diff options
Diffstat (limited to 'academic/perlprimer/01_sytaxerrors.patch')
| -rw-r--r-- | academic/perlprimer/01_sytaxerrors.patch | 157 |
1 files changed, 0 insertions, 157 deletions
diff --git a/academic/perlprimer/01_sytaxerrors.patch b/academic/perlprimer/01_sytaxerrors.patch deleted file mode 100644 index 45b9cd570d..0000000000 --- a/academic/perlprimer/01_sytaxerrors.patch +++ /dev/null @@ -1,157 +0,0 @@ -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)}; |