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academic/perlprimer: Updated for version 1.2.3_f7d3bd0.
academic/perlprimer: Updated for version 1.2.3_f7d3bd0.
Signed-off-by: David Spencer <idlemoor@slackbuilds.org>pull/47/head
Petar Petrov
7 years ago
committed by
David Spencer
David Spencer
6 changed files with 23 additions and 197 deletions
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157academic/perlprimer/01_sytaxerrors.patch
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11academic/perlprimer/02_fix-defined-slist.patch
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18academic/perlprimer/README
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24academic/perlprimer/perlprimer.SlackBuild
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8academic/perlprimer/perlprimer.info
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2academic/perlprimer/slack-desc
@ -1,157 +0,0 @@ |
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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, $l, 2)}; |
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@ -1,11 +0,0 @@ |
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--- orig/perlprimer.pl 2016-11-22 21:06:25.135978000 +0200
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+++ new/perlprimer.pl 2016-11-22 21:08:09.001971413 +0200
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@@ -5226,7 +5226,7 @@ sub generate_report {
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} |
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my ($hlist_sel) = $$hlist_ref->selectionGet; |
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- unless (defined(@$slist) && defined($hlist_sel)) {
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+ unless (@$slist && defined($hlist_sel)) {
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dialogue("The Generate Report function saves the statistics and alignment of a particular primer pair - please select a primer pair first"); |
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return; |
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} |
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