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157 lines
4.7 KiB
Diff
157 lines
4.7 KiB
Diff
Author: Steffen Moeller <steffen_moeller@gmx.de>
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Description: Fixes a series of errors indicated by Perl 5.18.
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Forwarded: https://sourceforge.net/p/perlprimer/patches/6/
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Index: git/perlprimer.pl
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===================================================================
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--- git.orig/perlprimer.pl
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+++ git/perlprimer.pl
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@@ -3093,23 +3093,24 @@
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# and because it's 3' primer-dimers that are the real problem in PCR.
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# create a binding array for each of the four bases
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- for $l (0 .. $pfl-1) {
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+ foreach $l (0 .. $pfl-1) {
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my $mbase = substr($fprimer_r, $l, 1);
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$primer_hash{$mbase}[$l]=1;
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- for $k qw(a g c t) {
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+ my @nucleotides = qw(a g c t);
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+ foreach $k (@nucleotides) {
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$primer_hash{$k}[$l] ||=0;
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}
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}
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# create the primer matrix
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my @primer_comp;
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- for $k (0 .. $prl-1) {
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+ foreach $k (0 .. $prl-1) {
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$primer_comp[$k]=$primer_hash{substr($rcomprlc, $k, 1)};
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}
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# read each combination from the matrix, calculate dG for each dimer
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my $pd_len = ($pd_full ? $pfl+$prl-1 : $pl-2);
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- for $k (0 .. $pd_len) {
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+ foreach $k (0 .. $pd_len) {
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$score[$k]=0;
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my $bind;
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my $score_p=0;
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@@ -3129,7 +3130,7 @@
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# }
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# read the binding data
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- for $l (0 .. $prl-1) {
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+ foreach $l (0 .. $prl-1) {
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if (($k-$l)<$pfl) {
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$bind .= $primer_comp[$l][$k-$l] if ($k-$l)>=0;
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} else {
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@@ -3148,7 +3149,7 @@
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# Find start and end of similarity
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my ($pb_init,$pb_end);
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- for $l (0 .. length($bind)-1) {
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+ foreach $l (0 .. length($bind)-1) {
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# at first I tried finding the initiating terminal bases with
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# regexps, but that was much slower ...
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if (substr($bind, $l, 1) eq "1") {
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@@ -3159,7 +3160,7 @@
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if (defined($pb_init)) {
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# deltaG calculation
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- for $l ($pb_init .. $pb_end-1) {
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+ foreach $l ($pb_init .. $pb_end-1) {
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next if substr($bind, $l, 2) eq "00";
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next if substr($bind, $l, 1) eq "2";
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$score_p+=$oligo_dG{substr($primer_f, $pfl-$k+$l-1, 2).substr($rprimer_r, $l, 2)};
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@@ -3228,44 +3229,44 @@
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# and because it's 3' primer-dimers that are the real problem in PCR.
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# create a binding array for each of the four bases
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- for $l (0 .. $pfl-1) {
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+ foreach $l (0 .. $pfl-1) {
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my $mbase = substr($fprimer_r, $l, 1);
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$primer_hash{$mbase}[$l]=1;
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- for $k qw(a g c t) {
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+ foreach $k (qw(a g c t)) {
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$primer_hash{$k}[$l] ||=0;
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}
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}
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# create the primer matrix
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my @primer_comp;
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- for $k (0 .. $prl-1) {
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- $primer_comp[$k]=$primer_hash{substr($rcomprlc, $k, 1)};
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+ foreach my $kk (0 .. $prl-1) {
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+ $primer_comp[$kk]=$primer_hash{substr($rcomprlc, $kk, 1)};
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}
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# print the matrix - for debugging
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print "$primer_f vs. $primer_r - full pd = $pd_full\n";
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print " \t";
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- for $l (0 .. $pfl-1) {
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+ foreach $l (0 .. $pfl-1) {
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my $mbase = substr($fprimer_r, $l, 1);
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print "$mbase ";
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}
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print "\n";
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- for $k (0 .. $prl-1) {
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- my $base = substr($rprimer_r, $k, 1);
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- print "$base:\t@{$primer_comp[$k]}\n";
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+ foreach my $kk (0 .. $prl-1) {
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+ my $base = substr($rprimer_r, $kk, 1);
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+ print "$base:\t@{$primer_comp[$kk]}\n";
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}
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my @binding_data;
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# read each combination from the matrix, calculate dG for each dimer
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my $pd_len = ($pd_full ? $pfl+$prl-1 : $pl-2);
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- for my $k (0 .. $pd_len) {
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- $score[$k]=0;
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+ foreach my $kk (0 .. $pd_len) {
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+ $score[$kk]=0;
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my $bind;
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my $score_p=0;
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# starting coords
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- my $pf_coord_start = ($k >= $pfl ? $pfl-1 : $k);
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- my $pr_coord_start = ($k - $pfl > 0 ? $k - $pfl : 0);
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+ my $pf_coord_start = ($kk >= $pfl ? $pfl-1 : $kk);
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+ my $pr_coord_start = ($kk - $pfl > 0 ? $kk - $pfl : 0);
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my ($pf_coord, $pr_coord, $first, $flag);
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# read through each combination finding multiple matches
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@@ -3285,7 +3286,7 @@
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}
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} elsif ($flag) {
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# end of a binding stretch
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- push @binding_data, [$k, $first, $bind] if $bind > 1;
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+ push @binding_data, [$kk, $first, $bind] if $bind > 1;
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$bind=0;
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$flag=0;
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}
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@@ -3325,7 +3326,7 @@
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# # }
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#
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# # read the binding data
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- # for $l (0 .. $prl-1) {
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+ # foreach $l (0 .. $prl-1) {
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# if (($k-$l)<$pfl) {
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# $bind .= $primer_comp[$l][$k-$l] if ($k-$l)>=0;
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# } else {
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@@ -3344,7 +3345,7 @@
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#
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# # Find start and end of similarity
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# my ($pb_init,$pb_end);
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- # for $l (0 .. length($bind)-1) {
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+ # foreach $l (0 .. length($bind)-1) {
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# # at first I tried finding the initiating terminal bases with
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# # regexps, but that was much slower ...
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# if (substr($bind, $l, 1) eq "1") {
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@@ -3355,7 +3356,7 @@
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#
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# if (defined($pb_init)) {
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# # deltaG calculation
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- # for $l ($pb_init .. $pb_end-1) {
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+ # foreach $l ($pb_init .. $pb_end-1) {
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# next if substr($bind, $l, 2) eq "00";
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# next if substr($bind, $l, 1) eq "2";
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# $score_p+=$oligo_dG{substr($primer_f, $pfl-$k+$l-1, 2).substr($rprimer_r, $l, 2)};
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