From: martinahansen Date: Wed, 8 Jul 2009 09:10:21 +0000 (+0000) Subject: added use strict to all biopieces X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=9bf550c4335d8860c5f6f9c4db0f385f1b36c1dd;p=biopieces.git added use strict to all biopieces git-svn-id: http://biopieces.googlecode.com/svn/trunk@558 74ccb610-7750-0410-82ae-013aeee3265d --- diff --git a/bp_bin/add_ident b/bp_bin/add_ident index f9cdac0..57a644a 100755 --- a/bp_bin/add_ident +++ b/bp_bin/add_ident @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; diff --git a/bp_bin/align_pair_seq b/bp_bin/align_pair_seq index bfa326b..1a9d673 100755 --- a/bp_bin/align_pair_seq +++ b/bp_bin/align_pair_seq @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::AlignTwoSeq; diff --git a/bp_bin/align_seq b/bp_bin/align_seq index 7f88042..af114e1 100755 --- a/bp_bin/align_seq +++ b/bp_bin/align_seq @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Align; diff --git a/bp_bin/analyze_bed b/bp_bin/analyze_bed index 16c53d5..5895104 100755 --- a/bp_bin/analyze_bed +++ b/bp_bin/analyze_bed @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::UCSC; diff --git a/bp_bin/analyze_seq b/bp_bin/analyze_seq index 53a9d64..b6f7d8c 100755 --- a/bp_bin/analyze_seq +++ b/bp_bin/analyze_seq @@ -27,6 +27,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Seq; diff --git a/bp_bin/analyze_tags b/bp_bin/analyze_tags index 63a0d32..181beb5 100755 --- a/bp_bin/analyze_tags +++ b/bp_bin/analyze_tags @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Seq; diff --git a/bp_bin/analyze_vals b/bp_bin/analyze_vals index 445b2db..91da15a 100755 --- a/bp_bin/analyze_vals +++ b/bp_bin/analyze_vals @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Calc; diff --git a/bp_bin/assemble_tag_contigs b/bp_bin/assemble_tag_contigs index 758a022..9b605ef 100755 --- a/bp_bin/assemble_tag_contigs +++ b/bp_bin/assemble_tag_contigs @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Filesys; diff --git a/bp_bin/bioscript b/bp_bin/bioscript index 48dfec2..f2e4cbd 100755 --- a/bp_bin/bioscript +++ b/bp_bin/bioscript @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces qw( get_record put_record ); use Data::Dumper; diff --git a/bp_bin/biostat b/bp_bin/biostat index 744710a..6a7d040 100755 --- a/bp_bin/biostat +++ b/bp_bin/biostat @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Common; diff --git a/bp_bin/blast_seq b/bp_bin/blast_seq index 2f12545..55d0530 100755 --- a/bp_bin/blast_seq +++ b/bp_bin/blast_seq @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Common; diff --git a/bp_bin/blat_seq b/bp_bin/blat_seq index 2fd60f6..220e7b3 100755 --- a/bp_bin/blat_seq +++ b/bp_bin/blat_seq @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Filesys; diff --git a/bp_bin/calc_bit_scores b/bp_bin/calc_bit_scores index 9de170d..4b930c3 100755 --- a/bp_bin/calc_bit_scores +++ b/bp_bin/calc_bit_scores @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Seq; diff --git a/bp_bin/calc_fixedstep b/bp_bin/calc_fixedstep index 27628fe..49c9a76 100755 --- a/bp_bin/calc_fixedstep +++ b/bp_bin/calc_fixedstep @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Filesys; diff --git a/bp_bin/complement_seq b/bp_bin/complement_seq index 193d9e4..348e058 100755 --- a/bp_bin/complement_seq +++ b/bp_bin/complement_seq @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Seq; diff --git a/bp_bin/compute b/bp_bin/compute index 359becd..0b2e280 100755 --- a/bp_bin/compute +++ b/bp_bin/compute @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Common; use Maasha::Biopieces; diff --git a/bp_bin/count_records b/bp_bin/count_records index 28b6157..cbe5f0d 100755 --- a/bp_bin/count_records +++ b/bp_bin/count_records @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Fasta; use Maasha::Biopieces; diff --git a/bp_bin/count_vals b/bp_bin/count_vals index 377af35..8081e5c 100755 --- a/bp_bin/count_vals +++ b/bp_bin/count_vals @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Filesys; use Maasha::Biopieces; diff --git a/bp_bin/create_blast_db b/bp_bin/create_blast_db index eee8357..8dc857e 100755 --- a/bp_bin/create_blast_db +++ b/bp_bin/create_blast_db @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Seq; use