adding bzip2 support in ruby

[biopieces.git] / code_perl / Maasha / Blast.pm

diff --git a/code_perl/Maasha/Blast.pm b/code_perl/Maasha/Blast.pm
index 5b8647bd0ee5c952d670b19f43a5d1e275846ad8..c5d70c30d8153531d1a4e1b5ab396876c5784b3d 100644 (file)
--- a/code_perl/Maasha/Blast.pm
+++ b/code_perl/Maasha/Blast.pm
@@ -1,6 +1,6 @@
 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
@@ -28,6 +28,7 @@ package Maasha::Blast;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Storable qw( dclone );
 use Data::Dumper;
@@ -108,12 +109,12 @@ sub xml_parse_blast
     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
     {
@@ -133,7 +134,7 @@ sub xml_parse_blast_ncbi
 
     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 } )
         {
@@ -147,8 +148,8 @@ sub xml_parse_blast_ncbi
 
                 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,
@@ -175,7 +176,7 @@ sub xml_parse_blast_blastcl3
 
     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 } )
         {
@@ -189,8 +190,8 @@ sub xml_parse_blast_blastcl3
 
                 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,
@@ -277,8 +278,8 @@ sub xml_parse_blast_subject
 
             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;