path: root/sci-biology/consed/files/consed-29-fix-perl-shebang.patch

Make perl shebangs portable, such that the scripts can also be used on Gentoo Prefix.
Rationale: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/

--- a/contributions/ace2fof
+++ b/contributions/ace2fof
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 
 # .-----------------------------------------------------------------------------------.
 # |                                                                                   |
@@ -107,6 +107,7 @@
 # |                                                                                   |
 # `-----------------------------------------------------------------------------------'
 #Fixed this file for taking Aracne's Ace file by syang 05152002
+use warnings;
 use strict;
 use POSIX qw(fmod);
 
--- a/contributions/ace2OligosWithComments.perl
+++ b/contributions/ace2OligosWithComments.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 #
 # ace2Oligos.perl
 #
@@ -18,6 +18,8 @@
 # Rev: 020528 to print comments in oligo tags upon request (Peter Kos)
 #
 
+use warnings;
+
 $szUsage = "\nUsage:  $0 (name of ace file) (name of oligo file) [Print|Comment|PrintComment]\n";
 
 die "$szUsage" if  (( $#ARGV != 1 ) && ( $#ARGV != 2 ));
--- a/contributions/aceContigs2Phds.perl
+++ b/contributions/aceContigs2Phds.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 #
 # aceContigs2Phd.perl
 #
@@ -13,6 +13,8 @@
 # Acknowledgements: Borrowed as much as I could from determineReadTypes.Perl
 #                   and fasta2Phd.perl
 
+use warnings;
+
 $szUsage = "Usage: aceContigs2Phds.perl [-s minimum-contig-size] <name of ace file>";
 $nContigLimit = 2000;
 
--- a/contributions/acestatus.pl
+++ b/contributions/acestatus.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 
 # acestatus.pl
 # author: Cliff Wollam
@@ -14,6 +14,7 @@
 # USAGE FROM THE COMMAND LINE:
 # acestatus.pl ace_filename
 
+use warnings;
 use strict;
 
 if($#ARGV >= 0) {
--- a/contributions/cons.perl
+++ b/contributions/cons.perl
@@ -1,5 +1,6 @@
-#!/usr/bin/perl
+#!/usr/bin/env perl
 
+use warnings;
 use strict;
 use Cwd;
 
--- a/contributions/mergeAces.perl
+++ b/contributions/mergeAces.perl
@@ -1,4 +1,4 @@
-#! /usr/local/bin/perl -w
+#!/usr/bin/env perl
 
 # Bugs and complaints to Bill Gilliland, billg@ucdavis.edu.
 # mergeAces.perl v. 0.2 5/22/01
@@ -9,6 +9,7 @@
 # project directory (if it doesn't already exist) with all the cgrams
 # and phd files of the original projects.
 
+use warnings;
 use Getopt::Long;
 use File::Copy;
 $pathRoot = $ENV{"PWD"};
--- a/contributions/phredPhrapWithPhdBalls
+++ b/contributions/phredPhrapWithPhdBalls
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 #
 # phredPhrapWithPhdBalls
 #    modified from phredPhrap by Ben Allen at LANL
@@ -73,6 +73,7 @@
 # Rev: 120312 to not duplicate consensus tags during miniassembly
 # Rev: 120717 Ben Allen (LANL) to use reads from phdballs as well as phd_dir
 
+use warnings;
 
 $szVersion = "120312";
 
--- a/contributions/recover_consensus_tags
+++ b/contributions/recover_consensus_tags
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 
 # Purpose:  Transfers all consensus tags from a set of old assemblies to
 #     a new assembly.  
@@ -14,6 +14,7 @@
 #  rct ace_filename <only ace file to be transfer (optional)>
 # You must be in the edit_dir where the ace file is located
 
+use warnings;
 use strict;
 
