[Bioperl-l] fasta format

[Smithies, Russell]

It's even easier as the script is already written for you :-)

bp_seqconvert.pl --from fasta --to fasta < file.in.fa > file.out.fa


--Russell


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Kevin Brown
> Sent: Thursday, 10 December 2009 4:26 a.m.
> To: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] fasta format
> 
> Even easier to accomplish in one step. Read in the fasta file and output
> it right to another fasta file with SeqIO
> 
> my $in = Bio::SeqIO->new(-format=>'fasta',-file=>$file);
> my $out = Bio::SeqIO->new(-format=>'fasta',-file=>'>file.fasta');
> while (my $seq = $in->next){$out->write_seq($seq);}
> 
> Kevin Brown
> Center for Innovations in Medicine
> Biodesign Institute
> Arizona State University
> 
> > -----Original Message-----
> > From: bioperl-l-bounces at lists.open-bio.org
> > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Amir Karger
> > Sent: Wednesday, December 09, 2009 8:02 AM
> > To: Jonas Schaer; bioperl-l at bioperl.org
> > Subject: Re: [Bioperl-l] fasta format
> >
> > > Is there any way to use these fasta files with diffrent length of
> > > lines with this fasta.pm module or will i have to change the format
> > > of my fasta-files(big databases...) ?
> > >
> >
> > Jonas,
> >
> > It's not Bioperl, but for a quick fix you can use the
> > Scriptome. Use the change_fasta_to_tab script
> > (http://sysbio.harvard.edu/csb/resources/computational/scripto
> > me/Windows/Tools/Change.html#change_a_fasta_file_into_tabular_
> > format__change_fasta_to_tab_) to change your FASTA into a
> > tab-delimited file. Then use the next tool
> > (change_tab_to_fasta) to change your files back.
> >
> > To use a tool: change the input and output file names on the
> > website, then cut and paste the Perl script from the green
> > box into a CMD window. The script works one sequence at a
> > time, so it doesn't need a lot of memory. (As long as you
> > have enough disk space to store the tab-delimited copy).
> >
> > The recreated FASTAs will be 60 characters per line (although
> > you can hand-edit the line after you paste it to be whatever
> > number of characters you'd like).
> >
> > Let me know if you have a problem.
> >
> > -Amir Karger
> > Life Sciences Research Computing, FAS IT
> > Harvard University
> >
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> 
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