From f7e5c1b54c562cc1b25fe419cacd4da9ac01f129 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Wed, 13 May 2009 07:39:58 +0000 Subject: [PATCH] moved all binaries and created symlinks instead git-svn-id: http://biopieces.googlecode.com/svn/trunk@373 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/00README | 2 +- bp_bin/add_ident | 7 +------ bp_bin/align_seq | 7 +------ bp_bin/analyze_bed | 7 +------ bp_bin/analyze_seq | 7 +------ bp_bin/analyze_tags | 7 +------ bp_bin/analyze_vals | 7 +------ bp_bin/assemble_tag_contigs | 7 +------ bp_bin/blast_seq | 7 +------ bp_bin/blat_seq | 7 +------ bp_bin/calc_bit_scores | 7 +------ bp_bin/calc_fixedstep | 7 +------ bp_bin/complement_seq | 7 +------ bp_bin/complexity_seq | 7 +------ bp_bin/compute | 7 +------ bp_bin/count_records | 7 +------ bp_bin/count_vals | 7 +------ bp_bin/create_blast_db | 7 +------ bp_bin/create_vmatch_index | 7 +------ bp_bin/create_weight_matrix | 7 +------ bp_bin/extract_seq | 7 +------ bp_bin/flip_tab | 7 +------ bp_bin/fold_seq | 7 +------ bp_bin/format_genome | 7 +------ bp_bin/get_genome_align | 7 +------ bp_bin/get_genome_phastcons | 7 +------ bp_bin/get_genome_seq | 7 +------ bp_bin/grab | 7 +------ bp_bin/head_records | 7 +------ bp_bin/invert_align | 7 +------ bp_bin/length_seq | 7 +------ bp_bin/length_vals | 7 +------ bp_bin/list_biopieces | 7 +------ bp_bin/list_genomes | 7 +------ bp_bin/match_seq | 7 +------ bp_bin/max_vals | 7 +------ bp_bin/mean_vals | 7 +------ bp_bin/median_vals | 7 +------ bp_bin/merge_records | 7 +------ bp_bin/merge_vals | 7 +------ bp_bin/min_vals | 7 +------ bp_bin/oligo_freq | 7 +------ bp_bin/patscan_seq | 7 +------ bp_bin/plot_chrdist | 7 +------ bp_bin/plot_histogram | 7 +------ bp_bin/plot_karyogram | 7 +------ bp_bin/plot_lendist | 7 +------ bp_bin/plot_matches | 7 +------ bp_bin/plot_phastcons_profiles | 7 +------ bp_bin/plot_seqlogo | 7 +------ bp_bin/print_usage | 7 +------ bp_bin/random_records | 7 +------ bp_bin/read_2bit | 7 +------ bp_bin/read_bed | 7 +------ bp_bin/read_blast_tab | 7 +------ bp_bin/read_embl | 7 +------ bp_bin/read_fasta | 7 +------ bp_bin/read_fixedstep | 7 +------ bp_bin/read_gff | 7 +------ bp_bin/read_mysql | 7 +------ bp_bin/read_phastcons | 7 +------ bp_bin/read_psl | 7 +------ bp_bin/read_soft | 7 +------ bp_bin/read_solexa | 7 +------ bp_bin/read_solid | 7 +------ bp_bin/read_stockholm | 7 +------ bp_bin/read_tab | 7 +------ bp_bin/read_ucsc_config | 7 +------ bp_bin/remove_adaptor | 7 +------ bp_bin/remove_indels | 7 +------ bp_bin/remove_keys | 7 +------ bp_bin/remove_mysql_tables | 7 +------ bp_bin/remove_ucsc_tracks | 7 +------ bp_bin/rename_keys | 7 +------ bp_bin/reverse_seq | 7 +------ bp_bin/shuffle_seq | 7 +------ bp_bin/soap_seq | 7 +------ bp_bin/sort_records | 7 +------ bp_bin/split_bed | 7 +------ bp_bin/split_seq | 7 +------ bp_bin/sum_vals | 7 +------ bp_bin/tile_seq | 7 +------ bp_bin/translate_seq | 7 +------ bp_bin/transliterate_seq | 7 +------ bp_bin/transliterate_vals | 7 +------ bp_bin/uniq_vals | 7 +------ bp_bin/upload_to_ucsc | 7 +------ bp_bin/uppercase_seq | 7 +------ bp_bin/vmatch_seq | 7 +------ bp_bin/write_2bit | 7 +------ bp_bin/write_align | 7 +------ bp_bin/write_bed | 7 +------ bp_bin/write_blast | 7 +------ bp_bin/write_fasta | 7 +------ bp_bin/write_fixedstep | 7 +------ bp_bin/write_psl | 7 +------ bp_bin/write_solid | 7 +------ bp_bin/write_tab | 7 +------ bp_bin/write_ucsc_config | 7 +------ code_perl/Maasha/bin/add_ident | 6 ++++++ code_perl/Maasha/bin/align_seq | 6 ++++++ code_perl/Maasha/bin/analyze_bed | 6 ++++++ code_perl/Maasha/bin/analyze_seq | 6 ++++++ code_perl/Maasha/bin/analyze_tags | 6 ++++++ code_perl/Maasha/bin/analyze_vals | 6 ++++++ code_perl/Maasha/bin/assemble_tag_contigs | 6 ++++++ code_perl/Maasha/bin/blast_seq | 6 ++++++ code_perl/Maasha/bin/blat_seq | 6 ++++++ code_perl/Maasha/bin/calc_bit_scores | 6 ++++++ code_perl/Maasha/bin/calc_fixedstep | 6 ++++++ code_perl/Maasha/bin/complement_seq | 6 ++++++ code_perl/Maasha/bin/complexity_seq | 6 ++++++ code_perl/Maasha/bin/compute | 6 ++++++ code_perl/Maasha/bin/count_records | 6 ++++++ code_perl/Maasha/bin/count_vals | 6 ++++++ code_perl/Maasha/bin/create_blast_db | 6 ++++++ code_perl/Maasha/bin/create_vmatch_index | 6 ++++++ code_perl/Maasha/bin/create_weight_matrix | 6 ++++++ code_perl/Maasha/bin/extract_seq | 6 ++++++ code_perl/Maasha/bin/flip_tab | 6 ++++++ code_perl/Maasha/bin/fold_seq | 6 ++++++ code_perl/Maasha/bin/format_genome | 6 ++++++ code_perl/Maasha/bin/get_genome_align | 6 ++++++ code_perl/Maasha/bin/get_genome_phastcons | 6 ++++++ code_perl/Maasha/bin/get_genome_seq | 6 ++++++ code_perl/Maasha/bin/grab | 6 ++++++ code_perl/Maasha/bin/head_records | 6 ++++++ code_perl/Maasha/bin/invert_align | 6 ++++++ code_perl/Maasha/bin/length_seq | 6 ++++++ code_perl/Maasha/bin/length_vals | 6 ++++++ code_perl/Maasha/bin/list_biopieces | 6 ++++++ code_perl/Maasha/bin/list_genomes | 6 ++++++ code_perl/Maasha/bin/match_seq | 6 ++++++ code_perl/Maasha/bin/max_vals | 6 ++++++ code_perl/Maasha/bin/mean_vals | 6 ++++++ code_perl/Maasha/bin/median_vals | 6 ++++++ code_perl/Maasha/bin/merge_records | 6 ++++++ code_perl/Maasha/bin/merge_vals | 6 ++++++ code_perl/Maasha/bin/min_vals | 6 ++++++ code_perl/Maasha/bin/oligo_freq | 6 ++++++ code_perl/Maasha/bin/patscan_seq | 6 ++++++ code_perl/Maasha/bin/plot_chrdist | 6 ++++++ code_perl/Maasha/bin/plot_histogram | 6 ++++++ code_perl/Maasha/bin/plot_karyogram | 6 ++++++ code_perl/Maasha/bin/plot_lendist | 6 ++++++ code_perl/Maasha/bin/plot_matches | 6 ++++++ code_perl/Maasha/bin/plot_phastcons_profiles | 6 ++++++ code_perl/Maasha/bin/plot_seqlogo | 6 ++++++ code_perl/Maasha/bin/print_usage | 6 ++++++ code_perl/Maasha/bin/random_records | 6 ++++++ code_perl/Maasha/bin/read_2bit | 6 ++++++ code_perl/Maasha/bin/read_bed | 6 ++++++ code_perl/Maasha/bin/read_blast_tab | 6 ++++++ code_perl/Maasha/bin/read_embl | 6 ++++++ code_perl/Maasha/bin/read_fasta | 6 ++++++ code_perl/Maasha/bin/read_fixedstep | 6 ++++++ code_perl/Maasha/bin/read_gff | 6 ++++++ code_perl/Maasha/bin/read_mysql | 6 ++++++ code_perl/Maasha/bin/read_phastcons | 6 ++++++ code_perl/Maasha/bin/read_psl | 6 ++++++ code_perl/Maasha/bin/read_soft | 6 ++++++ code_perl/Maasha/bin/read_solexa | 6 ++++++ code_perl/Maasha/bin/read_solid | 6 ++++++ code_perl/Maasha/bin/read_stockholm | 6 ++++++ code_perl/Maasha/bin/read_tab | 6 ++++++ code_perl/Maasha/bin/read_ucsc_config | 6 ++++++ code_perl/Maasha/bin/remove_adaptor | 6 ++++++ code_perl/Maasha/bin/remove_indels | 6 ++++++ code_perl/Maasha/bin/remove_keys | 6 ++++++ code_perl/Maasha/bin/remove_mysql_tables | 6 ++++++ code_perl/Maasha/bin/remove_ucsc_tracks | 6 ++++++ code_perl/Maasha/bin/rename_keys | 6 ++++++ code_perl/Maasha/bin/reverse_seq | 6 ++++++ code_perl/Maasha/bin/shuffle_seq | 6 ++++++ code_perl/Maasha/bin/soap_seq | 6 ++++++ code_perl/Maasha/bin/sort_records | 6 ++++++ code_perl/Maasha/bin/split_bed | 6 ++++++ code_perl/Maasha/bin/split_seq | 6 ++++++ code_perl/Maasha/bin/sum_vals | 6 ++++++ code_perl/Maasha/bin/tile_seq | 6 ++++++ code_perl/Maasha/bin/translate_seq | 6 ++++++ code_perl/Maasha/bin/transliterate_seq | 6 ++++++ code_perl/Maasha/bin/transliterate_vals | 6 ++++++ code_perl/Maasha/bin/uniq_vals | 6 ++++++ code_perl/Maasha/bin/upload_to_ucsc | 6 ++++++ code_perl/Maasha/bin/uppercase_seq | 6 ++++++ code_perl/Maasha/bin/vmatch_seq | 6 ++++++ code_perl/Maasha/bin/write_2bit | 6 ++++++ code_perl/Maasha/bin/write_align | 6 ++++++ code_perl/Maasha/bin/write_bed | 6 ++++++ code_perl/Maasha/bin/write_blast | 6 ++++++ code_perl/Maasha/bin/write_fasta | 6 ++++++ code_perl/Maasha/bin/write_fixedstep | 6 ++++++ code_perl/Maasha/bin/write_psl | 6 ++++++ code_perl/Maasha/bin/write_solid | 6 ++++++ code_perl/Maasha/bin/write_tab | 6 ++++++ code_perl/Maasha/bin/write_ucsc_config | 6 ++++++ code_python/Cjung/Args.pyc | Bin 5025 -> 5390 bytes 198 files changed, 687 insertions(+), 589 deletions(-) mode change 100755 => 120000 bp_bin/add_ident mode change 100755 => 120000 bp_bin/align_seq mode change 100755 => 120000 bp_bin/analyze_bed mode change 100755 => 120000 bp_bin/analyze_seq mode change 100755 => 120000 bp_bin/analyze_tags mode change 100755 => 120000 bp_bin/analyze_vals mode change 100755 => 120000 bp_bin/assemble_tag_contigs mode change 100755 => 120000 bp_bin/blast_seq mode change 100755 => 120000 bp_bin/blat_seq mode change 100755 => 120000 bp_bin/calc_bit_scores mode change 100755 => 120000 bp_bin/calc_fixedstep mode change 100755 => 120000 bp_bin/complement_seq mode change 100755 => 120000 bp_bin/complexity_seq mode change 100755 => 120000 bp_bin/compute mode change 100755 => 120000 bp_bin/count_records mode change 100755 => 120000 bp_bin/count_vals mode change 100755 => 120000 bp_bin/create_blast_db mode change 100755 => 120000 bp_bin/create_vmatch_index mode change 100755 => 120000 bp_bin/create_weight_matrix mode change 100755 => 120000 bp_bin/extract_seq mode change 100755 => 120000 bp_bin/flip_tab mode change 100755 => 120000 bp_bin/fold_seq mode change 100755 => 120000 bp_bin/format_genome mode change 100755 => 120000 bp_bin/get_genome_align mode change 100755 => 120000 bp_bin/get_genome_phastcons mode change 100755 => 120000 bp_bin/get_genome_seq mode change 100755 => 120000 bp_bin/grab mode change 100755 => 120000 bp_bin/head_records mode change 100755 => 120000 bp_bin/invert_align mode change 100755 => 120000 bp_bin/length_seq mode change 100755 => 120000 bp_bin/length_vals mode change 100755 => 120000 bp_bin/list_biopieces mode change 100755 => 120000 bp_bin/list_genomes mode change 100755 => 120000 bp_bin/match_seq mode change 100755 => 120000 bp_bin/max_vals mode change 100755 => 120000 bp_bin/mean_vals mode change 100755 => 120000 bp_bin/median_vals mode change 100755 => 120000 bp_bin/merge_records mode change 100755 => 120000 bp_bin/merge_vals mode change 100755 => 120000 bp_bin/min_vals mode change 100755 => 120000 bp_bin/oligo_freq mode change 100755 => 120000 bp_bin/patscan_seq mode change 100755 => 120000 bp_bin/plot_chrdist mode change 100755 => 120000 bp_bin/plot_histogram mode change 100755 => 120000 bp_bin/plot_karyogram mode change 100755 => 120000 bp_bin/plot_lendist mode change 100755 => 120000 bp_bin/plot_matches mode change 100755 => 120000 bp_bin/plot_phastcons_profiles mode change 100755 => 120000 bp_bin/plot_seqlogo mode change 100755 => 120000 bp_bin/print_usage mode change 100755 => 120000 bp_bin/random_records mode change 100755 => 120000 bp_bin/read_2bit mode change 100755 => 120000 bp_bin/read_bed mode change 100755 => 120000 bp_bin/read_blast_tab mode change 100755 => 120000 bp_bin/read_embl mode change 100755 => 120000 bp_bin/read_fasta mode change 100755 => 120000 bp_bin/read_fixedstep mode change 100755 => 120000 bp_bin/read_gff mode change 100755 => 120000 bp_bin/read_mysql mode change 100755 => 120000 bp_bin/read_phastcons mode change 100755 => 120000 bp_bin/read_psl mode change 100755 => 120000 bp_bin/read_soft mode change 100755 => 120000 bp_bin/read_solexa mode change 100755 => 120000 bp_bin/read_solid mode change 100755 => 120000 bp_bin/read_stockholm mode change 100755 => 120000 bp_bin/read_tab mode change 100755 => 120000 bp_bin/read_ucsc_config mode