 
--- a/contributions/revert_fof
+++ b/contributions/revert_fof
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 
 # PURPOSE:  If the user really screws up a read, to back out all changes.
 #           You must reassemble after using this.
@@ -19,6 +19,8 @@
 # phd extensions.
 # revert_fof use file of files to give reads to revert 3/14/01 SL
 
+use warnings;
+
 $szUsage = "Enter a file of files name, please!";
 
 die $szUsage if ( $#ARGV != 0 );
--- a/contributions/sff2phd.perl
+++ b/contributions/sff2phd.perl
@@ -1,4 +1,5 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
+use warnings;
 use strict;
  #          SFF to PHD files converter, with 454 paired reads and MID support
  #          Version 0.15 - 111229
--- a/contributions/sff2phd_Samborskyy
+++ b/contributions/sff2phd_Samborskyy
@@ -1,4 +1,5 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
+use warnings;
 use strict;
  #          SFF to PHD files converter, with 454 paired reads and MID support
  #          Version 0.10 - 101110
--- a/scripts/ace2Fasta.perl
+++ b/scripts/ace2Fasta.perl
@@ -1,7 +1,9 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 #
 # Purpose:  makes a contigs file out of an ace file
 
+use warnings;
+
 $szUsage = "Usage:  ace2Contigs.perl (ace file)";
 
 
--- a/scripts/ace2Oligos.perl
+++ b/scripts/ace2Oligos.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 #
 # ace2Oligos.perl
 #
@@ -16,6 +16,8 @@
 # Rev: 000330 to handle comments in oligo tags
 #
 
+use warnings;
+
 $szUsage = "Usage:  ace2Oligos.perl (name of ace file) (name of oligo file)";
 
 if ( $ARGV[0] eq "-V" || $ARGV[0] eq "-v" ) {
--- a/scripts/add454Reads.perl
+++ b/scripts/add454Reads.perl
@@ -1,11 +1,11 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 
 # add454Reads.perl
 # part of Consed package
 # 
 # DG with help from Hao Wang to screen vector
 
-
+use warnings;
 use File::Basename;
 
 
--- a/scripts/addReads2Consed.perl
+++ b/scripts/addReads2Consed.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 #
 #   Purpose:  called by consed in order to add new reads to an
 #       existing assembly without reassemblying
@@ -29,6 +29,7 @@
 #   Rev: 080320 (David Gordon) to use discrep_lists instead of alignments
 #   Rev: 130828 (David Gordon) to handle slashes (/) in read names
 
+use warnings;
 
 $szVersion = "130828";
 if ( $#ARGV >= 0 ) {
--- a/scripts/addSangerReads.perl
+++ b/scripts/addSangerReads.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 
 # addSangerReads.perl
 
@@ -32,7 +32,7 @@
 # added is printed in a report ending with ".log".  The name of this
 # file is listed in auto.fof
 
-
+use warnings;
 
 
 $szVersion = "120717";
--- a/scripts/addSolexaReads.perl
+++ b/scripts/addSolexaReads.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 
 # addSolexaReads.perl
 
@@ -54,7 +54,7 @@
 
 $szUsage = "addSolexaReads.perl -ace (ace file) -fastqfof (solexa files) -fasta (fasta file) -readsList (file of list of desired reads) where -readsList is optional";
 
-
+use warnings;
 use Getopt::Long;
 
 GetOptions( "ace=s" => \$szAceFile,
--- a/scripts/alignRNA2Genomic.perl
+++ b/scripts/alignRNA2Genomic.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 
 # alignRNA2Genomic.perl
 
@@ -6,6 +6,8 @@
 # consed-ready ace and phd ball with the RNA aligned against the
 # genomic with introns being represented by large gaps
 
+use warnings;
+
 $szVersion = "120717";
 
 if ( $#ARGV == 0 ) {
--- a/scripts/alignSolexaReads2Refs.perl
+++ b/scripts/alignSolexaReads2Refs.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 
 # Input: a file where each line looks like this:
 #    (solexa seq file) (read prefix)
@@ -10,6 +10,7 @@
 
