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|
Description: Make sure that iterator variable is explicitly decalred as
a lexcical using my keyword. See PBP, page 108. Add perl shebang.
From: Alex Mestiashvili <amestia@rsh2.donotuse.de>
--- gff2aplot.orig/src/gff2aplot.pl
+++ gff2aplot/src/gff2aplot.pl
@@ -1,3 +1,4 @@
+#!/usr/bin/perl
#
# %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# % GFF2APLOT %
@@ -1663,7 +1664,7 @@
&report( 'NO_CUSTOM_FOUND', $file );
last MAIN;
};
- LOAD: foreach $file (@custom_files) {
+ LOAD: foreach my $file (@custom_files) {
open( THIS, "< $file" )
|| ( &warn( 'FILE_NO_OPEN', $T, $file ), next LOAD );
&report( 'READ_CUSTOM_FILE', $file );
@@ -1934,7 +1935,7 @@
sub parse_GFF_files() {
&header("PARSING INPUT GFF RECORDS");
- LOAD: foreach $file (@data_files) {
+ LOAD: foreach my $file (@data_files) {
open( THIS, "< $file" )
|| ( &warn( 'FILE_NO_OPEN', $T, $file ), next LOAD );
$file eq '-' && ( $file = 'STANDARD INPUT' );
@@ -2665,13 +2666,13 @@
my ( $out, $v );
$out = 0; #
# print STDERR ("#"x40)."\n";
- foreach $v (qw/ FEATURE GROUP STRAND SOURCE SEQUENCE /) {
+ foreach my $v (qw/ FEATURE GROUP STRAND SOURCE SEQUENCE /) {
# print STDERR "### GET LAYER: $v ($name) : ".
# (defined($Defaults{$v}{$name})?$Defaults{$v}{$name}:"undef")."\n";
defined( $Defaults{$v}{$name} ) && ( $out = $Defaults{$v}{$name} );
}; # foreach
- foreach $v (@refs) {
+ foreach my $v (@refs) {
# print STDERR "### GET LAYER: $v ($name) : ".
# (defined($v->{$name})?$v->{$name}:"undef")."\n";
@@ -3002,7 +3003,7 @@
#
( $sq_a, $sq_b ) = @$_ra;
- foreach $naln (@$_ro) {
+ foreach my $naln (@$_ro) {
( $nm_a, $nm_b ) = split /:/o, $naln->[0], 2;
( "$nm_a" eq "$sq_a" && "$nm_b" eq "$sq_b" ) && do {
@$_ra = ( $nm_a, $nm_b );
@@ -3010,7 +3011,7 @@
};
}; # foreach $naln
# swapping
- foreach $naln (@$_ro) {
+ foreach my $naln (@$_ro) {
( $nm_a, $nm_b ) = split /:/o, $naln->[0], 2;
( "$nm_a" eq "$sq_b" && "$nm_b" eq "$sq_a" ) && do {
@$_ra = ( $nm_a, $nm_b );
@@ -3024,7 +3025,7 @@
sub search_seqname() {
my ( $sq_a, $sq_b, $_ro ) = @_;
my ( $a_found, $naln );
- foreach $naln (@$_ro) {
+ foreach my $naln (@$_ro) {
( $sq_a eq '.+' && defined($sq_b) && "$naln->[0]" eq "$sq_b" ) && next;
( $sq_a eq '.+' || "$naln->[0]" eq "$sq_a" ) && do {
$sq_a = $naln->[0];
@@ -4279,13 +4280,13 @@
my ( $out, $v );
# print STDERR ("#"x40)."\n";
- foreach $v (qw/ FEATURE GROUP STRAND SOURCE SEQUENCE /) {
+ foreach my $v (qw/ FEATURE GROUP STRAND SOURCE SEQUENCE /) {
defined( $Defaults{$v}{$name} ) && ( $out = $Defaults{$v}{$name} );
# print STDERR "### GET VAR VALUE: $v ($name) : ".
# (defined($Defaults{$v}{$name})?$Defaults{$v}{$name}:"undef")."\n";
}; # foreach
- foreach $v (@$refs) {
+ foreach my $v (@$refs) {
defined( $v->[$_prop]{$name} ) && ( $out = $v->[$_prop]{$name} );
# print STDERR "### GET VAR VALUE: $v ($name) : ".
|