change 100755 => 120000 bp_bin/remove_adaptor mode change 100755 => 120000 bp_bin/remove_indels mode change 100755 => 120000 bp_bin/remove_keys mode change 100755 => 120000 bp_bin/remove_mysql_tables mode change 100644 => 120000 bp_bin/remove_ucsc_tracks mode change 100755 => 120000 bp_bin/rename_keys mode change 100755 => 120000 bp_bin/reverse_seq mode change 100755 => 120000 bp_bin/shuffle_seq mode change 100755 => 120000 bp_bin/soap_seq mode change 100755 => 120000 bp_bin/sort_records mode change 100755 => 120000 bp_bin/split_bed mode change 100755 => 120000 bp_bin/split_seq mode change 100755 => 120000 bp_bin/sum_vals mode change 100755 => 120000 bp_bin/tile_seq mode change 100755 => 120000 bp_bin/translate_seq mode change 100755 => 120000 bp_bin/transliterate_seq mode change 100755 => 120000 bp_bin/transliterate_vals mode change 100755 => 120000 bp_bin/uniq_vals mode change 100755 => 120000 bp_bin/upload_to_ucsc mode change 100755 => 120000 bp_bin/uppercase_seq mode change 100755 => 120000 bp_bin/vmatch_seq mode change 100755 => 120000 bp_bin/write_2bit mode change 100755 => 120000 bp_bin/write_align mode change 100755 => 120000 bp_bin/write_bed mode change 100755 => 120000 bp_bin/write_blast mode change 100755 => 120000 bp_bin/write_fasta mode change 100755 => 120000 bp_bin/write_fixedstep mode change 100755 => 120000 bp_bin/write_psl mode change 100755 => 120000 bp_bin/write_solid mode change 100755 => 120000 bp_bin/write_tab mode change 100755 => 120000 bp_bin/write_ucsc_config create mode 100755 code_perl/Maasha/bin/add_ident create mode 100755 code_perl/Maasha/bin/align_seq create mode 100755 code_perl/Maasha/bin/analyze_bed create mode 100755 code_perl/Maasha/bin/analyze_seq create mode 100755 code_perl/Maasha/bin/analyze_tags create mode 100755 code_perl/Maasha/bin/analyze_vals create mode 100755 code_perl/Maasha/bin/assemble_tag_contigs create mode 100755 code_perl/Maasha/bin/blast_seq create mode 100755 code_perl/Maasha/bin/blat_seq create mode 100755 code_perl/Maasha/bin/calc_bit_scores create mode 100755 code_perl/Maasha/bin/calc_fixedstep create mode 100755 code_perl/Maasha/bin/complement_seq create mode 100755 code_perl/Maasha/bin/complexity_seq create mode 100755 code_perl/Maasha/bin/compute create mode 100755 code_perl/Maasha/bin/count_records create mode 100755 code_perl/Maasha/bin/count_vals create mode 100755 code_perl/Maasha/bin/create_blast_db create mode 100755 code_perl/Maasha/bin/create_vmatch_index create mode 100755 code_perl/Maasha/bin/create_weight_matrix create mode 100755 code_perl/Maasha/bin/extract_seq create mode 100755 code_perl/Maasha/bin/flip_tab create mode 100755 code_perl/Maasha/bin/fold_seq create mode 100755 code_perl/Maasha/bin/format_genome create mode 100755 code_perl/Maasha/bin/get_genome_align create mode 100755 code_perl/Maasha/bin/get_genome_phastcons create mode 100755 code_perl/Maasha/bin/get_genome_seq create mode 100755 code_perl/Maasha/bin/grab create mode 100755 code_perl/Maasha/bin/head_records create mode 100755 code_perl/Maasha/bin/invert_align create mode 100755 code_perl/Maasha/bin/length_seq create mode 100755 code_perl/Maasha/bin/length_vals create mode 100755 code_perl/Maasha/bin/list_biopieces create mode 100755 code_perl/Maasha/bin/list_genomes create mode 100755 code_perl/Maasha/bin/match_seq create mode 100755 code_perl/Maasha/bin/max_vals create mode 100755 code_perl/Maasha/bin/mean_vals create mode 100755 code_perl/Maasha/bin/median_vals create mode 100755 code_perl/Maasha/bin/merge_records create mode 100755 code_perl/Maasha/bin/merge_vals create mode 100755 code_perl/Maasha/bin/min_vals create mode 100755 code_perl/Maasha/bin/oligo_freq create mode 100755 code_perl/Maasha/bin/patscan_seq create mode 