[Bioperl-l] Problem with blast_sequence()
selvi
biselvi at gmail.com
Thu Dec 5 01:21:59 UTC 2013
I am new to bioperl. I ran the code below. and I did get the output. It shows
some html codes and output file is empty.
I searched this site .but not able to get the answer.( i tried the solutions
given)
I am using active perl(v.5.14.2) and bioperl-1.6.0
Please help me to get the solution.
Its urgent. I have to submit my assignmentdue by today.
use Bio::Perl;
use Bio::Tools::Run::RemoteBlast;
use Bio::SearchIO;
use warnings;
use strict;
# This is the 'easy' way for reading all sequences as Bio::Seq objects
# into array (we take file name from the first command line argument here):
my @seq_array = read_all_sequences($ARGV[0],'fasta');
my $c=@seq_array;
for(my $i=0;$i<$c;$i++)
{
print "\n",$seq_array[$i]->seq;
}
print"\n__________________________\n";
#Here we'll fetch a sequence:
foreach my $seq_object (@seq_array) {
my $blast_result="";
$blast_result= blast_sequence($seq_object);
my @s=split('.',$ARGV[0]);
my @v=split('|',$seq_object->display_id);
my $f_name=$s[0].$v[2];
print "\n***********************\n",$blast_result;
write_blast(">myblastreport123.txt", $blast_result);
}
--
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