Andreas Leimbach | 20 Feb 17:24 2013
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Re: Problem Parsing BLAST output to annotate FASTA file

oops, I just realized I had one loop to much in there. Adam is correct. 
Sorry.

The last part of the code I send you should look like this:

my $seqio = Bio::SeqIO->new(-format => 'fasta', -file => "$ARGV[1]");
while (my $seqobj = $seqio->next_seq) {
print ">$hits{$seqobj->display_id}\n";
my $nuc = $seqobj->seq();
print $nuc, "\n";
}

Cheers,
Andreas

--
Andreas Leimbach
Universität Münster
Institut für Hygiene
Mendelstr. 7
D-48149 Münster
Germany

Tel.: +49 (0)551 39 3843
E-Mail: andreas.leimbach <at> uni-wuerzburg.de

On 20.2.13 06:20, Ann Gregory wrote:
> Hi BioPerl,
>
> I am having issues with a BioPerl script. I have a blastxml file from a
> blastx blast and the original multifasta file containing the original
> nucleotides sequences.
>
> I want to take the blast result (ie. the blast description) and annotate my
> multifasta file.
>
> I have written 2 while loops that extract the blast descriptions as well as
> the nucleotide sequence from the multifasta file.
>
> My problem is that I cannot incorporate one of the while loops into the
> other without loosing the loop property of one of the loops. I would like
> to take the 1st blast description, then the 1st nucleotide sequence, then
> the 2nd blast description, then the 2nd nucleotide sequence and so
> on...just can figure out how to alternate the results.
>
> See script below:
>
>
> use warnings;
> use strict;
> use Bio::SearchIO;
> use Bio::SeqIO;
>
>
> my $search_in = Bio::SearchIO->new(-format => 'blastxml', -file =>
> "$ARGV[0]");
> while (my $result = $search_in->next_result) {
> while (my $hit = $result->next_hit) {
> while (my $hsp = $hit->next_hsp) {
> my $qd = $hit->description;
> print $qd, "\n";
> }
> }
> }
>
> my $seqio = Bio::SeqIO->new(-format => 'fasta', -file => "$ARGV[1]");
> while (my $seqobj = $seqio->next_seq) {
> my $nuc = $seqobj->seq();
> print $nuc, "\n";
> }--
> Ann (Nina) Gregory
> Graduate Student
> Rich Lab / Sullivan Lab
> Soil, Water, Environmental Science Department
> University of Arizona
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>

Gmane