100755 code_perl/Maasha/bin/plot_chrdist create mode 100755 code_perl/Maasha/bin/plot_histogram create mode 100755 code_perl/Maasha/bin/plot_karyogram create mode 100755 code_perl/Maasha/bin/plot_lendist create mode 100755 code_perl/Maasha/bin/plot_matches create mode 100755 code_perl/Maasha/bin/plot_phastcons_profiles create mode 100755 code_perl/Maasha/bin/plot_seqlogo create mode 100755 code_perl/Maasha/bin/print_usage create mode 100755 code_perl/Maasha/bin/random_records create mode 100755 code_perl/Maasha/bin/read_2bit create mode 100755 code_perl/Maasha/bin/read_bed create mode 100755 code_perl/Maasha/bin/read_blast_tab create mode 100755 code_perl/Maasha/bin/read_embl create mode 100755 code_perl/Maasha/bin/read_fasta create mode 100755 code_perl/Maasha/bin/read_fixedstep create mode 100755 code_perl/Maasha/bin/read_gff create mode 100755 code_perl/Maasha/bin/read_mysql create mode 100755 code_perl/Maasha/bin/read_phastcons create mode 100755 code_perl/Maasha/bin/read_psl create mode 100755 code_perl/Maasha/bin/read_soft create mode 100755 code_perl/Maasha/bin/read_solexa create mode 100755 code_perl/Maasha/bin/read_solid create mode 100755 code_perl/Maasha/bin/read_stockholm create mode 100755 code_perl/Maasha/bin/read_tab create mode 100755 code_perl/Maasha/bin/read_ucsc_config create mode 100755 code_perl/Maasha/bin/remove_adaptor create mode 100755 code_perl/Maasha/bin/remove_indels create mode 100755 code_perl/Maasha/bin/remove_keys create mode 100755 code_perl/Maasha/bin/remove_mysql_tables create mode 100644 code_perl/Maasha/bin/remove_ucsc_tracks create mode 100755 code_perl/Maasha/bin/rename_keys create mode 100755 code_perl/Maasha/bin/reverse_seq create mode 100755 code_perl/Maasha/bin/shuffle_seq create mode 100755 code_perl/Maasha/bin/soap_seq create mode 100755 code_perl/Maasha/bin/sort_records create mode 100755 code_perl/Maasha/bin/split_bed create mode 100755 code_perl/Maasha/bin/split_seq create mode 100755 code_perl/Maasha/bin/sum_vals create mode 100755 code_perl/Maasha/bin/tile_seq create mode 100755 code_perl/Maasha/bin/translate_seq create mode 100755 code_perl/Maasha/bin/transliterate_seq create mode 100755 code_perl/Maasha/bin/transliterate_vals create mode 100755 code_perl/Maasha/bin/uniq_vals create mode 100755 code_perl/Maasha/bin/upload_to_ucsc create mode 100755 code_perl/Maasha/bin/uppercase_seq create mode 100755 code_perl/Maasha/bin/vmatch_seq create mode 100755 code_perl/Maasha/bin/write_2bit create mode 100755 code_perl/Maasha/bin/write_align create mode 100755 code_perl/Maasha/bin/write_bed create mode 100755 code_perl/Maasha/bin/write_blast create mode 100755 code_perl/Maasha/bin/write_fasta create mode 100755 code_perl/Maasha/bin/write_fixedstep create mode 100755 code_perl/Maasha/bin/write_psl create mode 100755 code_perl/Maasha/bin/write_solid create mode 100755 code_perl/Maasha/bin/write_tab create mode 100755 code_perl/Maasha/bin/write_ucsc_config diff --git a/bp_bin/00README b/bp_bin/00README index 49d4a84..5991f9b 100644 --- a/bp_bin/00README +++ b/bp_bin/00README @@ -1,4 +1,4 @@ -This directory should only contain biopiece executables. +This directory should only contain symlinks to Biopiece executables. diff --git a/bp_bin/add_ident b/bp_bin/add_ident deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/add_ident +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/add_ident b/bp_bin/add_ident new file mode 120000 index 0000000..f557754 --- /dev/null +++ b/bp_bin/add_ident @@ -0,0 +1 @@ +../code_perl/Maasha/bin/add_ident \ No newline at end of file diff --git a/bp_bin/align_seq b/bp_bin/align_seq deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/align_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/align_seq