From 7c156d69589b299f887d88de26ea446120ddd2cd Mon Sep 17 00:00:00 2001 From: =?utf8?q?Carn=C3=AB=20Draug?= Date: Mon, 25 Jul 2011 19:57:54 +0100 Subject: [PATCH] scripts: replaced -w switch by use warnings --- scripts/DB/bp_biofetch_genbank_proxy.PLS | 3 ++- scripts/DB/bp_biogetseq.PLS | 3 ++- scripts/biblio/bp_biblio.PLS | 3 ++- scripts/searchio/bp_filter_search.PLS | 4 ++-- scripts/searchio/bp_hmmer_to_table.PLS | 3 ++- scripts/seq/bp_extract_feature_seq.PLS | 3 ++- scripts/seq/bp_make_mrna_protein.PLS | 3 ++- scripts/seq/bp_seqconvert.PLS | 3 ++- scripts/seq/bp_split_seq.PLS | 3 ++- scripts/seq/bp_translate_seq.PLS | 3 ++- scripts/seq/bp_unflatten_seq.PLS | 3 ++- scripts/seqstats/bp_aacomp.PLS | 3 ++- scripts/seqstats/bp_chaos_plot.PLS | 3 ++- scripts/seqstats/bp_gccalc.PLS | 3 ++- scripts/seqstats/bp_oligo_count.PLS | 3 ++- scripts/taxa/bp_taxid4species.PLS | 3 ++- scripts/tree/bp_nexus2nh.PLS | 3 ++- scripts/tree/bp_tree2pag.PLS | 3 ++- scripts/utilities/bp_dbsplit.PLS | 3 ++- scripts/utilities/bp_mask_by_search.PLS | 3 ++- scripts/utilities/bp_nrdb.PLS | 3 ++- scripts/utilities/bp_pairwise_kaks.PLS | 3 ++- scripts/utilities/bp_search2BSML.PLS | 3 ++- scripts/utilities/bp_search2alnblocks.PLS | 3 ++- scripts/utilities/bp_search2gff.PLS | 3 ++- scripts/utilities/bp_search2tribe.PLS | 3 ++- scripts/utilities/bp_seq_length.PLS | 3 ++- 27 files changed, 54 insertions(+), 28 deletions(-) diff --git a/scripts/DB/bp_biofetch_genbank_proxy.PLS b/scripts/DB/bp_biofetch_genbank_proxy.PLS index 44d0bede3..05deac528 100644 --- a/scripts/DB/bp_biofetch_genbank_proxy.PLS +++ b/scripts/DB/bp_biofetch_genbank_proxy.PLS @@ -1,7 +1,8 @@ -#!perl -w +#!perl # dbfetch style caching proxy for GenBank use strict; +use warnings; use CGI qw(:standard); use HTTP::Request::Common; use LWP::UserAgent; diff --git a/scripts/DB/bp_biogetseq.PLS b/scripts/DB/bp_biogetseq.PLS index cc2cdcbfc..7c7897b34 100644 --- a/scripts/DB/bp_biogetseq.PLS +++ b/scripts/DB/bp_biogetseq.PLS @@ -1,4 +1,4 @@ -#!perl -w +#!perl # # OBDA Registry compliant sequence retrieval script # @@ -10,6 +10,7 @@ use Bio::DB::Registry; use Bio::SeqIO; use Getopt::Long; use strict; +use warnings; my ($help, $format, $namespace, $dbname) = ('', 'embl', 'acc', 'embl'); GetOptions ("help" => \$help, "format=s" => \$format, diff --git a/scripts/biblio/bp_biblio.PLS b/scripts/biblio/bp_biblio.PLS index 12df00334..885184ef4 100644 --- a/scripts/biblio/bp_biblio.PLS +++ b/scripts/biblio/bp_biblio.PLS @@ -1,4 +1,4 @@ -#!perl -w +#!perl # # A client showing how to use Bio::Biblio module, a module for # accessing and querying a bibliographic repository. @@ -19,6 +19,7 @@ #----------------------------------------------------------------------------- use strict; +use warnings; sub get_usage { exec('perldoc',$0); diff --git a/scripts/searchio/bp_filter_search.PLS b/scripts/searchio/bp_filter_search.PLS index 