strip keyword substitution from perl scripts

bioperl · Jul 29, 2010 · 4017a48 · 4017a48
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commit 4017a48
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diff --git a/examples/align/aligntutorial.pl b/examples/align/aligntutorial.pl
@@ -1,6 +1,5 @@
 #!/usr/bin/perl -w
 
-# $Id$
 # An example of how to use the different alignment tools in bioperl
 # to align some sequences
 

diff --git a/examples/align/clustalw.pl b/examples/align/clustalw.pl
@@ -3,7 +3,6 @@
 # PURPOSE  : Demonstrate possible uses of Bio::Tools::Run::Alignment::Clustalw.pm
 # AUTHOR   : Peter Schattner schattner@alum.mit.edu
 # CREATED  : Oct 06 2000
-# REVISION : $Id$
 #
 # INSTALLATION
 #

diff --git a/examples/align/simplealign.pl b/examples/align/simplealign.pl
@@ -4,7 +4,6 @@
 # PURPOSE  : Simple driver for Bio::SimpleAlign
 # AUTHOR   : Ewan Birney birney@sanger.ac.uk 
 # CREATED  : Tue Oct 27 1998
-# REVISION : $Id$
 #
 # INSTALLATION
 #    If you have installed bioperl using the standard

diff --git a/examples/biblio/biblio-eutils-example.pl b/examples/biblio/biblio-eutils-example.pl
@@ -1,5 +1,4 @@
 #!/usr/bin/perl -w
-# $Id$
 =head1 NAME
 
 biblio-eutils-example.pl

diff --git a/examples/biblio/biblio-soap-example.pl b/examples/biblio/biblio-soap-example.pl
@@ -1,5 +1,4 @@
 #!/usr/bin/perl -w
-# $Id$
 =head1 NAME
 
 biblio-soap-example.pl

diff --git a/examples/contributed/nmrpdb_parse.pl b/examples/contributed/nmrpdb_parse.pl
@@ -1,5 +1,4 @@
 #!/usr/bin/perl -w
-# $Id$
 use strict;
 
 # This program will read in an NMR derived PDB file containing

diff --git a/examples/contributed/prosite2perl.pl b/examples/contributed/prosite2perl.pl
@@ -1,5 +1,4 @@
 #!/usr/bin/perl -w
-# $Id$
 # prosite2perl -- convert Prosite patterns to Perl regular expressions
 #
 # Jordan Dimov (jdimov@cis.clarion.edu)

diff --git a/examples/liveseq/change_gene.pl b/examples/liveseq/change_gene.pl
@@ -1,5 +1,4 @@
 #!/usr/bin/perl
-# $Id$
 
 use strict;
 use Bio::LiveSeq::IO::BioPerl;

diff --git a/examples/make_primers.pl b/examples/make_primers.pl
@@ -1,5 +1,4 @@
 #!/usr/bin/perl -w
-# $Id$
 # Author: cckim@stanford.edu
 
 # Description: This program designs primers for constructing knockouts

diff --git a/examples/popgen/parse_calc_stats.pl b/examples/popgen/parse_calc_stats.pl
@@ -1,6 +1,5 @@
 #!/usr/bin/perl -w
 # Author: Jason Stajich, jason@bioperl.org
-# $Id$
 # $Revision: 6576 $
 
 use strict;

diff --git a/examples/rev_and_trans.pl b/examples/rev_and_trans.pl
@@ -4,7 +4,6 @@
 # PURPOSE  : Simple driver for Bio::Seq revcom and translate
 # AUTHOR   : Ewan Birney birney@sanger.ac.uk 
 # CREATED  : Tue Oct 27 1998
-# REVISION : $Id$
 #
 # INSTALLATION
 #    If you have installed bioperl using the standard

diff --git a/examples/root/exceptions1.pl b/examples/root/exceptions1.pl
@@ -14,7 +14,6 @@
 #
 # Author: Steve Chervitz <sac@bioperl.org>
 #
-# $Id$
 
 use strict;
 use lib qw(lib/ ../../);

diff --git a/examples/root/exceptions2.pl b/examples/root/exceptions2.pl
@@ -12,7 +12,6 @@
 #
 # Author: Steve Chervitz <sac@bioperl.org>
 #
-# $Id$
 
 use strict;
 

diff --git a/examples/root/exceptions3.pl b/examples/root/exceptions3.pl
@@ -14,7 +14,6 @@
 #
 # Author: Steve Chervitz <sac@bioperl.org>
 #
-# $Id$
 
 use strict;
 use lib qw(lib/ ../../);

diff --git a/examples/root/exceptions4.pl b/examples/root/exceptions4.pl
@@ -9,7 +9,6 @@
 #
 # Author: Steve Chervitz <sac@bioperl.org>
 #
-# $Id$
 
