path: root/perl-shebangs.patch

From eae2a63c25fcb95e6fc1e6e062215ad1e8b24345 Mon Sep 17 00:00:00 2001
From: Christian Krause <kizkizzbangbang@googlemail.com>
Date: Thu, 16 Jul 2015 12:33:10 +0200
Subject: [PATCH] use more portable /usr/bin/env perl for scripts

This is useful, e.g. if your perl is not installed in /usr/bin or you
want to give a specific perl precendence over the one installed in
/usr/bin. Wherever there was `perl -w` there is now `use warnings;`.
---
 cd-hit-2d-para.pl                     | 3 ++-
 cd-hit-auxtools/cd-hit-dup-PE-out.pl  | 2 +-
 cd-hit-div.pl                         | 2 +-
 cd-hit-para.pl                        | 3 ++-
 clstr2tree.pl                         | 2 +-
 clstr2txt.pl                          | 2 +-
 clstr2xml.pl                          | 2 +-
 clstr_cut.pl                          | 2 +-
 clstr_merge.pl                        | 2 +-
 clstr_merge_noorder.pl                | 2 +-
 clstr_quality_eval.pl                 | 2 +-
 clstr_quality_eval_by_link.pl         | 2 +-
 clstr_reduce.pl                       | 2 +-
 clstr_renumber.pl                     | 2 +-
 clstr_rep.pl                          | 2 +-
 clstr_reps_faa_rev.pl                 | 2 +-
 clstr_rev.pl                          | 2 +-
 clstr_select.pl                       | 2 +-
 clstr_select_rep.pl                   | 2 +-
 clstr_size_histogram.pl               | 2 +-
 clstr_size_stat.pl                    | 2 +-
 clstr_sort_by.pl                      | 2 +-
 clstr_sort_prot_by.pl                 | 2 +-
 clstr_sql_tbl.pl                      | 2 +-
 clstr_sql_tbl_sort.pl                 | 2 +-
 make_multi_seq.pl                     | 2 +-
 plot_2d.pl                            | 2 +-
 plot_len1.pl                          | 2 +-
 psi-cd-hit/cd-hit-div.pl              | 2 +-
 psi-cd-hit/clstr_select_rep.pl        | 2 +-
 psi-cd-hit/clstr_select_seq.pl        | 2 +-
 psi-cd-hit/fetch_fasta_by_ids.pl      | 2 +-
 psi-cd-hit/fetch_fasta_exclude_ids.pl | 2 +-
 psi-cd-hit/psi-2d.pl                  | 2 +-
 psi-cd-hit/psi-cd-hit-local.pl        | 3 ++-
 psi-cd-hit/psi-cd-hit.pl              | 4 +++-
 36 files changed, 41 insertions(+), 36 deletions(-)

diff --git a/cd-hit-2d-para.pl b/cd-hit-2d-para.pl
index 3cab955..9aa2d8a 100755
--- a/cd-hit-2d-para.pl
+++ b/cd-hit-2d-para.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 # =============================================================================
 # CD-HIT
 # http://cd-hit.org/
@@ -11,6 +11,7 @@
 #                                      Email liwz@sdsc.edu
 # =============================================================================
 
+use warnings;
 use strict;
 no strict "refs";
 
diff --git a/cd-hit-auxtools/cd-hit-dup-PE-out.pl b/cd-hit-auxtools/cd-hit-dup-PE-out.pl
index bfe5af3..f035229 100755
--- a/cd-hit-auxtools/cd-hit-dup-PE-out.pl
+++ b/cd-hit-auxtools/cd-hit-dup-PE-out.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 my $script_name = $0;
 my $script_dir = $0;
diff --git a/cd-hit-div.pl b/cd-hit-div.pl
index e349394..db8d942 100755
--- a/cd-hit-div.pl
+++ b/cd-hit-div.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 #not like cd-hit-div, this script do not sort input
 #or throw away seq
diff --git a/cd-hit-para.pl b/cd-hit-para.pl
index 33f1a1b..db62e38 100755
--- a/cd-hit-para.pl
+++ b/cd-hit-para.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 # =============================================================================
 # CD-HIT
 # http://cd-hit.org/
@@ -11,6 +11,7 @@
 #                                      Email liwz@sdsc.edu
 # =============================================================================
 
