academic/perlprimer: Updated for version 1.1.21.

Signed-off-by: David Spencer <idlemoor@slackbuilds.org>

1 files changed, 157 insertions, 0 deletions

diff --git a/academic/perlprimer/01_sytaxerrors.patch b/academic/perlprimer/01_sytaxerrors.patch
new file mode 100644
index 0000000000..45b9cd570d
--- /dev/null
+++ b/academic/perlprimer/01_sytaxerrors.patch
@@ -0,0 +1,157 @@
+Author: Steffen Moeller <steffen_moeller@gmx.de>
+Description: Fixes a series of errors indicated by Perl 5.18.
+Forwarded: https://sourceforge.net/p/perlprimer/patches/6/
+
+Index: git/perlprimer.pl
+===================================================================
+--- git.orig/perlprimer.pl
++++ git/perlprimer.pl
+@@ -3093,23 +3093,24 @@
+ 	# and because it's 3' primer-dimers that are the real problem in PCR.
+ 	
+ 	# create a binding array for each of the four bases
+-	for $l (0 .. $pfl-1) {
++	foreach $l (0 .. $pfl-1) {
+ 		my $mbase = substr($fprimer_r, $l, 1);
+ 		$primer_hash{$mbase}[$l]=1;
+-		for $k qw(a g c t) {
++		my @nucleotides = qw(a g c t);
++		foreach $k (@nucleotides) {
+ 			$primer_hash{$k}[$l] ||=0;
+ 		}
+ 	}
+ 		
+ 	# create the primer matrix
+ 	my @primer_comp;
+-	for $k (0 .. $prl-1) {
++	foreach $k (0 .. $prl-1) {
+ 		$primer_comp[$k]=$primer_hash{substr($rcomprlc, $k, 1)};
+ 	}
+ 		
+ 	# read each combination from the matrix, calculate dG for each dimer
+ 	my $pd_len = ($pd_full ? $pfl+$prl-1 : $pl-2);
+-	for $k (0 .. $pd_len) {
++	foreach $k (0 .. $pd_len) {
+ 		$score[$k]=0;
+ 		my $bind;
+ 		my $score_p=0;
+@@ -3129,7 +3130,7 @@
+ 		# }
+ 		
+ 		# read the binding data
+-		for $l (0 .. $prl-1) {
++		foreach $l (0 .. $prl-1) {
+ 			if (($k-$l)<$pfl) {
+ 				$bind .= $primer_comp[$l][$k-$l] if ($k-$l)>=0;
+ 			} else {
+@@ -3148,7 +3149,7 @@
+ 		
+ 		# Find start and end of similarity
+ 		my ($pb_init,$pb_end);
+-		for $l (0 .. length($bind)-1) {
++		foreach $l (0 .. length($bind)-1) {
+ 			# at first I tried finding the initiating terminal bases with
+ 			# regexps, but that was much slower ...
+ 			if (substr($bind, $l, 1) eq "1") {
+@@ -3159,7 +3160,7 @@
+ 				
+ 		if (defined($pb_init)) {
+ 			# deltaG calculation
+-			for $l ($pb_init .. $pb_end-1) {
++			foreach $l ($pb_init .. $pb_end-1) {
+ 				next if substr($bind, $l, 2) eq "00";
+ 				next if substr($bind, $l, 1) eq "2";
+ 				$score_p+=$oligo_dG{substr($primer_f, $pfl-$k+$l-1, 2).substr($rprimer_r, $l, 2)};
+@@ -3228,44 +3229,44 @@
+ 	# and because it's 3' primer-dimers that are the real problem in PCR.
+ 	
+ 	# create a binding array for each of the four bases
+-	for $l (0 .. $pfl-1) {
++	foreach $l (0 .. $pfl-1) {
+ 		my $mbase = substr($fprimer_r, $l, 1);