b/bp_bin/align_seq new file mode 120000 index 0000000..0000796 --- /dev/null +++ b/bp_bin/align_seq @@ -0,0 +1 @@ +../code_perl/Maasha/bin/align_seq \ No newline at end of file diff --git a/bp_bin/analyze_bed b/bp_bin/analyze_bed deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/analyze_bed +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/analyze_bed b/bp_bin/analyze_bed new file mode 120000 index 0000000..6f0d8ca --- /dev/null +++ b/bp_bin/analyze_bed @@ -0,0 +1 @@ +../code_perl/Maasha/bin/analyze_bed \ No newline at end of file diff --git a/bp_bin/analyze_seq b/bp_bin/analyze_seq deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/analyze_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/analyze_seq b/bp_bin/analyze_seq new file mode 120000 index 0000000..ac17cf2 --- /dev/null +++ b/bp_bin/analyze_seq @@ -0,0 +1 @@ +../code_perl/Maasha/bin/analyze_seq \ No newline at end of file diff --git a/bp_bin/analyze_tags b/bp_bin/analyze_tags deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/analyze_tags +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/analyze_tags b/bp_bin/analyze_tags new file mode 120000 index 0000000..3cb9f03 --- /dev/null +++ b/bp_bin/analyze_tags @@ -0,0 +1 @@ +../code_perl/Maasha/bin/analyze_tags \ No newline at end of file diff --git a/bp_bin/analyze_vals b/bp_bin/analyze_vals deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/analyze_vals +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/analyze_vals b/bp_bin/analyze_vals new file mode 120000 index 0000000..c25d2e8 --- /dev/null +++ b/bp_bin/analyze_vals @@ -0,0 +1 @@ +../code_perl/Maasha/bin/analyze_vals \ No newline at end of file diff --git a/bp_bin/assemble_tag_contigs b/bp_bin/assemble_tag_contigs deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/assemble_tag_contigs +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/assemble_tag_contigs b/bp_bin/assemble_tag_contigs new file mode 120000 index 0000000..2352792 --- /dev/null +++ b/bp_bin/assemble_tag_contigs @@ -0,0 +1 @@ +../code_perl/Maasha/bin/assemble_tag_contigs \ No newline at end of file diff --git a/bp_bin/blast_seq b/bp_bin/blast_seq deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/blast_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/blast_seq b/bp_bin/blast_seq new file mode 120000 index 0000000..27d57ad --- /dev/null +++ b/bp_bin/blast_seq @@ -0,0 +1 @@ +../code_perl/Maasha/bin/blast_seq \ No newline at end of file diff --git a/bp_bin/blat_seq b/bp_bin/blat_seq deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/blat_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/blat_seq b/bp_bin/blat_seq new file mode 120000 index 0000000..eb77e30 --- /dev/null +++ b/bp_bin/blat_seq @@ -0,0 +1 @@ +../code_perl/Maasha/bin/blat_seq \ No newline at end of file diff --git a/bp_bin/calc_bit_scores b/bp_bin/calc_bit_scores deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/calc_bit_scores +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/calc_bit_scores b/bp_bin/calc_bit_scores new file mode 120000 index 0000000..7105a3a --- /dev/null +++ b/bp_bin/calc_bit_scores @@ -0,0 +1 @@ +../code_perl/Maasha/bin/calc_bit_scores \ No newline at end of file diff --git a/bp_bin/calc_fixedstep b/bp_bin/calc_fixedstep deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/calc_fixedstep +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/calc_fixedstep b/bp_bin/calc_fixedstep new file mode 120000 index 0000000..b177a75 --- /dev/null +++ b/bp_bin/calc_fixedstep @@ -0,0 +1 @@ +../code_perl/Maasha/bin/calc_fixedstep \ No newline at end of file diff --git a/bp_bin/complement_seq b/bp_bin/complement_seq deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/complement_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/complement_seq