[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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