+use warnings;
 use strict;
 no strict "refs";
 
diff --git a/clstr2tree.pl b/clstr2tree.pl
index 73fd37a..56d9fe2 100755
--- a/clstr2tree.pl
+++ b/clstr2tree.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 $clstr = shift;
 $fr = shift; # for nr80.clstr $fr = 0.8
diff --git a/clstr2txt.pl b/clstr2txt.pl
index 902b083..127537e 100755
--- a/clstr2txt.pl
+++ b/clstr2txt.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 my $no = 0;
 my $clstr_no = "";
diff --git a/clstr2xml.pl b/clstr2xml.pl
index 10d828c..ba8264a 100755
--- a/clstr2xml.pl
+++ b/clstr2xml.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 #usage: clstr_xml.pl [-len|-size] level1.clstr [level2.clstr level3.clstr ...]
 #purpose: to create xml file from cd-hit or hierarchical cd-hit(h-cd-hit) results
diff --git a/clstr_cut.pl b/clstr_cut.pl
index 498f180..ae0264c 100755
--- a/clstr_cut.pl
+++ b/clstr_cut.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 #keep only top $no proteins in cluster
 
diff --git a/clstr_merge.pl b/clstr_merge.pl
index 3fe108e..9186777 100755
--- a/clstr_merge.pl
+++ b/clstr_merge.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 # the order of clusters need to be identical
 my ($master_clstr, @clstr) = @ARGV;
diff --git a/clstr_merge_noorder.pl b/clstr_merge_noorder.pl
index f8acdfc..0852aee 100755
--- a/clstr_merge_noorder.pl
+++ b/clstr_merge_noorder.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 # order of clusters don't need to be the same
 # but then I have to read everything into memory
diff --git a/clstr_quality_eval.pl b/clstr_quality_eval.pl
index 62f2a3d..060ab01 100755
--- a/clstr_quality_eval.pl
+++ b/clstr_quality_eval.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 ## calculate the sensitivity and specificity of clusters
 ## if the input fasta file has pre-defined classification term
diff --git a/clstr_quality_eval_by_link.pl b/clstr_quality_eval_by_link.pl
index 8fba8df..140c05c 100755
--- a/clstr_quality_eval_by_link.pl
+++ b/clstr_quality_eval_by_link.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 ## calculate the sensitivity and specificity of clusters
 ## if the input fasta file has pre-defined classification term
diff --git a/clstr_reduce.pl b/clstr_reduce.pl
index 990f4ad..3621025 100755
--- a/clstr_reduce.pl
+++ b/clstr_reduce.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 
 $file90 = shift;
diff --git a/clstr_renumber.pl b/clstr_renumber.pl
index b542304..c66088d 100755
--- a/clstr_renumber.pl
+++ b/clstr_renumber.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 $no = 0;
 while($ll=<>){
   if ($ll =~ /^>Cluster (\d+)/) {
diff --git a/clstr_rep.pl b/clstr_rep.pl
index 0ebeb88..84b86b3 100755
--- a/clstr_rep.pl
+++ b/clstr_rep.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 $rep = "";
 $no = 0;
diff --git a/clstr_reps_faa_rev.pl b/clstr_reps_faa_rev.pl
index 80a4a8a..3574b2b 100755
--- a/clstr_reps_faa_rev.pl
+++ b/clstr_reps_faa_rev.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 # output single fasta file
 # for each cluster output at least $cutoff seqs
 
diff --git a/clstr_rev.pl b/clstr_rev.pl
index d7efdcc..71134e2 100755
--- a/clstr_rev.pl
+++ b/clstr_rev.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 # if nr90 from nr100 and
 #    nr80 from nr90, so I have nr90.clstr and nr80.clstr
 # but, in nr80.clstr, some gi numbers whose from nr100 are there
diff --git a/clstr_select.pl b/clstr_select.pl
index 1b168d9..dc70147 100755
--- a/clstr_select.pl
+++ b/clstr_select.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 #my $by = shift;
 my $min;
diff --git a/clstr_select_rep.pl b/clstr_select_rep.pl
index 80c7b7e..f7c38f4 100755
--- a/clstr_select_rep.pl
+++ b/clstr_select_rep.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 #my $by = shift;
 my $min;
diff --git a/clstr_size_histogram.pl b/clstr_size_histogram.pl
index 01ecb63..b726e46 100755
--- a/clstr_size_histogram.pl
+++ b/clstr_size_histogram.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 if(@ARGV==0){
    print "Usage:\n\tclstr_size_histogram.pl [-bin N] clstr_file\n";
diff --git a/clstr_size_stat.pl b/clstr_size_stat.pl
index b234b06..ecda7db 100755
--- a/clstr_size_stat.pl
+++ b/clstr_size_stat.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 if(@ARGV==0){
    print "Usage:\n\tclstr_size_stat.pl clstr_file\n";
diff --git a/clstr_sort_by.pl b/clstr_sort_by.pl
index 82e9cf8..adb12d8 100755
--- a/clstr_sort_by.pl
+++ b/clstr_sort_by.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 my $sort_by_what = shift;
    $sort_by_what = "no" unless $sort_by_what;
diff --git a/clstr_sort_prot_by.pl b/clstr_sort_prot_by.pl
index 64f19e2..0832b99 100755
--- a/clstr_sort_prot_by.pl
+++ b/clstr_sort_prot_by.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 my $sort_by = shift;
    $sort_by = "len" unless ($sort_by);
diff --git a/clstr_sql_tbl.pl b/clstr_sql_tbl.pl
index f2dba07..68bfd7d 100755
--- a/clstr_sql_tbl.pl
+++ b/clstr_sql_tbl.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 if(@ARGV==0){
   print "Usage:\n\tclstr_sql_tbl.pl clstr_file tbl_file\n";
diff --git a/clstr_sql_tbl_sort.pl b/clstr_sql_tbl_sort.pl
index 67d60a8..3dfe9c4 100755
--- a/clstr_sql_tbl_sort.pl
+++ b/clstr_sql_tbl_sort.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 if(@ARGV==0){
    print "Usage:\n\tclstr_sql_tbl_sort.pl table_file level\n";
diff --git a/make_multi_seq.pl b/make_multi_seq.pl
index 7b05636..3678654 100755
--- a/make_multi_seq.pl
+++ b/make_multi_seq.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 #note you have to use "-d 0" in the cd-hit run
 #note you better to use "-g 1" in the cd-hit run
diff --git a/plot_2d.pl b/plot_2d.pl
index 418a5cf..91342ca 100755
--- a/plot_2d.pl
+++ b/plot_2d.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 use Image::Magick;
 
