From e1e61f6b2e3f51a98c0be95573d6955dc921a697 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Thu, 26 Jun 2008 06:30:38 +0000 Subject: [PATCH] this will probably break git-svn-id: http://biopieces.googlecode.com/svn/trunk@24 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/add_ident | 2 +- bp_bin/align_seq | 2 +- bp_bin/analyze_bed | 2 +- bp_bin/analyze_seq | 2 +- bp_bin/analyze_tags | 2 +- bp_bin/analyze_vals | 2 +- bp_bin/blast_seq | 2 +- bp_bin/blat_seq | 2 +- bp_bin/calc_bit_scores | 2 +- bp_bin/complement_seq | 2 +- bp_bin/complexity_seq | 2 +- bp_bin/compute | 2 +- bp_bin/count_records | 2 +- bp_bin/count_vals | 2 +- bp_bin/create_blast_db | 2 +- bp_bin/create_vmatch_index | 2 +- bp_bin/create_weight_matrix | 2 +- bp_bin/extract_seq | 2 +- bp_bin/flip_tab | 2 +- bp_bin/fold_seq | 2 +- bp_bin/get_genome_align | 2 +- bp_bin/get_genome_phastcons | 2 +- bp_bin/get_genome_seq | 2 +- bp_bin/grab | 2 +- bp_bin/head_records | 2 +- bp_bin/invert_align | 2 +- bp_bin/length_seq | 2 +- bp_bin/length_vals | 2 +- bp_bin/list_biotools | 2 +- bp_bin/match_seq | 2 +- bp_bin/max_vals | 2 +- bp_bin/mean_vals | 2 +- bp_bin/median_vals | 2 +- bp_bin/merge_vals | 2 +- bp_bin/min_vals | 2 +- bp_bin/oligo_freq | 2 +- bp_bin/patscan_seq | 2 +- bp_bin/plot_chrdist | 2 +- bp_bin/plot_histogram | 2 +- bp_bin/plot_karyogram | 2 +- bp_bin/plot_lendist | 2 +- bp_bin/plot_matches | 2 +- bp_bin/plot_phastcons_profiles | 2 +- bp_bin/plot_seqlogo | 2 +- bp_bin/print_usage | 2 +- bp_bin/random_records | 2 +- bp_bin/read_2bit | 2 +- bp_bin/read_align | 2 +- bp_bin/read_bed | 2 +- bp_bin/read_blast_tab | 2 +- bp_bin/read_embl | 2 +- bp_bin/read_fasta | 2 +- bp_bin/read_gff | 2 +- bp_bin/read_mysql | 2 +- bp_bin/read_phastcons | 2 +- bp_bin/read_psl | 2 +- bp_bin/read_soft | 2 +- bp_bin/read_solexa | 2 +- bp_bin/read_solid | 2 +- bp_bin/read_stockholm | 2 +- bp_bin/read_tab | 2 +- bp_bin/remove_indels | 2 +- bp_bin/remove_keys | 2 +- bp_bin/rename_keys | 2 +- bp_bin/reverse_seq | 2 +- bp_bin/shuffle_seq | 2 +- bp_bin/sort_records | 2 +- bp_bin/split_bed | 2 +- bp_bin/split_seq | 2 +- bp_bin/sum_vals | 2 +- bp_bin/tile_seq | 2 +- bp_bin/translate_seq | 2 +- bp_bin/transliterate_seq | 2 +- bp_bin/transliterate_vals | 2 +- bp_bin/uniq_vals | 2 +- bp_bin/upload_to_ucsc | 2 +- bp_bin/uppercase_seq | 2 +- bp_bin/vmatch_seq | 2 +- bp_bin/write_2bit | 2 +- bp_bin/write_align | 2 +- bp_bin/write_bed | 2 +- bp_bin/write_blast | 2 +- bp_bin/write_fasta | 2 +- bp_bin/write_psl | 2 +- bp_bin/write_solid | 2 +- bp_bin/write_tab | 2 +- code_perl/Maasha/{Biotools.pm => Biopieces.pm} | 2 +- 87 files changed, 87 insertions(+), 87 deletions(-) rename code_perl/Maasha/{Biotools.pm => Biopieces.pm} (99%) diff --git a/bp_bin/add_ident b/bp_bin/add_ident index c8c800f..4cd1d44 100755 --- a/bp_bin/add_ident +++ b/bp_bin/add_ident @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/align_seq b/bp_bin/align_seq index c8c800f..4cd1d44 100755 --- a/bp_bin/align_seq +++ b/bp_bin/align_seq @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/analyze_bed b/bp_bin/analyze_bed index c8c800f..4cd1d44 100755 --- a/bp_bin/analyze_bed +++ b/bp_bin/analyze_bed @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/analyze_seq b/bp_bin/analyze_seq index c8c800f..4cd1d44 100755 --- a/bp_bin/analyze_seq +++ b/bp_bin/analyze_seq @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/analyze_tags b/bp_bin/analyze_tags index c8c800f..4cd1d44 100755 --- a/bp_bin/analyze_tags +++ b/bp_bin/analyze_tags @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/analyze_vals