2d2919523..d534e4248 100644 --- a/scripts/searchio/bp_filter_search.PLS +++ b/scripts/searchio/bp_filter_search.PLS @@ -1,6 +1,6 @@ -#!perl -w +#!perl use strict; - +use warnings; =head1 NAME diff --git a/scripts/searchio/bp_hmmer_to_table.PLS b/scripts/searchio/bp_hmmer_to_table.PLS index 734121ee0..a24db61da 100644 --- a/scripts/searchio/bp_hmmer_to_table.PLS +++ b/scripts/searchio/bp_hmmer_to_table.PLS @@ -1,5 +1,6 @@ -#!perl -w +#!perl use strict; +use warnings; =head1 NAME diff --git a/scripts/seq/bp_extract_feature_seq.PLS b/scripts/seq/bp_extract_feature_seq.PLS index f43a9b617..7d4ad600a 100644 --- a/scripts/seq/bp_extract_feature_seq.PLS +++ b/scripts/seq/bp_extract_feature_seq.PLS @@ -1,5 +1,6 @@ -#!perl -w +#!perl use strict; +use warnings; # Author Jason Stajich =head1 NAME diff --git a/scripts/seq/bp_make_mrna_protein.PLS b/scripts/seq/bp_make_mrna_protein.PLS index c47e26678..c37c31021 100644 --- a/scripts/seq/bp_make_mrna_protein.PLS +++ b/scripts/seq/bp_make_mrna_protein.PLS @@ -1,4 +1,4 @@ -#!perl -w +#!perl # =head1 NAME @@ -32,6 +32,7 @@ and the translate() method =cut use strict; +use warnings; use Bio::SeqIO; use Getopt::Long; diff --git a/scripts/seq/bp_seqconvert.PLS b/scripts/seq/bp_seqconvert.PLS index af09e99cf..ffce31958 100644 --- a/scripts/seq/bp_seqconvert.PLS +++ b/scripts/seq/bp_seqconvert.PLS @@ -1,6 +1,7 @@ -#!perl -w +#!perl use strict; +use warnings; use Getopt::Long; use Bio::SeqIO; diff --git a/scripts/seq/bp_split_seq.PLS b/scripts/seq/bp_split_seq.PLS index 3b12e66b5..2b2158ac6 100644 --- a/scripts/seq/bp_split_seq.PLS +++ b/scripts/seq/bp_split_seq.PLS @@ -1,5 +1,6 @@ -#!perl -w +#!perl use strict; +use warnings; =head1 NAME diff --git a/scripts/seq/bp_translate_seq.PLS b/scripts/seq/bp_translate_seq.PLS index 6745fd783..7d44b6017 100644 --- a/scripts/seq/bp_translate_seq.PLS +++ b/scripts/seq/bp_translate_seq.PLS @@ -1,5 +1,6 @@ -#!perl -w +#!perl use strict; +use warnings; =head1 NAME diff --git a/scripts/seq/bp_unflatten_seq.PLS b/scripts/seq/bp_unflatten_seq.PLS index 93a3b7d00..1eb1d67b5 100644 --- a/scripts/seq/bp_unflatten_seq.PLS +++ b/scripts/seq/bp_unflatten_seq.PLS @@ -1,5 +1,6 @@ -#!perl -w +#!perl use strict; +use warnings; # Author Chris Mungall =head1 NAME diff --git a/scripts/seqstats/bp_aacomp.PLS b/scripts/seqstats/bp_aacomp.PLS index 3b98a595f..a7dd4827e 100644 --- a/scripts/seqstats/bp_aacomp.PLS +++ b/scripts/seqstats/bp_aacomp.PLS @@ -1,5 +1,6 @@ -#!perl -w +#!perl use strict; +use warnings; use Carp; use Bio::SeqIO; diff --git a/scripts/seqstats/bp_chaos_plot.PLS b/scripts/seqstats/bp_chaos_plot.PLS index d44c88000..dac5bbb7a 100644 --- a/scripts/seqstats/bp_chaos_plot.PLS +++ b/scripts/seqstats/bp_chaos_plot.PLS @@ -1,6 +1,7 @@ -#!perl -w +#!perl use strict; +use warnings; use Bio::SeqIO; use Getopt::Long; diff --git a/scripts/seqstats/bp_gccalc.PLS b/scripts/seqstats/bp_gccalc.PLS