[Bioperl-l] Bio::Index::Fasta return object problem

[Brian Osborne]

David,

OK. One problem is that your code wants an id like 'sptrembl|Q9V2U7|Q9V2U7',
not 'Q9V2U7', I don't think fetch() will work with this id in your code as
written. To use a specific substring in the fasta header you need to write a
function that finds this substring. Take a look at the III.1.2 section in
bptutorial for more information
(http://bioperl.org/Core/Latest/bptutorial.html).

Brian O.


-----Original Message-----
From: bioperl-l-bounces at bioperl.org [mailto:bioperl-l-bounces at bioperl.org]On
Behalf Of david vilanova
Sent: Monday, April 28, 2003 10:41 AM
To: jason at cgt.mc.duke.edu
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Bio::Index::Fasta return object problem


Here are two of the sequences I try to retrieve from the indexed file.
>sptrembl|Q9V2U7|Q9V2U7 ABC transporter permease (Fragment).
MLYVGLPYMVNSGRDGFLMVNEELENVSRTLGASKIKTFFNISLPLIKNNLVSGSILTFA
RGISEVGAILIVAYFPKTTPVLILDRFNEYGLSSSKPISVIMIVLSIVLFSVFRLVRYNK
K
>sptrembl|Q977F6|Q977F6 FtsY.
MALLQSDVEMQVAEEILETIREKLIGETRKQVESTGQLVSEALHDALYEVISVGQFDFDQ
RIAEADKPVTLIFTGINGVGKTTTIAKLAKYFEKQGYSTVLANGDTYRAGANEQIREHAE
ALDKKLIAHEQGGDPAAVIYDGVEYAEAHDIDIVLGDTAGRLHTSNDLMAQLEKIDRVVG
PDLTLFVDEAVAGQDAVERARQFNDAAAIDGAILTKADADSNGGAAISIAYVTGKPILFL
GVGQGYDHIEKFDPEQMVERLLGEDE
I use:
my @ids = qw(Q9V2U7 Q977F6);
foreach my $id (@ids) {
my $seq = $inx->fetch($id); # Returns Bio::Seq object
$out->write_seq($seq);
}

It still gives the exception.



> Bio::Seq ISA Bio::PrimarySeqI
>
> You might want some code to verify that $seq is defined - it is
> possible you aren't actually retrieving anything when you call fetch.
> Just do a grep "accession" filename
>
> If the accession doesn't match exactly you need to write your own
> id_parser function which will (For example) drop the .1 or some thing.
>
> Also you really don't want to be calling
> for $id ($Index_File_Name) {
> you want to be calling
> for $id ( @accession ) {
> }
>
> where @accession is the list of accession numbers or unique Ids you
> want to retrieve with
>
>
>
> On Mon, 28 Apr 2003, [iso-8859-1] david vilanova wrote:
>
>> Dear all,
>> I have some problems when I try to retreive sequences from an indexed
>> file. The Index::Fasta  seems to return a Bio::Seq object however the
>> method write_seq requires a valid Bio::PrimarySeqI object. How can I
>> can go through this problem.
>>
>> Thanks
>> ------------- EXCEPTION  -------------
>> MSG: Did not provide a valid Bio::PrimarySeqI object
>> STACK Bio::SeqIO::fasta::write_seq
>> /usr/local/psu/bioperl-live/Bio/SeqIO/fasta.pm:175
>> STACK toplevel fasta.pl:21
>>
>>
>> use Bio::Index::Fasta;
>> use strict;
>>
>> my ($Index_File_Name,$Fasta_File) = @ARGV;
>> my $inx = Bio::Index::Fasta->new(
>> '-filename' => $Index_File_Name,
>> '-write_flag' => 1);
>> $inx->make_index($Fasta_File);
>>
>> # Print out several sequences present in the index
>> # in Fasta format
>>
>> my $out = Bio::SeqIO->new('-format' => 'Fasta','-fh' => \*STDOUT);
>>
>> foreach my $id ($Index_File_Name) {
>> my $seq = $inx->fetch($id); # Returns Bio::Seq object
>> $out->write_seq($seq);#requires a valid Bio::PrimarySeqI object
>> }
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at bioperl.org
>> http://bioperl.org/mailman/listinfo/bioperl-l
>>
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu



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