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] "; $nContigLimit = 2000; --- a/contributions/acestatus.pl +++ b/contributions/acestatus.pl @@ -1,4 +1,4 @@ -#!/usr/bin/perl -w +#!/usr/bin/env perl # acestatus.pl # author: Cliff Wollam @@ -14,6 +14,7 @@ # USAGE FROM THE COMMAND LINE: # acestatus.pl ace_filename +use warnings; use strict; if($#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 # 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 "; --- 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 \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" ) {