 # Output: a list of alignment files
 
+use warnings;
 
 defined( $szConsedHome = $ENV{'CONSED_HOME'} ) ||
     ( $szConsedHome = "/usr/local/genome" );
--- a/scripts/amplifyTranscripts.perl
+++ b/scripts/amplifyTranscripts.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 
 # PURPOSE: runs consed -autoPCRAmplify in order to pick pcr primers 
 #    for a large group of regions
@@ -40,7 +40,7 @@
 #   That is, the left primers are given in top strand orientation, and
 #   the right primers are given in bottom strand orientation.
 
-
+use warnings;
 
 defined( $szConsedHome = $ENV{'CONSED_HOME'} ) ||
     ( $szConsedHome = "/usr/local/genome" );
--- a/scripts/autoPrimers.perl
+++ b/scripts/autoPrimers.perl
@@ -1,5 +1,6 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 
+use warnings;
 
 $szUsage = "autoPrimers.perl (fasta file of targets)";
 $szVersion = "141226";
--- a/scripts/bam2Ace.perl
+++ b/scripts/bam2Ace.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 
 
 # Purpose:  runs:
@@ -6,6 +6,7 @@
 #  2) consed -renameDuplicates
 #  3) consed -removeColumnsOfPads
 
+use warnings;
 
 $szUsage = "usage: bam2Ace.perl -bamFile (bam file) -regionsFile (regions file) (see README.txt for format of the regions file) -exec (consed executable name) -newAceFile (new ace file name) where the -exec (exec) is optional";
 
--- a/scripts/convertBedToBamScape.perl
+++ b/scripts/convertBedToBamScape.perl
@@ -1,4 +1,6 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
+
+use warnings;
 
 $szUsage = "usage: convertBedToBamScape.perl (Bed file) (BamScape file) (fasta file of all sequences) (conversion of reference names--optional)";
 
--- a/scripts/countEditedBases.perl
+++ b/scripts/countEditedBases.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 #
 # countEditedBases.perl
 #
@@ -11,6 +11,8 @@
 #
 #
 
+use warnings;
+
 while(<>) {
 	if ( /^CO / ) {
 		@aWords = split;
--- a/scripts/determineReadTypes.perl
+++ b/scripts/determineReadTypes.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 #  determineReadTypes.perl
 #  
 #  Purpose:  to write into the phd file information about the template 
@@ -173,6 +173,7 @@
 #
 ###############################################################
 
+use warnings;
 
 # you can remove or comment out this line when you are satisfied with
 # your customized version of this file.
--- a/scripts/fasta2Ace.perl
+++ b/scripts/fasta2Ace.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 #
 # manyFasta2Ace.perl
 #
@@ -13,6 +13,7 @@
 #
 # NOTE:  you must run this in edit_dir 
 
+use warnings;
 use Getopt::Long;
 
 $szRevision = "141212";
--- a/scripts/fasta2PhdBall.perl
+++ b/scripts/fasta2PhdBall.perl
@@ -1,4 +1,6 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
+
+use warnings;
 
 $nQuality = 20;
 
--- a/scripts/fasta2Phd.perl
+++ b/scripts/fasta2Phd.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 #
 # fasta2Phd.perl
 #
@@ -20,6 +20,7 @@
 #            June 2002, Bill Gilliland to allow the user to specify 
 #                the quality value
 
+use warnings;
 use Getopt::Long;
 GetOptions( "quality=i" => \$qualityValue);
  
--- a/scripts/fastq2Phrap.perl
+++ b/scripts/fastq2Phrap.perl
@@ -1,4 +1,6 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
+
+use warnings;
 
 $szUsage = "fastq2Phrap.perl (fastq) or for paired reads fastq2Phrap.perl (fastq1) (fastq2) where fastq1 and fastq2 have corresponding mate pairs--e.g., the 5th read in fastq1 is the mate of the 5th read in fastq2--these fastq files are assumed to be in ../solexa_dir--not the current directory\n";
 