 
 # Setting this variable simulates not having Error.pm installed.

diff --git a/examples/searchio/custom_writer.pl b/examples/searchio/custom_writer.pl
@@ -30,7 +30,6 @@
 #   STDERR: Progress info.
 #
 # Author: Steve Chervitz <sac@bioperl.org>
-# Revision: $Id$
 
 package MyBlastWriter;
 

diff --git a/examples/searchio/hitwriter.pl b/examples/searchio/hitwriter.pl
@@ -38,7 +38,6 @@
 #   Bio::SearchIO
 #
 # Author: Steve Chervitz <sac@bioperl.org>
-# Revision: $Id$
 
 use strict;
 use lib '../../';

diff --git a/examples/searchio/hspwriter.pl b/examples/searchio/hspwriter.pl
@@ -36,7 +36,6 @@
 #   Bio::SearchIO
 #
 # Author: Steve Chervitz <sac@bioperl.org>
-# Revision: $Id$
 
 use strict;
 use lib '../../';

diff --git a/examples/searchio/htmlwriter.pl b/examples/searchio/htmlwriter.pl
@@ -24,7 +24,6 @@
 #   Bio::SearchIO
 #
 # Author: Steve Chervitz <sac@bioperl.org>
-# Revision: $Id$
 
 
 use strict;

diff --git a/examples/searchio/psiblast_features.pl b/examples/searchio/psiblast_features.pl
@@ -21,7 +21,6 @@
 #   Bio::SearchIO::psiblast
 #
 # Author: Steve Chervitz <sac@bioperl.org>
-# Revision: $Id$
 
 use strict;
 use lib '../../';

diff --git a/examples/searchio/psiblast_iterations.pl b/examples/searchio/psiblast_iterations.pl
@@ -13,7 +13,6 @@
 #   Bio::Search::Iteration::IterationI
 #
 # Author: Steve Chervitz <sac@bioperl.org>
-# Revision: $Id$
 
 use strict;
 use lib '../../';

diff --git a/examples/searchio/rawwriter.pl b/examples/searchio/rawwriter.pl
@@ -20,7 +20,6 @@
 #   Bio::SearchIO::psiblast
 #
 # Author: Steve Chervitz <sac@bioperl.org>
-# Revision: $Id$
 #
 # TODO: 
 #   * Implement a Bio::SearchIO::Writer::HSPTextWriter object

diff --git a/examples/searchio/resultwriter.pl b/examples/searchio/resultwriter.pl
@@ -34,7 +34,6 @@
 #   Bio::SearchIO
 #
 # Author: Steve Chervitz <sac@bioperl.org>
-# Revision: $Id$
 
 
 use strict;

diff --git a/examples/tools/extract_genes.pl b/examples/tools/extract_genes.pl
@@ -1,5 +1,4 @@
 #!/usr/bin/perl -w
-# $Id$
 =pod
 
 =head1 NAME

diff --git a/examples/tools/psw.pl b/examples/tools/psw.pl
@@ -4,7 +4,6 @@
 # PURPOSE  : Simple driver for Bio::Tools::pSW
 # AUTHOR   : Ewan Birney birney@sanger.ac.uk 
 # CREATED  : Tue Oct 27 1998
-# REVISION : $Id$
 #
 # INSTALLATION
 #  

diff --git a/examples/tools/reverse-translate.pl b/examples/tools/reverse-translate.pl
@@ -1,5 +1,4 @@
 #!/usr/bin/perl -w
-# $Id$
 
 =head1 NAME
 

diff --git a/examples/tools/run_primer3.pl b/examples/tools/run_primer3.pl
@@ -1,5 +1,4 @@
 #!/usr/bin/perl -w
-# $Id$
 