Maasha::Fasta; diff --git a/bp_bin/create_vmatch_index b/bp_bin/create_vmatch_index index aed4ca7..f27e255 100755 --- a/bp_bin/create_vmatch_index +++ b/bp_bin/create_vmatch_index @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Common; use Maasha::Biopieces; diff --git a/bp_bin/create_weight_matrix b/bp_bin/create_weight_matrix index 8c5089b..ac7d12c 100755 --- a/bp_bin/create_weight_matrix +++ b/bp_bin/create_weight_matrix @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Common; use Maasha::Biopieces; diff --git a/bp_bin/extract_seq b/bp_bin/extract_seq index ee1a004..d5760d5 100755 --- a/bp_bin/extract_seq +++ b/bp_bin/extract_seq @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; diff --git a/bp_bin/flip_tab b/bp_bin/flip_tab index 7f520bc..74fca2e 100755 --- a/bp_bin/flip_tab +++ b/bp_bin/flip_tab @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Matrix; diff --git a/bp_bin/fold_seq b/bp_bin/fold_seq index 6563107..1207cfe 100755 --- a/bp_bin/fold_seq +++ b/bp_bin/fold_seq @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; diff --git a/bp_bin/format_genome b/bp_bin/format_genome index 844e5af..dbd4182 100755 --- a/bp_bin/format_genome +++ b/bp_bin/format_genome @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Fasta; use Maasha::Biopieces; diff --git a/bp_bin/get_genome_align b/bp_bin/get_genome_align index 664e6b5..566ea6e 100755 --- a/bp_bin/get_genome_align +++ b/bp_bin/get_genome_align @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Common; diff --git a/bp_bin/get_genome_phastcons b/bp_bin/get_genome_phastcons index 0790bb0..8531d26 100755 --- a/bp_bin/get_genome_phastcons +++ b/bp_bin/get_genome_phastcons @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Filesys; diff --git a/bp_bin/get_genome_seq b/bp_bin/get_genome_seq index 5292b72..dbbc9d4 100755 --- a/bp_bin/get_genome_seq +++ b/bp_bin/get_genome_seq @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Filesys; diff --git a/bp_bin/grab b/bp_bin/grab index 1be030a..8728f81 100755 --- a/bp_bin/grab +++ b/bp_bin/grab @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Common; diff --git a/bp_bin/head_records b/bp_bin/head_records index 9ae3918..d88c222 100755 --- a/bp_bin/head_records +++ b/bp_bin/head_records @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; diff --git a/bp_bin/indel_seq b/bp_bin/indel_seq index 4fe3d3d..f5288d6 100755 --- a/bp_bin/indel_seq +++ b/bp_bin/indel_seq @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Common; use Maasha::Biopieces; diff --git a/bp_bin/invert_align b/bp_bin/invert_align index 28ccac0..e798687 100755 --- a/bp_bin/invert_align +++ b/bp_bin/invert_align @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Align; diff --git a/bp_bin/length_seq b/bp_bin/length_seq index 4a94333..4e8d0e3 100755 --- a/bp_bin/length_seq +++ b/bp_bin/length_seq @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; diff --git a/bp_bin/length_vals b/bp_bin/length_vals index b7ed3c4..29451b8 100755 --- a/bp_bin/length_vals +++ b/bp_bin/length_vals @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; diff --git a/bp_bin/list_biopieces b/bp_bin/list_biopieces index bf17d01..e36d52e 100755 --- a/bp_bin/list_biopieces +++ b/bp_bin/list_biopieces @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Common; use Maasha::Biopieces; diff --git a/bp_bin/list_genomes b/bp_bin/list_genomes index 2c8fb1d..f5e6d4d 100755 --- a/bp_bin/list_genomes +++ b/bp_bin/list_genomes @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Common; use Maasha::Biopieces; diff --git a/bp_bin/match_seq b/bp_bin/match_seq index dd1ac63..bb95a3f 100755 --- a/bp_bin/match_seq +++ b/bp_bin/match_seq @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Match; diff --git a/bp_bin/max_vals b/bp_bin/max_vals index 4d42fcf..4cb794b 100755 --- a/bp_bin/max_vals +++ b/bp_bin/max_vals @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; diff --git a/bp_bin/mean_vals b/bp_bin/mean_vals index 45a1707..f29a4fc 100755 --- a/bp_bin/mean_vals +++ b/bp_bin/mean_vals @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; diff --git a/bp_bin/median_vals b/bp_bin/median_vals index 9256cf5..91cdd36 100755 --- a/bp_bin/median_vals +++ b/bp_bin/median_vals @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Calc; diff --git a/bp_bin/merge_records b/bp_bin/merge_records index a452c7a..7294590 100755 --- a/bp_bin/merge_records +++ b/bp_bin/merge_records @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Common; diff --git a/bp_bin/merge_vals b/bp_bin/merge_vals index c6c6cfe..963fbfc 100755 --- a/bp_bin/merge_vals +++ b/bp_bin/merge_vals @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; diff --git a/bp_bin/min_vals b/bp_bin/min_vals index ed355d4..bff25a7 100755 --- a/bp_bin/min_vals +++ b/bp_bin/min_vals @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; diff --git a/bp_bin/mutate_seq b/bp_bin/mutate_seq index 2000e9d..b77ffcf 100755 --- a/bp_bin/mutate_seq +++ b/bp_bin/mutate_seq @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Common; use Maasha::Biopieces; diff --git a/bp_bin/oligo_freq b/bp_bin/oligo_freq index 008bcbe..53029b6 100755 --- a/bp_bin/oligo_freq +++ b/bp_bin/oligo_freq @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; diff --git a/bp_bin/patscan_seq b/bp_bin/patscan_seq index 07dd685..2d828f6 100755 --- a/bp_bin/patscan_seq +++ b/bp_bin/patscan_seq @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Common; diff --git a/bp_bin/plot_chrdist b/bp_bin/plot_chrdist index 172d3dc..9e3ba41 100755 --- a/bp_bin/plot_chrdist +++ b/bp_bin/plot_chrdist @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Plot; diff --git a/bp_bin/plot_histogram b/bp_bin/plot_histogram index f04068f..4950305 100755 --- a/bp_bin/plot_histogram +++ b/bp_bin/plot_histogram @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Plot; diff --git a/bp_bin/plot_karyogram b/bp_bin/plot_karyogram index a486190..2e3748b 100755 --- a/bp_bin/plot_karyogram +++ b/bp_bin/plot_karyogram @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Plot; diff --git a/bp_bin/plot_lendist b/bp_bin/plot_lendist index 0138c66..dfc0abb 100755 --- a/bp_bin/plot_lendist +++ b/bp_bin/plot_lendist @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Plot; diff --git a/bp_bin/plot_matches b/bp_bin/plot_matches index 3aa016e..3fc25ad 100755 --- a/bp_bin/plot_matches +++ b/bp_bin/plot_matches @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Plot; diff --git a/bp_bin/plot_phastcons_profiles b/bp_bin/plot_phastcons_profiles index 89835c3..82db056 100755 --- a/bp_bin/plot_phastcons_profiles +++ b/bp_bin/plot_phastcons_profiles @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Plot; diff --git a/bp_bin/plot_seqlogo b/bp_bin/plot_seqlogo index ce30a73..3495c9e 100755 --- a/bp_bin/plot_seqlogo +++ b/bp_bin/plot_seqlogo @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Plot; diff --git a/bp_bin/print_wiki b/bp_bin/print_wiki index 1c581d2..f766c8b 100755 --- a/bp_bin/print_wiki +++ b/bp_bin/print_wiki @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Gwiki; diff --git a/bp_bin/random_records b/bp_bin/random_records index 12986d1..b700dc1 100755 --- a/bp_bin/random_records +++ b/bp_bin/random_records @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Filesys; diff --git a/bp_bin/read_2bit b/bp_bin/read_2bit index fe5878e..7eebe05 100755 --- a/bp_bin/read_2bit +++ b/bp_bin/read_2bit @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Filesys; diff --git a/bp_bin/read_bed b/bp_bin/read_bed index 8d270cb..2815749 100755 --- a/bp_bin/read_bed +++ b/bp_bin/read_bed @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Filesys; diff --git a/bp_bin/read_blast_tab b/bp_bin/read_blast_tab index 61aabc6..26d4089 100755 --- a/bp_bin/read_blast_tab +++ b/bp_bin/read_blast_tab @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Filesys; diff --git a/bp_bin/read_embl b/bp_bin/read_embl index 50b24e5..496a5d8 100755 --- a/bp_bin/read_embl +++ b/bp_bin/read_embl @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Filesys; diff --git a/bp_bin/read_fasta b/bp_bin/read_fasta index 488465d..91d8ad2 100755 --- a/bp_bin/read_fasta +++ b/bp_bin/read_fasta @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Filesys; diff --git a/bp_bin/read_fixedstep b/bp_bin/read_fixedstep index 932ebe6..64d949c 100755 --- a/bp_bin/read_fixedstep +++ b/bp_bin/read_fixedstep @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Filesys; diff --git a/bp_bin/read_gff b/bp_bin/read_gff index d3785b6..b3d36db 100755 --- a/bp_bin/read_gff +++ b/bp_bin/read_gff @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Filesys; diff --git a/bp_bin/read_mysql b/bp_bin/read_mysql index 8abc908..ff96a81 100755 --- a/bp_bin/read_mysql +++ b/bp_bin/read_mysql @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::SQL; diff --git a/bp_bin/read_psl b/bp_bin/read_psl index bcba5ee..0d7fe35 100755 --- a/bp_bin/read_psl +++ b/bp_bin/read_psl @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Filesys; diff --git a/bp_bin/read_soft b/bp_bin/read_soft index 9e44f59..78adc84 100755 --- a/bp_bin/read_soft +++ b/bp_bin/read_soft @@ -27,6 +27,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Filesys; diff --git a/bp_bin/read_solexa b/bp_bin/read_solexa index fb3a988..dc5d237 100755 --- a/bp_bin/read_solexa +++ b/bp_bin/read_solexa @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Filesys; diff --git a/bp_bin/read_solid b/bp_bin/read_solid index 8a66618..193cd52 100755 --- a/bp_bin/read_solid +++ b/bp_bin/read_solid @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Filesys; diff --git a/bp_bin/read_stockholm b/bp_bin/read_stockholm index 400c8a7..597e9e9 100755 --- a/bp_bin/read_stockholm +++ b/bp_bin/read_stockholm @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Filesys; diff --git a/bp_bin/read_tab b/bp_bin/read_tab index cf37a12..3c78230 100755 --- a/bp_bin/read_tab +++ b/bp_bin/read_tab @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Filesys; use Maasha::Biopieces; diff --git a/bp_bin/read_ucsc_config b/bp_bin/read_ucsc_config index fed3f83..4317ae3 100755 --- a/bp_bin/read_ucsc_config +++ b/bp_bin/read_ucsc_config @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Filesys; diff --git a/bp_bin/remove_adaptor b/bp_bin/remove_adaptor index f037055..14a7f89 100755 --- a/bp_bin/remove_adaptor +++ b/bp_bin/remove_adaptor @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Common; diff --git a/bp_bin/remove_indels b/bp_bin/remove_indels index 59bbd4f..3156b44 100755 --- a/bp_bin/remove_indels +++ b/bp_bin/remove_indels @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; diff --git a/bp_bin/remove_keys b/bp_bin/remove_keys index a61e763..6e00043 100755 --- a/bp_bin/remove_keys +++ b/bp_bin/remove_keys @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; diff --git a/bp_bin/remove_mysql_tables b/bp_bin/remove_mysql_tables index b25b79d..1419cbc 100755 --- a/bp_bin/remove_mysql_tables +++ b/bp_bin/remove_mysql_tables @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Common; diff --git a/bp_bin/remove_ucsc_tracks b/bp_bin/remove_ucsc_tracks index 52d7ee6..4148da8 100755 --- a/bp_bin/remove_ucsc_tracks +++ b/bp_bin/remove_ucsc_tracks @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Common; diff --git a/bp_bin/rename_keys b/bp_bin/rename_keys index b8d85be..b0dc229 100755 --- a/bp_bin/rename_keys +++ b/bp_bin/rename_keys @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; diff --git a/bp_bin/reverse_seq b/bp_bin/reverse_seq index 7d13727..019245e 100755 --- a/bp_bin/reverse_seq +++ b/bp_bin/reverse_seq @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; diff --git a/bp_bin/shuffle_seq b/bp_bin/shuffle_seq index 11d4c91..165fbda 100755 --- a/bp_bin/shuffle_seq +++ b/bp_bin/shuffle_seq @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Seq; diff --git a/bp_bin/soap_seq b/bp_bin/soap_seq index 67d53e9..e6417f5 100755 --- a/bp_bin/soap_seq +++ b/bp_bin/soap_seq @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Common; diff --git a/bp_bin/sort_records b/bp_bin/sort_records index f6e4234..af8edbc 100755 --- a/bp_bin/sort_records +++ b/bp_bin/sort_records @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; diff --git a/bp_bin/split_bed b/bp_bin/split_bed index 5fbdf40..bd708a4 100755 --- a/bp_bin/split_bed +++ b/bp_bin/split_bed @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; diff --git a/bp_bin/split_seq b/bp_bin/split_seq index b8aa503..518565d 100755 --- a/bp_bin/split_seq +++ b/bp_bin/split_seq @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; diff --git a/bp_bin/split_vals b/bp_bin/split_vals index f654523..93cac4a 100755 --- a/bp_bin/split_vals +++ b/bp_bin/split_vals @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; diff --git a/bp_bin/sum_vals b/bp_bin/sum_vals index 2db00ff..b672de3 100755 --- a/bp_bin/sum_vals +++ b/bp_bin/sum_vals @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; diff --git a/bp_bin/tile_seq b/bp_bin/tile_seq index d0f9562..9a7dcfd 100755 --- a/bp_bin/tile_seq +++ b/bp_bin/tile_seq @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Align; diff --git a/bp_bin/translate_seq b/bp_bin/translate_seq index 663012b..ba6b07f 100755 --- a/bp_bin/translate_seq +++ b/bp_bin/translate_seq @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Seq; diff --git a/bp_bin/transliterate_seq b/bp_bin/transliterate_seq index a53c62a..a81d328 100755 --- a/bp_bin/transliterate_seq +++ b/bp_bin/transliterate_seq @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; diff --git a/bp_bin/transliterate_vals b/bp_bin/transliterate_vals index 502939a..3877ad4 100755 --- a/bp_bin/transliterate_vals +++ b/bp_bin/transliterate_vals @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; diff --git a/bp_bin/uniq_vals b/bp_bin/uniq_vals index c9bf842..0bc6ce0 100755 --- a/bp_bin/uniq_vals +++ b/bp_bin/uniq_vals @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; diff --git a/bp_bin/upload_to_ucsc b/bp_bin/upload_to_ucsc index 72ef8c4..aac4928 100755 --- a/bp_bin/upload_to_ucsc +++ b/bp_bin/upload_to_ucsc @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Common; use Maasha::Biopieces; diff --git a/bp_bin/uppercase_seq b/bp_bin/uppercase_seq index 3b4b941..e5acdf8 100755 --- a/bp_bin/uppercase_seq +++ b/bp_bin/uppercase_seq @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; diff --git a/bp_bin/vmatch_seq b/bp_bin/vmatch_seq index 9b8f952..c02b98d 100755 --- a/bp_bin/vmatch_seq +++ b/bp_bin/vmatch_seq @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Data::Dumper; use Maasha::Biopieces; diff --git a/bp_bin/write_2bit b/bp_bin/write_2bit index 1f1575e..12e330d 100755 --- a/bp_bin/write_2bit +++ b/bp_bin/write_2bit @@ -29,6 +29,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Fasta; use Maasha::Biopieces; diff --git a/bp_bin/write_align b/bp_bin/write_align index 4692f86..f0a0598 100755 --- a/bp_bin/write_align +++ b/bp_bin/write_align @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Align; diff --git a/bp_bin/write_bed b/bp_bin/write_bed index 3b486fd..51cdc75 100755 --- a/bp_bin/write_bed +++ b/bp_bin/write_bed @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::UCSC::BED; diff --git a/bp_bin/write_blast b/bp_bin/write_blast index ba65a2b..b3f6c72 100755 --- a/bp_bin/write_blast +++ b/bp_bin/write_blast @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Fasta; use Maasha::Biopieces; diff --git a/bp_bin/write_fasta b/bp_bin/write_fasta index b6dd344..52f8a70 100755 --- a/bp_bin/write_fasta +++ b/bp_bin/write_fasta @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Fasta; use Maasha::Biopieces; diff --git a/bp_bin/write_fixedstep b/bp_bin/write_fixedstep index 97f8f21..f79873d 100755 --- a/bp_bin/write_fixedstep +++ b/bp_bin/write_fixedstep @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::UCSC::Wiggle; diff --git a/bp_bin/write_psl b/bp_bin/write_psl index 6ff8fef..776676d 100755 --- a/bp_bin/write_psl +++ b/bp_bin/write_psl @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::UCSC::PSL; diff --git a/bp_bin/write_solid b/bp_bin/write_solid index 01b8220..7723f76 100755 --- a/bp_bin/write_solid +++ b/bp_bin/write_solid @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::Fasta; diff --git a/bp_bin/write_tab b/bp_bin/write_tab index 2ed2ce8..b512d94 100755 --- a/bp_bin/write_tab +++ b/bp_bin/write_tab @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Fasta; use Maasha::Biopieces; diff --git a/bp_bin/write_ucsc_config b/bp_bin/write_ucsc_config index 5d2e2d5..2c8654a 100755 --- a/bp_bin/write_ucsc_config +++ b/bp_bin/write_ucsc_config @@ -26,6 +26,7 @@ # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< +use warnings; use strict; use Maasha::Biopieces; use Maasha::UCSC;