[Bioperl-l] Parsing multi-record genbank file

[Fields, Christopher J]

… and not to point out the obvious, but the output is listed as a fasta file but the format you give is ‘genbank’, so the output will be genbank.

-c

On Nov 7, 2013, at 8:00 PM, Fields, Christopher J <cjfields at illinois.edu> wrote:

> A lot of problems in this one; try:
> 
> use Bio::SeqIO;
> use Bio::Seq;
> 
> my $seqio_in = Bio::SeqIO->new(-file => "ls_orchid.gbk" , '-format' => 'genbank');
> my $seqio_out = Bio::SeqIO->new(-file => '>sequence.fasta', -format => 'genbank' );
> 
> while ( my $seq = $seqio_in->next_seq ) {
>    $seqio_out->write_seq($seq);
> }
> 
> chris
> 
> On Nov 7, 2013, at 3:23 PM, Robert Johnson <robjohn7000 at gmail.com> wrote:
> 
>> Hi,
>> 
>> I would be happy if someone could help me get the following code to output
>> the sequences (including the ids)  of all records in the input file (
>> http://biopython.org/DIST/docs/tutorial/examples/ls_orchid.gbk):
>> 
>> use Bio::SeqIO;
>> use Bio::Seq;
>> use Bio::DB::GenBank;
>> 
>> $seq_obj = Bio::SeqIO->new(-file => "ls_orchid.gbk" , '-format' =>
>> 'genbank');
>> $seqio_obj2 = Bio::SeqIO->new(-file => '>sequence.fasta', -format =>
>> 'genbank' );
>> 
>> while ( my $seq = $seq_obj->next_seq() ) {
>> print "Sequence ",$seq->id ($seq_obj)"\n";
>> #print $seq_obj->seq,"\n";
>> $seqio_obj2->write_seq($seq_obj);
>> }
>> 
>> Thank you
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> 
> 
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