b/bp_bin/analyze_vals index c8c800f..4cd1d44 100755 --- a/bp_bin/analyze_vals +++ b/bp_bin/analyze_vals @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/blast_seq b/bp_bin/blast_seq index c8c800f..4cd1d44 100755 --- a/bp_bin/blast_seq +++ b/bp_bin/blast_seq @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/blat_seq b/bp_bin/blat_seq index c8c800f..4cd1d44 100755 --- a/bp_bin/blat_seq +++ b/bp_bin/blat_seq @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/calc_bit_scores b/bp_bin/calc_bit_scores index c8c800f..4cd1d44 100755 --- a/bp_bin/calc_bit_scores +++ b/bp_bin/calc_bit_scores @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/complement_seq b/bp_bin/complement_seq index c8c800f..4cd1d44 100755 --- a/bp_bin/complement_seq +++ b/bp_bin/complement_seq @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/complexity_seq b/bp_bin/complexity_seq index c8c800f..4cd1d44 100755 --- a/bp_bin/complexity_seq +++ b/bp_bin/complexity_seq @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/compute b/bp_bin/compute index c8c800f..4cd1d44 100755 --- a/bp_bin/compute +++ b/bp_bin/compute @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/count_records b/bp_bin/count_records index c8c800f..4cd1d44 100755 --- a/bp_bin/count_records +++ b/bp_bin/count_records @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/count_vals b/bp_bin/count_vals index c8c800f..4cd1d44 100755 --- a/bp_bin/count_vals +++ b/bp_bin/count_vals @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/create_blast_db b/bp_bin/create_blast_db index c8c800f..4cd1d44 100755 --- a/bp_bin/create_blast_db +++ b/bp_bin/create_blast_db @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/create_vmatch_index b/bp_bin/create_vmatch_index index c8c800f..4cd1d44 100755 --- a/bp_bin/create_vmatch_index +++ b/bp_bin/create_vmatch_index @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/create_weight_matrix b/bp_bin/create_weight_matrix index c8c800f..4cd1d44 100755 --- a/bp_bin/create_weight_matrix +++ b/bp_bin/create_weight_matrix @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/extract_seq b/bp_bin/extract_seq index c8c800f..4cd1d44 100755 --- a/bp_bin/extract_seq +++ b/bp_bin/extract_seq @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/flip_tab b/bp_bin/flip_tab index c8c800f..4cd1d44 100755 --- a/bp_bin/flip_tab +++ b/bp_bin/flip_tab @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/fold_seq b/bp_bin/fold_seq index c8c800f..4cd1d44 100755 --- a/bp_bin/fold_seq +++ b/bp_bin/fold_seq @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/get_genome_align b/bp_bin/get_genome_align index c8c800f..4cd1d44 100755 --- a/bp_bin/get_genome_align +++ b/bp_bin/get_genome_align @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/get_genome_phastcons b/bp_bin/get_genome_phastcons index c8c800f..4cd1d44 100755 --- a/bp_bin/get_genome_phastcons +++ b/bp_bin/get_genome_phastcons @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/get_genome_seq b/bp_bin/get_genome_seq index c8c800f..4cd1d44 100755 --- a/bp_bin/get_genome_seq +++ b/bp_bin/get_genome_seq @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/grab b/bp_bin/grab index c8c800f..4cd1d44 100755 --- a/bp_bin/grab +++ b/bp_bin/grab @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/head_records b/bp_bin/head_records index c8c800f..4cd1d44 100755 --- a/bp_bin/head_records +++ b/bp_bin/head_records @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/invert_align b/bp_bin/invert_align index c8c800f..4cd1d44 100755 --- a/bp_bin/invert_align +++ b/bp_bin/invert_align @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/length_seq b/bp_bin/length_seq index c8c800f..4cd1d44 100755 --- a/bp_bin/length_seq +++ b/bp_bin/length_seq @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/length_vals b/bp_bin/length_vals index c8c800f..4cd1d44 100755 --- a/bp_bin/length_vals +++ b/bp_bin/length_vals @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/list_biotools b/bp_bin/list_biotools index c8c800f..4cd1d44 100755 --- a/bp_bin/list_biotools +++ b/bp_bin/list_biotools @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/match_seq b/bp_bin/match_seq index c8c800f..4cd1d44 100755 --- a/bp_bin/match_seq +++ b/bp_bin/match_seq @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/max_vals b/bp_bin/max_vals index c8c800f..4cd1d44 100755 --- a/bp_bin/max_vals +++ b/bp_bin/max_vals @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/mean_vals b/bp_bin/mean_vals index c8c800f..4cd1d44 100755 --- a/bp_bin/mean_vals +++ b/bp_bin/mean_vals @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/median_vals b/bp_bin/median_vals index c8c800f..4cd1d44 100755 --- a/bp_bin/median_vals +++ b/bp_bin/median_vals @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/merge_vals b/bp_bin/merge_vals index c8c800f..4cd1d44 100755 --- a/bp_bin/merge_vals +++ b/bp_bin/merge_vals @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/min_vals b/bp_bin/min_vals index c8c800f..4cd1d44 100755 --- a/bp_bin/min_vals +++ b/bp_bin/min_vals @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/oligo_freq b/bp_bin/oligo_freq index c8c800f..4cd1d44 100755 --- a/bp_bin/oligo_freq +++ b/bp_bin/oligo_freq @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/patscan_seq b/bp_bin/patscan_seq index c8c800f..4cd1d44 100755 --- a/bp_bin/patscan_seq +++ b/bp_bin/patscan_seq @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/plot_chrdist b/bp_bin/plot_chrdist index c8c800f..4cd1d44 100755 --- a/bp_bin/plot_chrdist +++ b/bp_bin/plot_chrdist @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/plot_histogram b/bp_bin/plot_histogram index c8c800f..4cd1d44 100755 --- a/bp_bin/plot_histogram +++ b/bp_bin/plot_histogram @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/plot_karyogram b/bp_bin/plot_karyogram index c8c800f..4cd1d44 100755 --- a/bp_bin/plot_karyogram +++ b/bp_bin/plot_karyogram @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/plot_lendist b/bp_bin/plot_lendist index c8c800f..4cd1d44 100755 --- a/bp_bin/plot_lendist +++ b/bp_bin/plot_lendist @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/plot_matches b/bp_bin/plot_matches index c8c800f..4cd1d44 100755 --- a/bp_bin/plot_matches +++ b/bp_bin/plot_matches @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/plot_phastcons_profiles b/bp_bin/plot_phastcons_profiles index c8c800f..4cd1d44 100755 --- a/bp_bin/plot_phastcons_profiles +++ b/bp_bin/plot_phastcons_profiles @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/plot_seqlogo b/bp_bin/plot_seqlogo index c8c800f..4cd1d44 100755 --- a/bp_bin/plot_seqlogo +++ b/bp_bin/plot_seqlogo @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/print_usage b/bp_bin/print_usage index c8c800f..4cd1d44 100755 --- a/bp_bin/print_usage +++ b/bp_bin/print_usage @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/random_records b/bp_bin/random_records index c8c800f..4cd1d44 100755 --- a/bp_bin/random_records +++ b/bp_bin/random_records @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/read_2bit b/bp_bin/read_2bit