Member Avatar for Inking

Good day, I was looking for a good subroutine to parse BLAST records without using BioPerl. I have to open a BlAST results file and then use regular expressions to parse out the query, BESTHIT (highest E-Value), E-value, and the identities. I have to parse them out and then print it out to a file.

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  • Latest Post Latest Post by Anthony Cameron
Member Avatar for Anthony Cameron

Good day, I was looking for a good subroutine to parse BLAST records without using BioPerl. I have to open a BlAST results file and then use regular expressions to parse out the query, BESTHIT (highest E-Value), E-value, and the identities. I have to parse them out and then print it out to a file.

I understand you don't want to use BioPerl and I was searching for you but I did not come up with a good subroutine. I will continue to look though.

Member Avatar for Anthony Cameron

Good day, I was looking for a good subroutine to parse BLAST records without using BioPerl. I have to open a BlAST results file and then use regular expressions to parse out the query, BESTHIT (highest E-Value), E-value, and the identities. I have to parse them out and then print it out to a file.

I am not sure if this is helpful but I think you need to follow code similar to this:

!/usr/bin/perl-w

use strict;
use warnings;
use BeginPerlBioinfo;

#Declare and initialize variables
my $beginning_annotation='';
my $ending_annotation='';
my %alignments=();
my $alignment='';
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