package Maasha::Blast;
-# Copyright (C) 2007 Martin A. Hansen.
+# Copyright (C) 2007-2009 Martin A. Hansen.
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+use warnings;
use strict;
use Storable qw( dclone );
use Data::Dumper;
if ( $doctype eq '<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">' )
{
print STDERR qq(Parsing blastcl3 results ...\n);
- $results = &xml_parse_blast_blastcl3( $fh );
+ $results = xml_parse_blast_blastcl3( $fh );
}
elsif ( $doctype eq '<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">' )
{
print STDERR qq(Parsing NCBI blast results ...\n);
- $results = &xml_parse_blast_ncbi( $fh );
+ $results = xml_parse_blast_ncbi( $fh );
}
else
{
my ( $blast_record, $line, @blast_query, @blast_subject, $query, $subject, @results );
- while ( $blast_record = &xml_get_blast_record( $fh ) and scalar @{ $blast_record } > 0 )
+ while ( $blast_record = xml_get_blast_record( $fh ) and scalar @{ $blast_record } > 0 )
{
foreach $line ( @{ $blast_record } )
{
if ( $line =~ /<\/Iteration_hits>/ )
{
- $query = &xml_parse_blast_query( \@blast_query );
- $subject = &xml_parse_blast_subject( \@blast_subject );
+ $query = xml_parse_blast_query( \@blast_query );
+ $subject = xml_parse_blast_subject( \@blast_subject );
push @results, {
"QUERY" => $query,
my ( $blast_record, $line, @blast_query, @blast_subject, $query, $subject, @results );
- while ( $blast_record = &xml_get_blast_record( $fh ) and scalar @{ $blast_record } > 0 )
+ while ( $blast_record = xml_get_blast_record( $fh ) and scalar @{ $blast_record } > 0 )
{
foreach $line ( @{ $blast_record } )
{
if ( $line =~ /<\/Iteration_hits>/ )
{
- $query = &xml_parse_blast_query( \@blast_query );
- $subject = &xml_parse_blast_subject( \@blast_subject );
+ $query = xml_parse_blast_query( \@blast_query );
+ $subject = xml_parse_blast_subject( \@blast_subject );
push @results, {
"QUERY" => $query,
if ( $line =~ /<\/Hit_hsps>/ )
{
- $hit = &xml_parse_blast_hit( \@blast_hit );
- $hsps = &xml_parse_blast_hsps( \@blast_hsps );
+ $hit = xml_parse_blast_hit( \@blast_hit );
+ $hsps = xml_parse_blast_hsps( \@blast_hsps );
$hit->{ "HSPS" } = $hsps;