index c8c800f..4cd1d44 100755 --- a/bp_bin/read_2bit +++ b/bp_bin/read_2bit @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/read_align b/bp_bin/read_align index c8c800f..4cd1d44 100755 --- a/bp_bin/read_align +++ b/bp_bin/read_align @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/read_bed b/bp_bin/read_bed index c8c800f..4cd1d44 100755 --- a/bp_bin/read_bed +++ b/bp_bin/read_bed @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/read_blast_tab b/bp_bin/read_blast_tab index c8c800f..4cd1d44 100755 --- a/bp_bin/read_blast_tab +++ b/bp_bin/read_blast_tab @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/read_embl b/bp_bin/read_embl index c8c800f..4cd1d44 100755 --- a/bp_bin/read_embl +++ b/bp_bin/read_embl @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/read_fasta b/bp_bin/read_fasta index c8c800f..4cd1d44 100755 --- a/bp_bin/read_fasta +++ b/bp_bin/read_fasta @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/read_gff b/bp_bin/read_gff index c8c800f..4cd1d44 100755 --- a/bp_bin/read_gff +++ b/bp_bin/read_gff @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/read_mysql b/bp_bin/read_mysql index c8c800f..4cd1d44 100755 --- a/bp_bin/read_mysql +++ b/bp_bin/read_mysql @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/read_phastcons b/bp_bin/read_phastcons index c8c800f..4cd1d44 100755 --- a/bp_bin/read_phastcons +++ b/bp_bin/read_phastcons @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/read_psl b/bp_bin/read_psl index c8c800f..4cd1d44 100755 --- a/bp_bin/read_psl +++ b/bp_bin/read_psl @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/read_soft b/bp_bin/read_soft index c8c800f..4cd1d44 100755 --- a/bp_bin/read_soft +++ b/bp_bin/read_soft @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/read_solexa b/bp_bin/read_solexa index c8c800f..4cd1d44 100755 --- a/bp_bin/read_solexa +++ b/bp_bin/read_solexa @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/read_solid b/bp_bin/read_solid index c8c800f..4cd1d44 100755 --- a/bp_bin/read_solid +++ b/bp_bin/read_solid @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/read_stockholm b/bp_bin/read_stockholm index c8c800f..4cd1d44 100755 --- a/bp_bin/read_stockholm +++ b/bp_bin/read_stockholm @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/read_tab b/bp_bin/read_tab index c8c800f..4cd1d44 100755 --- a/bp_bin/read_tab +++ b/bp_bin/read_tab @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/remove_indels b/bp_bin/remove_indels index c8c800f..4cd1d44 100755 --- a/bp_bin/remove_indels +++ b/bp_bin/remove_indels @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/remove_keys b/bp_bin/remove_keys index c8c800f..4cd1d44 100755 --- a/bp_bin/remove_keys +++ b/bp_bin/remove_keys @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/rename_keys b/bp_bin/rename_keys index c8c800f..4cd1d44 100755 --- a/bp_bin/rename_keys +++ b/bp_bin/rename_keys @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/reverse_seq b/bp_bin/reverse_seq index c8c800f..4cd1d44 100755 --- a/bp_bin/reverse_seq +++ b/bp_bin/reverse_seq @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/shuffle_seq b/bp_bin/shuffle_seq index c8c800f..4cd1d44 100755 --- a/bp_bin/shuffle_seq +++ b/bp_bin/shuffle_seq @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/sort_records b/bp_bin/sort_records index c8c800f..4cd1d44 100755 --- a/bp_bin/sort_records +++ b/bp_bin/sort_records @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/split_bed b/bp_bin/split_bed index c8c800f..4cd1d44 100755 --- a/bp_bin/split_bed +++ b/bp_bin/split_bed @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/split_seq b/bp_bin/split_seq index c8c800f..4cd1d44 100755 --- a/bp_bin/split_seq +++ b/bp_bin/split_seq @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/sum_vals b/bp_bin/sum_vals index c8c800f..4cd1d44 100755 --- a/bp_bin/sum_vals +++ b/bp_bin/sum_vals @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/tile_seq b/bp_bin/tile_seq index c8c800f..4cd1d44 100755 --- a/bp_bin/tile_seq +++ b/bp_bin/tile_seq @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/translate_seq b/bp_bin/translate_seq index c8c800f..4cd1d44 100755 --- a/bp_bin/translate_seq +++ b/bp_bin/translate_seq @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/transliterate_seq b/bp_bin/transliterate_seq index c8c800f..4cd1d44 100755 --- a/bp_bin/transliterate_seq +++ b/bp_bin/transliterate_seq @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/transliterate_vals b/bp_bin/transliterate_vals index c8c800f..4cd1d44 100755 --- a/bp_bin/transliterate_vals +++ b/bp_bin/transliterate_vals @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/uniq_vals b/bp_bin/uniq_vals index c8c800f..4cd1d44 100755 --- a/bp_bin/uniq_vals +++ b/bp_bin/uniq_vals @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/upload_to_ucsc b/bp_bin/upload_to_ucsc index c8c800f..4cd1d44 100755 --- a/bp_bin/upload_to_ucsc +++ b/bp_bin/upload_to_ucsc @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/uppercase_seq b/bp_bin/uppercase_seq index c8c800f..4cd1d44 100755 --- a/bp_bin/uppercase_seq +++ b/bp_bin/uppercase_seq @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/vmatch_seq b/bp_bin/vmatch_seq index c8c800f..4cd1d44 100755 --- a/bp_bin/vmatch_seq +++ b/bp_bin/vmatch_seq @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/write_2bit b/bp_bin/write_2bit index c8c800f..4cd1d44 100755 --- a/bp_bin/write_2bit +++ b/bp_bin/write_2bit @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/write_align b/bp_bin/write_align index c8c800f..4cd1d44 100755 --- a/bp_bin/write_align +++ b/bp_bin/write_align @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/write_bed b/bp_bin/write_bed index c8c800f..4cd1d44 100755 --- a/bp_bin/write_bed +++ b/bp_bin/write_bed @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/write_blast b/bp_bin/write_blast index c8c800f..4cd1d44 100755 --- a/bp_bin/write_blast +++ b/bp_bin/write_blast @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/write_fasta b/bp_bin/write_fasta index c8c800f..4cd1d44 100755 --- a/bp_bin/write_fasta +++ b/bp_bin/write_fasta @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/write_psl b/bp_bin/write_psl index c8c800f..4cd1d44 100755 --- a/bp_bin/write_psl +++ b/bp_bin/write_psl @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/write_solid b/bp_bin/write_solid index c8c800f..4cd1d44 100755 --- a/bp_bin/write_solid +++ b/bp_bin/write_solid @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/bp_bin/write_tab b/bp_bin/write_tab index c8c800f..4cd1d44 100755 --- a/bp_bin/write_tab +++ b/bp_bin/write_tab @@ -3,4 +3,4 @@ use warnings; use strict; -use Maasha::Biotools; +use Maasha::Biopieces; diff --git a/code_perl/Maasha/Biotools.pm b/code_perl/Maasha/Biopieces.pm similarity index 99% rename from code_perl/Maasha/Biotools.pm rename to code_perl/Maasha/Biopieces.pm index 50d7e9b..b42a994 100644 --- a/code_perl/Maasha/Biotools.pm +++ b/code_perl/Maasha/Biopieces.pm @@ -1,4 +1,4 @@ -package Maasha::Biotools; +package Maasha::Biopieces; # Copyright (C) 2007-2008 Martin A. Hansen. -- 2.39.5