academic/perlprimer: Fixed syntax error.
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Petar Petrov
Erik Hanson
parent
ad51632962
commit
437e34b650
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@ -17,9 +17,9 @@ PerlPrimer's current features include the following:
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to be in-frame
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- QPCR primer design without manual intron-exon boundary entry
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For details and citation:
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Marshall OJ. PerlPrimer: cross-platform, graphical primer design for
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standard, bisulphite and real-time PCR. Bioinformatics 2004
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20(15):2471-2472
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An optional run-time dependency is spidey, for Real Time PCR.
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For Real Time PCR, spidey is required.
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For details and citation:
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Marshall OJ. PerlPrimer: cross-platform, graphical primer design for
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standard, bisulphite and real-time PCR. Bioinformatics 2004
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20(15):2471-2472
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@ -2,7 +2,7 @@
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# Slackware build script for perlprimer
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# Copyright 2011 Petar Petrov, ppetrov@paju.oulu.fi
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# Copyright 2011-2014 Petar Petrov, petar.petrov@student.oulu.fi
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# All rights reserved.
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#
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# Redistribution and use of this script, with or without modification, is
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@ -24,7 +24,7 @@
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PRGNAM=perlprimer
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VERSION=${VERSION:-1.1.21}
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BUILD=${BUILD:-1}
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BUILD=${BUILD:-2}
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TAG=${TAG:-_SBo}
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ARCH=noarch
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@ -44,10 +44,13 @@ tar xvf $CWD/$PRGNAM-$VERSION.tar.bz2
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cd $PRGNAM-$VERSION
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chown -R root:root .
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find -L . \
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\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \
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-exec chmod 755 {} \; -o \
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\( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
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-exec chmod 644 {} \;
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\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
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-o -perm 511 \) -exec chmod 755 {} \; -o \
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\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
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-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
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# Thanks to Debian for the patch!
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patch -p1 -i $CWD/sytaxerrors.patch
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install -D -m755 perlprimer.pl $PKG/usr/bin/perlprimer.pl
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install -D -m644 gcg.603 $PKG/usr/share/$PRGNAM/gcg.603
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@ -7,4 +7,4 @@ DOWNLOAD_x86_64=""
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MD5SUM_x86_64=""
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REQUIRES="libwww-perl perl-tk"
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MAINTAINER="Petar Petrov"
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EMAIL="ppetrov@paju.oulu.fi"
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EMAIL="petar.petrov@student.oulu.fi"
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@ -0,0 +1,157 @@
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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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