index 1744bfb6b..b699d41bf 100644 --- a/scripts/seqstats/bp_gccalc.PLS +++ b/scripts/seqstats/bp_gccalc.PLS @@ -1,6 +1,7 @@ -#!perl -w +#!perl use strict; +use warnings; use Bio::SeqIO; use Bio::Tools::SeqStats; diff --git a/scripts/seqstats/bp_oligo_count.PLS b/scripts/seqstats/bp_oligo_count.PLS index 9e67d1f5b..1281b8470 100644 --- a/scripts/seqstats/bp_oligo_count.PLS +++ b/scripts/seqstats/bp_oligo_count.PLS @@ -1,4 +1,4 @@ -#!perl -w +#!perl # # oligomer_freq.pl # We use this to determine what primers are useful for frequent priming of @@ -20,6 +20,7 @@ use Getopt::Long; ######################### use strict; +use warnings; my ($format, $infile, $help, $outfile, $oligomerlength) = ('fasta'); GetOptions( diff --git a/scripts/taxa/bp_taxid4species.PLS b/scripts/taxa/bp_taxid4species.PLS index dd3c1c927..4322b28e3 100644 --- a/scripts/taxa/bp_taxid4species.PLS +++ b/scripts/taxa/bp_taxid4species.PLS @@ -1,4 +1,4 @@ -#!perl -w +#!perl # Author: Jason Stajich # Purpose: Retrieve the NCBI Taxa ID for organism(s) @@ -8,6 +8,7 @@ use LWP::UserAgent; use XML::Twig; use strict; +use warnings; use Getopt::Long; my $verbose = 0; my $plain = 0; diff --git a/scripts/tree/bp_nexus2nh.PLS b/scripts/tree/bp_nexus2nh.PLS index 5abf36a73..b5eeabee1 100644 --- a/scripts/tree/bp_nexus2nh.PLS +++ b/scripts/tree/bp_nexus2nh.PLS @@ -1,4 +1,4 @@ -#!perl -w +#!perl =head1 NAME @@ -24,6 +24,7 @@ Convert Nexus Tree files into Newick/New Hampshire format tree files. =cut use strict; +use warnings; use Bio::TreeIO; use Getopt::Long; diff --git a/scripts/tree/bp_tree2pag.PLS b/scripts/tree/bp_tree2pag.PLS index 371bb7db7..cfde7e90b 100644 --- a/scripts/tree/bp_tree2pag.PLS +++ b/scripts/tree/bp_tree2pag.PLS @@ -1,4 +1,4 @@ -#!perl -w +#!perl =head1 NAME @@ -25,6 +25,7 @@ so. Also Pagel parsing is not yet available in bioperl. =cut use strict; +use warnings; use Bio::TreeIO; use Getopt::Long; my ($iformat,$oformat) = ('newick', 'pag'); diff --git a/scripts/utilities/bp_dbsplit.PLS b/scripts/utilities/bp_dbsplit.PLS index 3a10ea2aa..8607ada0b 100644 --- a/scripts/utilities/bp_dbsplit.PLS +++ b/scripts/utilities/bp_dbsplit.PLS @@ -1,4 +1,4 @@ -#!perl -w +#!perl #-*-Perl-*- =head1 NAME @@ -56,6 +56,7 @@ Jason Stajich, jason-at-bioperl-dot-org =cut use strict; +use warnings; use Bio::SeqIO; use Bio::SeqIO::MultiFile; diff --git a/scripts/utilities/bp_mask_by_search.PLS b/scripts/utilities/bp_mask_by_search.PLS index a6e5edea0..be46f7cc0 100644 --- a/scripts/utilities/bp_mask_by_search.PLS +++ b/scripts/utilities/bp_mask_by_search.PLS @@ -1,4 +1,4 @@ -#!perl -w +#!perl # Author: Jason Stajich @@ -59,6 +59,7 @@ Jason Stajich, jason-at-bioperl-dot-org. use strict; +use warnings; use Bio::SeqIO; use Bio::SearchIO; use Getopt::Long; diff --git a/scripts/utilities/bp_nrdb.PLS b/scripts/utilities/bp_nrdb.PLS index c1a40b99a..08183142d 100644 --- a/scripts/utilities/bp_nrdb.PLS +++ b/scripts/utilities/bp_nrdb.PLS @@ -1,4 +1,4 @@ -#!perl -w +#!perl # Author Jason Stajich # @@ -41,6 +41,7 @@ Jason Stajich, jason-at-bioperl-dot-org =cut use strict; +use warnings; use Bio::SeqIO; use Getopt::Long; diff --git a/scripts/utilities/bp_pairwise_kaks.PLS b/scripts/utilities/bp_pairwise_kaks.PLS index 92a09f901..3129b9401 100644 --- a/scripts/utilities/bp_pairwise_kaks.PLS +++ b/scripts/utilities/bp_pairwise_kaks.PLS @@ -1,5 +1,6 @@ -#!perl -w +#!perl use strict; +use warnings; # Author Jason Stajich =head1 NAME diff --git a/scripts/utilities/bp_search2BSML.PLS b/scripts/utilities/bp_search2BSML.PLS index 9d3ecf880..1fdc2c22f 100644 --- a/scripts/utilities/bp_search2BSML.PLS +++ b/scripts/utilities/bp_search2BSML.PLS @@ -1,4 +1,4 @@ -#!perl -w +#!perl # Author: Jason Stajich # Description: Turn SearchIO parseable report(s) into a GFF report @@ -37,6 +37,7 @@ Jason Stajich, jason-at-bioperl-dot-org =cut use strict; +use warnings; use Getopt::Long; use Bio::SearchIO; diff --git a/scripts/utilities/bp_search2alnblocks.PLS b/scripts/utilities/bp_search2alnblocks.PLS index c4ba8f945..5f4a8a77d 100644 --- a/scripts/utilities/bp_search2alnblocks.PLS +++ b/scripts/utilities/bp_search2alnblocks.PLS @@ -1,4 +1,4 @@ -#!perl -w +#!perl # Author: Jason Stajich # Description: Turn SearchIO parseable report(s) into a set of Aligned blocks # @@ -48,6 +48,7 @@ Jason Stajich, jason-at-bioperl-dot-org. use strict; +use warnings; use Bio::SearchIO; use Bio::AlignIO; diff --git a/scripts/utilities/bp_search2gff.PLS b/scripts/utilities/bp_search2gff.PLS index ec1154b6f..a13993089 100644 --- a/scripts/utilities/bp_search2gff.PLS +++ b/scripts/utilities/bp_search2gff.PLS @@ -1,4 +1,4 @@ -#!perl -w +#!perl # Author: Jason Stajich # Description: Turn SearchIO parseable report(s) into a GFF report @@ -68,6 +68,7 @@ Hilmar Lapp, hlapp-at-gmx-dot-net =cut use strict; +use warnings; use Bio::Tools::GFF; use Getopt::Long; use Bio::SearchIO; diff --git a/scripts/utilities/bp_search2tribe.PLS b/scripts/utilities/bp_search2tribe.PLS index 2ee1acc07..c32a0dd8a 100644 --- a/scripts/utilities/bp_search2tribe.PLS +++ b/scripts/utilities/bp_search2tribe.PLS @@ -1,4 +1,4 @@ -#!perl -w +#!perl # Author: Jason Stajich # Description: Turn SearchIO parseable report(s) into a TRIBE matrix @@ -43,6 +43,7 @@ Jason Stajich, jason-at-bioperl-dot-org =cut use strict; +use warnings; use Bio::SearchIO; use Bio::SearchIO::FastHitEventBuilder; # employ a speedup use Getopt::Long; diff --git a/scripts/utilities/bp_seq_length.PLS b/scripts/utilities/bp_seq_length.PLS index abf1ff907..2fc9113b0 100644 --- a/scripts/utilities/bp_seq_length.PLS +++ b/scripts/utilities/bp_seq_length.PLS @@ -1,4 +1,4 @@ -#!perl -w +#!perl =head1 NAME @@ -44,6 +44,7 @@ Jason Stajich Ejason@bioperl.orgE =cut use strict; +use warnings; use Bio::SeqIO; use Getopt::Long; -- 2.11.4.GIT