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gentoo-overlay/sci-biology/consed/files/consed-29-fix-perl-shebang....

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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" ) {
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