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

[david vilanova]

Here it is...

# Complete code for making an index for several
# fasta files
use lib '/usr/local/psu/bioperl-live';
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);
my @ids = qw( Q977F6 Q9V306 );
foreach my $id (@ids) {
my $seq = $inx->fetch($id); # Returns Bio::Seq object
$out->write_seq($seq);
}


> David,
>
> Hmm. Can you show us the code after you made the change I suggested?
>
> Thanks again,
>
> Brian O.
>
>
> -----Original Message-----
> From: david vilanova [mailto:danova at andorra.ad]
> Sent: Monday, April 28, 2003 10:09 AM
> To: brian_osborne at cognia.com
> Cc: bioperl-l at bioperl.org
> Subject: RE: [Bioperl-l] Bio::Index::Fasta return object problem
>
> Hi brian,
> doesn't work for me. Still give the same problem exception. I picked up
> the code from the Bio::Index::Fasta module documentation which comes
> with the last bioperl release and costumised a little bit.
>
>
>> David,
>>
>> Your loop doesn't look right to me. Try something like:
>>
>> my @ids = qw( AC1111 B45455 );
>>
>> foreach my $id (@ids) {
>>  my $seq = $inx->fetch($id); # Returns Bio::Seq object
>>  $out->write_seq($seq);#requires a valid Bio::PrimarySeqI object
>> }
>>
>> Is your code derived from some example code?
>>
>> 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 9:47 AM
>> To: bioperl-l at bioperl.org
>> Subject: [Bioperl-l] Bio::Index::Fasta return object problem
>>
>> 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
>> }
>>
>>
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