[Bioperl-l] write protein sequence by Bio::SeqIO

[Remo Sanges]

suhoiy wrote:

> No, it did not work. :( In fact, the $seq from $in has the correct alphabet 
> "protein", but the write_seq method will change it to "dna".


I have try
you then can add a line whit the function molecule for the seq object

my $seq = $in->next_seq;


#adding this work well    ###

#############################

$seq->molecule('protein');###

#############################
$out->write_seq($seq);


> 
> thansk anyway. :)


nothing


> 
> 
> ---Original Message---
> From: Remo Sanges<sanges@biogem.it>
> Subject: Re: [Bioperl-l] write protein sequence by Bio::SeqIO
>  
> 
>>suhoiy wrote:
>>
>>
>>>Hello all,
>>>
>>>I am sorry to bother you. There is a problem in my code. I want to write a protein
>>>sequence in genbank format, but the code change it to nucleic acid sequence. For
>>>example:
>>>
>>>========
>>>my $in   = Bio::SeqIO->new(  '-format' => 'genbank', 
>>>                                             '-file'   => 'sample.genpept',
>>>		             );
>>>my $out  = Bio::SeqIO->new('-format' => 'genbank',
>>>                                            '-file' => '>sampleout.genpept',
>>>                                          );
>>>my $seq = $in->next_seq;
>>>$out->write_seq($seq);
>>>========
>>>
>>
>>I thing, if the input file is ok and contains protein sequenences, you
>>should set the '-alphabet' format in the constructor new:
>>
>>my $in   = Bio::SeqIO->new(  '-format' => 'genbank',
>>                            '-file'   => 'sample.genpept',
>>                            'alphabet'=> 'protein'           );
>>
>>my $out  = Bio::SeqIO->new(  '-format' => 'genbank',
>>                            '-file' => '>sampleout.genpept',
>>                            '-alphabet'=> 'protein'          );
>>
>>my $seq = $in->next_seq;
>>$out->write_seq($seq);
>>
>>I havn't try but I thing it should go
>>
>>Let me know!|
>>
>>
>>>the locus line of origin sequence is:
>>>LOCUS       108_LYCES                102 aa            linear   PLN 15-JUL-1999
>>>
>>>while the locus line of the output sequence is:
>>>LOCUS       108_LYCES                102 bp    linear  linear   PLN 15-JUL-1999
>>>
>>>I use bioperl 1.0.2. there are these lines in the write_seq method in Bio::SeqIO::genbank:
>>>
>>>========
>>>    if( !$seq->can('molecule') || ! defined ($mol = $seq->molecule()) ) {
>>>	$mol = $seq->alphabet || 'DNA';
>>>    }
>>>========
>>>
>>>many thanks for your help!
>>>
>>
>>you are welcome!
>>
>>
>>
>>>suhoiy
>>>
>>>
>>>
>>>
>>>_______________________________________________
>>>Bioperl-l mailing list
>>>Bioperl-l@bioperl.org
>>>http://bioperl.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
>>__________________________________
>>Remo Sanges
>>BioGeM
>>Gene Expression Core Lab
>>Via Pietro Castellino 111
>>80131 NaplesItaly
>>+39 081 6132265
>>sanges@biogem.it
>>sanges@iigb.na.cnr.it
>>__________________________________
>>
>>
>>
>>
>>
> 
>  
> ---End of Message---
> 
> 
__________________________________
Remo Sanges

BioGeM
Gene Expression Core Lab
Via Pietro Castellino 111
80131 NaplesItaly
+39 081 6132303
sanges@biogem.it
sanges@iigb.na.cnr.it
__________________________________