--- a/scripts/filter454Reads.perl
+++ b/scripts/filter454Reads.perl
@@ -1,6 +1,6 @@
-#!/usr/bin/perl -w
-
+#!/usr/bin/env perl
 
+use warnings;
 use File::Basename;
 
 
--- a/scripts/findSequenceMatchesForConsed.perl
+++ b/scripts/findSequenceMatchesForConsed.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 
 # findSequenceMatchesForConsed.perl
 
@@ -16,6 +16,8 @@
 # REVISIONS: 021127 (DG) to write (project).(date).(time).fasta instead of
 #    (project).fasta.screen.ace.1.(date).(time).fasta
 
+use warnings;
+
 $szVersion = "021127";
 
 $szUsage = "Usage: findSequenceMatchesForConsed.perl (ace file) (crossmatch parameters, if any)";
--- a/scripts/fixContigEnd.perl
+++ b/scripts/fixContigEnd.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 
 # fixContigEnd.perl
 
@@ -7,6 +7,7 @@
 # consed -ace (acefile) -fixContigEnds
 #
 
+use warnings;
 
 $szUsage = "fixContigEnd.perl (fasta file of reads for input) (fof for ace file, output)";
 
--- a/scripts/lib2Phd.perl
+++ b/scripts/lib2Phd.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 #
 # lib2Phd.perl
 #
@@ -23,6 +23,8 @@
 #    accept fasta library files as input.  The output file is named 
 #    according to the first, non-space block of text on each fasta defline. 
 
+use warnings;
+
 $nQuality = 20;
 
 $szUsage = "Usage: lib2Phd.perl <name of file with fasta library>";
--- a/scripts/makePhdBall.perl
+++ b/scripts/makePhdBall.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 
 # PURPOSE: concatenate all phd file into a single phd.ball 
 #          for the purpose of fast startup of consed
@@ -9,6 +9,7 @@
 #
 # February 2008, David Gordon
 
+use warnings;
 
 if ( $#ARGV >= 0 ) {
    if ( $ARGV[0] eq "-v" || $ARGV[0] eq "-V" ) {
--- a/scripts/makeRegionsFile.perl
+++ b/scripts/makeRegionsFile.perl
@@ -1,10 +1,12 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 
 # makeRegionsFile.perl
 # To be used with consed -bam2Ace
 # Takes a fasta file of sequences and makes a regions file that
 # specifies the entire length of each sequence.
 
+use warnings;
+
 $szUsage = "makeRegionsFile.perl (name of fasta file)";
 
 $szVersion = "110914";
--- a/scripts/orderPrimerPairs.perl
+++ b/scripts/orderPrimerPairs.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 
 # PURPOSE: puts the primers in 96 well format for ordering.  
 #  creates a file that can be emailed to
@@ -13,6 +13,8 @@
 #         2) a file of primer pairs, sorted by product size
 #         3) a fasta file of the primers, for your convenience for analysis
 
+use warnings;
+
 $| = 1;
 
 $szUsage = "orderPrimerPairs.perl";
--- a/scripts/phd2Ace.perl
+++ b/scripts/phd2Ace.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 #
 # phd2Ace.perl
 #
@@ -13,6 +13,8 @@
 # REV:  981002 (David Gordon) for new ace format
 #       981210 (DG) to eliminate warning message
 
+use warnings;
+
 $szPhdDirPath = "../phd_dir";
 
 $szUsage = "Usage: phd2Ace.perl <filename (without directory) of phd file>\nThe phd file is assumed to reside in $szPhdDirPath";
--- a/scripts/phredPhrap
+++ b/scripts/phredPhrap
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 #
 # phredPhrap
 #
@@ -70,6 +70,8 @@
 # Rev: 110609 to allow masking of vector sequence when doing miniassemblies
 # Rev: 120312 to not duplicate consensus tags during miniassembly
 
