = $in->next_seq) { $out->write_seq($seq) };
> 
> This only seems to find the first EMBL record in my example
> files. For example, this simple file has just two contig records:
> http://biopython.open-bio.org/SRC/biopython/Tests/EMBL/Human_contigs.embl
> 
> This is just the first two records taken from a much larger EMBL file
> rel_con_hum_01_r102.dat downloaded and uncompressed from:
> ftp://ftp.ebi.ac.uk/pub/databases/embl/release/rel_con_hum_01_r102.dat.gz
> 
> Trying both these examples as input, BioPerl just gives a single
> GenBank record as output (the first EMBL entry in the input).
> 
> Is this a BioPerl bug, or am I missing something?
> 
> Peter
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l