diff --git a/plot_len1.pl b/plot_len1.pl
index efcdfe0..e8be6e3 100755
--- a/plot_len1.pl
+++ b/plot_len1.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 $file90 = shift;
 $segs = shift;
diff --git a/psi-cd-hit/cd-hit-div.pl b/psi-cd-hit/cd-hit-div.pl
index e349394..db8d942 100755
--- a/psi-cd-hit/cd-hit-div.pl
+++ b/psi-cd-hit/cd-hit-div.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 #not like cd-hit-div, this script do not sort input
 #or throw away seq
diff --git a/psi-cd-hit/clstr_select_rep.pl b/psi-cd-hit/clstr_select_rep.pl
index b465586..63db0ce 100755
--- a/psi-cd-hit/clstr_select_rep.pl
+++ b/psi-cd-hit/clstr_select_rep.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 my $by = shift;
 my $min;
diff --git a/psi-cd-hit/clstr_select_seq.pl b/psi-cd-hit/clstr_select_seq.pl
index fd7bb8b..598b0e9 100755
--- a/psi-cd-hit/clstr_select_seq.pl
+++ b/psi-cd-hit/clstr_select_seq.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 my $by = shift;
 my $min;
diff --git a/psi-cd-hit/fetch_fasta_by_ids.pl b/psi-cd-hit/fetch_fasta_by_ids.pl
index bfdbb26..9c17504 100755
--- a/psi-cd-hit/fetch_fasta_by_ids.pl
+++ b/psi-cd-hit/fetch_fasta_by_ids.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 my ($gi_file, $seq_file) = @ARGV;
 
diff --git a/psi-cd-hit/fetch_fasta_exclude_ids.pl b/psi-cd-hit/fetch_fasta_exclude_ids.pl
index 90e237e..13d061a 100755
--- a/psi-cd-hit/fetch_fasta_exclude_ids.pl
+++ b/psi-cd-hit/fetch_fasta_exclude_ids.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 my ($gi_file, $seq_file) = @ARGV;
 
diff --git a/psi-cd-hit/psi-2d.pl b/psi-cd-hit/psi-2d.pl
index ab3f655..f3884a3 100755
--- a/psi-cd-hit/psi-2d.pl
+++ b/psi-cd-hit/psi-2d.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
 
 my $script_name = $0;
diff --git a/psi-cd-hit/psi-cd-hit-local.pl b/psi-cd-hit/psi-cd-hit-local.pl
index a77c7f7..e7866c3 100755
--- a/psi-cd-hit/psi-cd-hit-local.pl
+++ b/psi-cd-hit/psi-cd-hit-local.pl
@@ -1,7 +1,8 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 ################################################################################
 ######### PSI-cd-hit written by Weizhong Li at http://cd-hit.org
 ################################################################################
+use warnings;
 our $pid       = $$;
 our $db_in     = "";   ###################
 our $db_out    = "";   # input / output
diff --git a/psi-cd-hit/psi-cd-hit.pl b/psi-cd-hit/psi-cd-hit.pl
index af99e52..35aaeda 100755
--- a/psi-cd-hit/psi-cd-hit.pl
+++ b/psi-cd-hit/psi-cd-hit.pl
@@ -1,8 +1,10 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 ################################################################################
 ######### PSI-cd-hit written by Weizhong Li at http://cd-hit.org
 ################################################################################
 
+use warnings;
+
 our $script_name = $0;
 our $script_dir = $0;
    $script_dir =~ s/[^\/]+$//;