 =head1 NAME
 

diff --git a/examples/tools/seq_pattern.pl b/examples/tools/seq_pattern.pl
@@ -7,7 +7,6 @@
 #           nucleotide or peptide sequences).
 # AUTHOR  : Steve Chervitz (sac@bioperl.org)
 # CREATED : 28 Aug 1997
-# REVISION: $Id$
 # USAGE   : seq_pattern.pl -h
 # COMMENTS: 
 #    This is a driver script for the Bio::Tools::SeqPattern.pm Bioperl module

diff --git a/examples/tools/standaloneblast.pl b/examples/tools/standaloneblast.pl
@@ -4,7 +4,6 @@
 # PURPOSE  : Demonstrate possible uses of Bio::Tools::StandAloneBlast.pm
 # AUTHOR   : Peter Schattner schattner@alum.mit.edu
 # CREATED  : Nov 01 2000
-# REVISION : $Id$
 #
 # INSTALLATION
 #

diff --git a/maintenance/authors.pl b/maintenance/authors.pl
@@ -1,5 +1,4 @@
 #!/usr/bin/perl -w
-# $Id$
 #
 =head1 NAME
 

diff --git a/maintenance/cvs2cl_by_file.pl b/maintenance/cvs2cl_by_file.pl
@@ -25,9 +25,6 @@
 ###                                                        ###
 ##############################################################
 
-## $Revision$
-## $Date$
-## $Author$
 ##
 
 use strict;

diff --git a/maintenance/modules.pl b/maintenance/modules.pl
@@ -1,5 +1,4 @@
 #!/usr/bin/perl -w
-# $Id$
 #
 =head1 NAME
 

diff --git a/maintenance/pod.pl b/maintenance/pod.pl
@@ -1,5 +1,4 @@
 #!/usr/bin/perl -w
-# $Id$
 #
 =head1 NAME
 

diff --git a/maintenance/version.pl b/maintenance/version.pl
@@ -1,5 +1,4 @@
 #!/usr/bin/perl -w
-# $Id$
 #
 =head1 version
 

diff --git a/scripts/Bio-DB-GFF/bulk_load_gff.PLS b/scripts/Bio-DB-GFF/bulk_load_gff.PLS
@@ -1,5 +1,4 @@
 #!/usr/bin/perl
-# $Id$
 
 use strict;
 # use lib './blib/lib';

diff --git a/scripts/Bio-DB-GFF/fast_load_gff.PLS b/scripts/Bio-DB-GFF/fast_load_gff.PLS
@@ -1,5 +1,4 @@
 #!/usr/bin/perl
-# $Id$
 
 use strict;
 # use lib './blib/lib';

diff --git a/scripts/Bio-DB-GFF/genbank2gff.PLS b/scripts/Bio-DB-GFF/genbank2gff.PLS
@@ -2,7 +2,6 @@
 
 use lib '.';
 
-# $Id$
 use strict;
 use Bio::DB::GFF;
 use Getopt::Long;

diff --git a/scripts/Bio-DB-GFF/generate_histogram.PLS b/scripts/Bio-DB-GFF/generate_histogram.PLS
@@ -1,5 +1,4 @@
 #!/usr/bin/perl
-# $Id$
 
 use strict;
 use lib '.','./blib','../../blib/lib';

diff --git a/scripts/Bio-DB-GFF/process_sgd.PLS b/scripts/Bio-DB-GFF/process_sgd.PLS
@@ -1,6 +1,5 @@
 #!/usr/bin/perl -w
 
-# $Id$
 # This script will convert from SGD format to GFF format
 # See http://db.yeastgenome.org/schema/Schema.html
 

diff --git a/scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS b/scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS
@@ -1,5 +1,4 @@
 #!/usr/bin/perl
-# $Id$
 
 use strict;
 

diff --git a/scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS b/scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS
@@ -1,5 +1,4 @@
 #!/usr/bin/env perl
-# $Id$
 # AUTHOR: malcolm.cook@stowers-institute.org
 
 use strict;

diff --git a/scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS b/scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS
@@ -1,5 +1,4 @@
 #!/usr/bin/perl
-# $Id$
 
 use strict;
 

diff --git a/scripts/DB/biofetch_genbank_proxy.PLS b/scripts/DB/biofetch_genbank_proxy.PLS
@@ -1,5 +1,4 @@
 #!perl -w
-# $Id$
 