+use warnings;
+
 $szVersion = "120312";
 
 
--- a/scripts/picard2Regions.perl
+++ b/scripts/picard2Regions.perl
@@ -1,10 +1,12 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 
 # PURPOSE: takes a file of locations in the format for bamScape custom
 # navigation (Picard IntervalList format), adds 2000 bases of context
 # to each side of each location, and prints a region file in format to
 # be used by bam2Ace
 
+use warnings;
+
 $szRevision = "140903"; # David Gordon
 
 if ( defined( $ARGV[0] ) &&
--- a/scripts/removeReads
+++ b/scripts/removeReads
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 #
 # PURPOSE:  removes a list of chromats from an assembly.  After running this,
 #   you must reassemble to create an ace file without the given phd files.
@@ -16,6 +16,8 @@
 #        removeReads (name of fof's)
 #
 
+use warnings;
+
 $szUsage = "Usage: removeReads listOfReads.fof";
 
 die "$szUsage" if ( $#ARGV != 0 );
--- a/scripts/revertToUneditedRead
+++ b/scripts/revertToUneditedRead
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 #
 # PURPOSE:  If the user really screws up a read, to back out all changes.
 #           You must reassemble after using this.
@@ -16,6 +16,7 @@
 # REV:  7/24/98 (DG)
 # REV:  8/28/2013 (DG) to handle readnames with slashes (/)
 
+use warnings;
 
 $szUsage = "Usage: revertToUneditedRead (read name without any .phd.# extension)";
 
--- a/scripts/selectOneRegion.perl
+++ b/scripts/selectOneRegion.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 
 # selectOneRegion.perl
 # 
@@ -11,6 +11,7 @@
 # and you will create an ace file chr15_51000000.ace  or chr15_51000000.ace.1 
 # (or higher extension)
 
+use warnings;
 use Getopt::Long;
 
 
--- a/scripts/selectRegions.perl
+++ b/scripts/selectRegions.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 
 # selectRegions.perl
 # 
@@ -43,7 +43,7 @@
 # my_new_ace.ace says what the ace file should be called (the
 # extension may not start at 1 if there is already a .1
 
-
+use warnings;
 
 $SIG{__WARN__} = dieWhenGetWarning;
 sub dieWhenGetWarning {
--- a/scripts/tagRepeats.perl
+++ b/scripts/tagRepeats.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 #
 # PROGRAM:  tagRepeats.perl
 # PURPOSE:  to put consensus tags on any found ALU or any other 
@@ -10,6 +10,7 @@
 # INPUTS:   The ace file.  You must also provide a fasta file of the 
 #           ALU or any other sequence you want to tag
 
+use warnings;
 
 $szVersion = "090209";
 if ( $#ARGV >= 0 ) {
--- a/scripts/testSocket.perl
+++ b/scripts/testSocket.perl
@@ -1,7 +1,8 @@
-#! /usr/local/bin/perl -w
+#!/usr/bin/env perl
  
 # open a socket to consed
- 
+
+use warnings;
 use IO::Socket;
  
 # Consed makes a file which has nothing but the port number.
--- a/scripts/transferConsensusTags.perl
+++ b/scripts/transferConsensusTags.perl
@@ -1,4 +1,4 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
 #
 # Purpose:  Transfers consensus tags from an old assembly to
 #     a new assembly.  
@@ -44,6 +44,8 @@
 # Nov 2001, DG to handle cloneEnd tags which have orientation
 # Mar 2012, DG to prevent duplicating tags after miniassembly
 
+use warnings;
+
 $szUsage = "Usage:  transferConsensusTags.perl (old ace file) (new ace file) (file of list of old contigs with consensus tags to be transferred)";
 
 if ( $ARGV[0] eq "-V" || $ARGV[0] eq "-v" ) {