+ 		$primer_hash{$mbase}[$l]=1;
+-		for $k qw(a g c t) {
++		foreach $k (qw(a g c t)) {
+ 			$primer_hash{$k}[$l] ||=0;
+ 		}
+ 	}
+ 		
+ 	# create the primer matrix
+ 	my @primer_comp;
+-	for $k (0 .. $prl-1) {
+-		$primer_comp[$k]=$primer_hash{substr($rcomprlc, $k, 1)};
++	foreach my $kk (0 .. $prl-1) {
++		$primer_comp[$kk]=$primer_hash{substr($rcomprlc, $kk, 1)};
+ 	}
+ 	
+ 	# print the matrix - for debugging
+ 	print "$primer_f vs. $primer_r - full pd = $pd_full\n";
+ 	print "  \t";
+-	for $l (0 .. $pfl-1) {
++	foreach $l (0 .. $pfl-1) {
+ 		my $mbase = substr($fprimer_r, $l, 1);
+ 		print "$mbase ";
+ 	}
+ 	print "\n";
+-	for $k (0 .. $prl-1) {
+-		my $base = substr($rprimer_r, $k, 1);
+-		print "$base:\t@{$primer_comp[$k]}\n";
++	foreach my $kk (0 .. $prl-1) {
++		my $base = substr($rprimer_r, $kk, 1);
++		print "$base:\t@{$primer_comp[$kk]}\n";
+ 	}
+ 	
+ 	my @binding_data;
+ 	# read each combination from the matrix, calculate dG for each dimer
+ 	my $pd_len = ($pd_full ? $pfl+$prl-1 : $pl-2);
+-	for my $k (0 .. $pd_len) {
+-		$score[$k]=0;
++	foreach my $kk (0 .. $pd_len) {
++		$score[$kk]=0;
+ 		my $bind;
+ 		my $score_p=0;
+ 		
+ 		# starting coords
+-		my $pf_coord_start = ($k >= $pfl ? $pfl-1 : $k);
+-		my $pr_coord_start = ($k - $pfl > 0 ? $k - $pfl : 0);
++		my $pf_coord_start = ($kk >= $pfl ? $pfl-1 : $kk);
++		my $pr_coord_start = ($kk - $pfl > 0 ? $kk - $pfl : 0);
+ 		my ($pf_coord, $pr_coord, $first, $flag);
+ 		
+ 		# read through each combination finding multiple matches
+@@ -3285,7 +3286,7 @@
+ 				}
+ 			} elsif ($flag) {
+ 				# end of a binding stretch
+-				push @binding_data, [$k, $first, $bind] if $bind > 1;
++				push @binding_data, [$kk, $first, $bind] if $bind > 1;
+ 				$bind=0;
+ 				$flag=0;
+ 			}
+@@ -3325,7 +3326,7 @@
+ 		# # }
+ 				# 
+ 		# # read the binding data
+-		# for $l (0 .. $prl-1) {
++		# foreach $l (0 .. $prl-1) {
+ 			# if (($k-$l)<$pfl) {
+ 				# $bind .= $primer_comp[$l][$k-$l] if ($k-$l)>=0;
+ 			# } else {
+@@ -3344,7 +3345,7 @@
+ 		# 
+ 		# # Find start and end of similarity
+ 		# my ($pb_init,$pb_end);
+-		# for $l (0 .. length($bind)-1) {
++		# foreach $l (0 .. length($bind)-1) {
+ 			# # at first I tried finding the initiating terminal bases with
+ 			# # regexps, but that was much slower ...
+ 			# if (substr($bind, $l, 1) eq "1") {
+@@ -3355,7 +3356,7 @@
+ 				# 
+ 		# if (defined($pb_init)) {
+ 			# # deltaG calculation
+-			# for $l ($pb_init .. $pb_end-1) {
++			# foreach $l ($pb_init .. $pb_end-1) {
+ 				# next if substr($bind, $l, 2) eq "00";
+ 				# next if substr($bind, $l, 1) eq "2";
+ 				# $score_p+=$oligo_dG{substr($primer_f, $pfl-$k+$l-1, 2).substr($rprimer_r, $l, 2)};