 # dbfetch style caching proxy for GenBank
 use strict;

diff --git a/scripts/DB/biogetseq.PLS b/scripts/DB/biogetseq.PLS
@@ -1,5 +1,4 @@
 #!perl -w
-# $Id$
 #
 # OBDA Registry compliant sequence retrieval script
 #

diff --git a/scripts/DB/flanks.PLS b/scripts/DB/flanks.PLS
@@ -1,6 +1,5 @@
 #!perl
 # -*-Perl-*-
-# $Id$
 #
 # Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
 # Finding flanking sequences for a variant.

diff --git a/scripts/biblio/biblio.PLS b/scripts/biblio/biblio.PLS
@@ -16,7 +16,6 @@
 #   martin.senger@gmail.com
 #   February 2002
 #
-#   $Id$
 #-----------------------------------------------------------------------------
 
 use strict;

diff --git a/scripts/das/das_server.pl b/scripts/das/das_server.pl
@@ -1,7 +1,6 @@
 #!/usr/bin/perl
 
 # minimal annotation server
-# $Id$
 
 use strict;
 use Apache::DBI;

diff --git a/scripts/index/bp_seqret.PLS b/scripts/index/bp_seqret.PLS
@@ -1,5 +1,4 @@
 #!/usr/bin/perl -w
-# $Id$
 # -*-Perl-*- mode (for emacs)
 
 =head1 NAME

diff --git a/scripts/popgen/composite_LD.PLS b/scripts/popgen/composite_LD.PLS
@@ -1,6 +1,5 @@
 #!/usr/bin/perl -w
 # -*-Perl-*- 
-# $Id$
 
 =head1 NAME 
 

diff --git a/scripts/popgen/heterogeneity_test.PLS b/scripts/popgen/heterogeneity_test.PLS
@@ -1,6 +1,5 @@
 #!/usr/bin/perl -w
 # -*-Perl-*- (for my emacs)
-# $Id$
 
 use strict;
 

diff --git a/scripts/searchio/filter_search.PLS b/scripts/searchio/filter_search.PLS
@@ -1,7 +1,6 @@
 #!perl -w
 use strict;
 
-# $Id$
 
 
 =head1 NAME

diff --git a/scripts/searchio/parse_hmmsearch.PLS b/scripts/searchio/parse_hmmsearch.PLS
@@ -1,5 +1,4 @@
 #!/usr/bin/perl -w
-# $Id$
 
 use strict;
 

diff --git a/scripts/seq/extract_feature_seq.PLS b/scripts/seq/extract_feature_seq.PLS
@@ -1,6 +1,5 @@
 #!perl -w
 use strict;
-# $Id$
 # Author Jason Stajich <jason@bioperl.org>
 
 =head1 NAME

diff --git a/scripts/seq/make_mrna_protein.PLS b/scripts/seq/make_mrna_protein.PLS
@@ -1,5 +1,4 @@
 #!perl -w
-# $Id$
 #
 =head1 NAME
 

diff --git a/scripts/seq/seqconvert.PLS b/scripts/seq/seqconvert.PLS
@@ -1,5 +1,4 @@
 #!perl -w
-# $Id$
 
 use strict;
 use Getopt::Long;

diff --git a/scripts/seq/seqretsplit.PLS b/scripts/seq/seqretsplit.PLS
@@ -1,5 +1,4 @@
 #!/usr/bin/perl -w
-# $Id$
 #
 =head1 NAME
 

diff --git a/scripts/seq/split_seq.PLS b/scripts/seq/split_seq.PLS
@@ -1,6 +1,5 @@
 #!perl -w
 use strict;
-# $Id$
 
 =head1 NAME
-Original file line number
+Diff line change
@@ Expand Up / @@ -14,7 +14,6 @@ @@
     #
     # Author: Steve Chervitz <sac@bioperl.org>
     #
-    # $Id$
     use strict;
     use lib qw(lib/ ../../);
@@ Expand Down @@