Asking for help on the bioperl mailing list. WAS: [Bioperl-l] seqIO

[Lincoln Stein]

Hi Desmond and Others who Write to this Mailing List for Help,

The bioperl mailing list welcomes requests for help from programmers of all 
levels of experience.  However, as the recent thread indicates, a great deal 
of unhelpful and redundant traffic can be generated when the question is 
vague.

It would really help us all if next time you state the problem explicitly and 
concisely, as in "I have a file that contains EMBL sequences, I've read them 
into an array and want to print the results out as FASTA format."  Note that 
this is still underspecified because some people will understand this to mean 
that you've created an array in which each element is a line from the EMBL 
file, while others will think you've created one element per EMBL entry.  But 
it's much better than showing us a fragment of nonfunctional code taken out 
of context and then asking us "why doesn't bioperl work the way I think it 
should."

Also your problem raises another question.  Why did you read the EMBL file 
into a string array rather than using Bio::SeqIO from the beginning to do it?

Lincoln

On Tuesday 07 October 2003 09:16 pm, Desmond Lim wrote:
> Hi Lincoln,
>
> Thanks but what am I to do after this?
>
> I have a file that contains EMBL sequences. And I'm reading it into an
> array, manipulating it and then print it a file in fasta format.
>
> I know how to use the:
>
> my $seq_in = Bio::SeqIO->new('-file' => filename1, '-format' => 'embl');
> my $seq_out = Bio::SeqIO->new('-file' => filename2, '-format' => 'fasta');
>
> while ( my $inseq = $seq_in->next_seq ) {
>   $seq_out->write_seq($inseq);
> }
>
> But I don't have a file for filename1 but an array. Is there a way for
> reading the array (the manipulated embl one) and then write it as a fasta
> file?
>
> Thanks.
>
> -----Original Message-----
> From: Lincoln Stein [mailto:lstein at cshl.edu]
> Sent: Wednesday, October 08, 2003 7:18 AM
> To: Desmond Lim; Hilmar Lapp; BioPerl
> Subject: Re: [Bioperl-l] seqIO
>
>
> If you have an array of sequences then you can just create them using
> Bio::Seq:
>
> 	@bioperl_sequences = map {Bio::Seq->new(-seq=>$_)} @raw_seq;
>
> Lincoln
>
> On Tuesday 07 October 2003 12:45 am, Desmond Lim wrote:
> > > What made you think it would accept a -ph parameter? Besides, if
> > > there was
> > > one you'd have to provide an array reference.
> >
> > I didn't think it would work but I wanted to try it out.
> >
> > What I'm trying to do is get SeqIO to accept an array of sequences and
> > not a file.
> >
> > Desmond
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l

-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
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