b/bp_bin/complement_seq new file mode 120000 index 0000000..c45e684 --- /dev/null +++ b/bp_bin/complement_seq @@ -0,0 +1 @@ +../code_perl/Maasha/bin/complement_seq \ No newline at end of file diff --git a/bp_bin/complexity_seq b/bp_bin/complexity_seq deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/complexity_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/complexity_seq b/bp_bin/complexity_seq new file mode 120000 index 0000000..e67a447 --- /dev/null +++ b/bp_bin/complexity_seq @@ -0,0 +1 @@ +../code_perl/Maasha/bin/complexity_seq \ No newline at end of file diff --git a/bp_bin/compute b/bp_bin/compute deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/compute +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/compute b/bp_bin/compute new file mode 120000 index 0000000..073fa40 --- /dev/null +++ b/bp_bin/compute @@ -0,0 +1 @@ +../code_perl/Maasha/bin/compute \ No newline at end of file diff --git a/bp_bin/count_records b/bp_bin/count_records deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/count_records +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/count_records b/bp_bin/count_records new file mode 120000 index 0000000..ba524a8 --- /dev/null +++ b/bp_bin/count_records @@ -0,0 +1 @@ +../code_perl/Maasha/bin/count_records \ No newline at end of file diff --git a/bp_bin/count_vals b/bp_bin/count_vals deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/count_vals +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/count_vals b/bp_bin/count_vals new file mode 120000 index 0000000..2574094 --- /dev/null +++ b/bp_bin/count_vals @@ -0,0 +1 @@ +../code_perl/Maasha/bin/count_vals \ No newline at end of file diff --git a/bp_bin/create_blast_db b/bp_bin/create_blast_db deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/create_blast_db +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/create_blast_db b/bp_bin/create_blast_db new file mode 120000 index 0000000..f7b9637 --- /dev/null +++ b/bp_bin/create_blast_db @@ -0,0 +1 @@ +../code_perl/Maasha/bin/create_blast_db \ No newline at end of file diff --git a/bp_bin/create_vmatch_index b/bp_bin/create_vmatch_index deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/create_vmatch_index +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/create_vmatch_index b/bp_bin/create_vmatch_index new file mode 120000 index 0000000..6590fad --- /dev/null +++ b/bp_bin/create_vmatch_index @@ -0,0 +1 @@ +../code_perl/Maasha/bin/create_vmatch_index \ No newline at end of file diff --git a/bp_bin/create_weight_matrix b/bp_bin/create_weight_matrix deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/create_weight_matrix +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/create_weight_matrix b/bp_bin/create_weight_matrix new file mode 120000 index 0000000..17345c6 --- /dev/null +++ b/bp_bin/create_weight_matrix @@ -0,0 +1 @@ +../code_perl/Maasha/bin/create_weight_matrix \ No newline at end of file diff --git a/bp_bin/extract_seq b/bp_bin/extract_seq deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/extract_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/extract_seq b/bp_bin/extract_seq new file mode 120000 index 0000000..bd5293f --- /dev/null +++ b/bp_bin/extract_seq @@ -0,0 +1 @@ +../code_perl/Maasha/bin/extract_seq \ No newline at end of file diff --git a/bp_bin/flip_tab b/bp_bin/flip_tab deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/flip_tab +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/flip_tab b/bp_bin/flip_tab new file mode 120000 index 0000000..2703aa5 --- /dev/null +++ b/bp_bin/flip_tab @@ -0,0 +1 @@ +../code_perl/Maasha/bin/flip_tab \ No newline at end of file diff --git a/bp_bin/fold_seq b/bp_bin/fold_seq deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/fold_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/fold_seq b/bp_bin/fold_seq new file mode 120000 index 0000000..c5f3728 --- /dev/null +++ b/bp_bin/fold_seq @@ -0,0 +1 @@ +../code_perl/Maasha/bin/fold_seq \ No newline at end of file diff --git a/bp_bin/format_genome b/bp_bin/format_genome deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/format_genome +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/format_genome b/bp_bin/format_genome new file mode 120000 index 0000000..c4b373b --- /dev/null +++ b/bp_bin/format_genome @@ -0,0 +1 @@ +../code_perl/Maasha/bin/format_genome \ No newline at end of file diff --git a/bp_bin/get_genome_align b/bp_bin/get_genome_align deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/get_genome_align +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/get_genome_align b/bp_bin/get_genome_align new file mode 120000 index 0000000..65d4851 --- /dev/null +++ b/bp_bin/get_genome_align @@ -0,0 +1 @@ +../code_perl/Maasha/bin/get_genome_align \ No newline at end of file diff --git a/bp_bin/get_genome_phastcons b/bp_bin/get_genome_phastcons deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/get_genome_phastcons +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/get_genome_phastcons b/bp_bin/get_genome_phastcons new file mode 120000 index 0000000..e725c69 --- /dev/null +++ b/bp_bin/get_genome_phastcons @@ -0,0 +1 @@ +../code_perl/Maasha/bin/get_genome_phastcons \ No newline at end of file diff --git a/bp_bin/get_genome_seq b/bp_bin/get_genome_seq deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/get_genome_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/get_genome_seq b/bp_bin/get_genome_seq new file mode 120000 index 0000000..3f6c4cc --- /dev/null +++ b/bp_bin/get_genome_seq @@ -0,0 +1 @@ +../code_perl/Maasha/bin/get_genome_seq \ No newline at end of file diff --git a/bp_bin/grab b/bp_bin/grab deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/grab +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/grab b/bp_bin/grab new file mode 120000 index 0000000..3319f75 --- /dev/null +++ b/bp_bin/grab @@ -0,0 +1 @@ +../code_perl/Maasha/bin/grab \ No newline at end of file diff --git a/bp_bin/head_records b/bp_bin/head_records deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/head_records +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/head_records b/bp_bin/head_records new file mode 120000 index 0000000..db1b690 --- /dev/null +++ b/bp_bin/head_records @@ -0,0 +1 @@ +../code_perl/Maasha/bin/head_records \ No newline at end of file diff --git a/bp_bin/invert_align b/bp_bin/invert_align deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/invert_align +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/invert_align b/bp_bin/invert_align new file mode 120000 index 0000000..40c0b38 --- /dev/null +++ b/bp_bin/invert_align @@ -0,0 +1 @@ +../code_perl/Maasha/bin/invert_align \ No newline at end of file diff --git a/bp_bin/length_seq b/bp_bin/length_seq deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/length_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/length_seq b/bp_bin/length_seq new file mode 120000 index 0000000..b3a16a7 --- /dev/null +++ b/bp_bin/length_seq @@ -0,0 +1 @@ +../code_perl/Maasha/bin/length_seq \ No newline at end of file diff --git a/bp_bin/length_vals b/bp_bin/length_vals deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/length_vals +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/length_vals b/bp_bin/length_vals new file mode 120000 index 0000000..4651536 --- /dev/null +++ b/bp_bin/length_vals @@ -0,0 +1 @@ +../code_perl/Maasha/bin/length_vals \ No newline at end of file diff --git a/bp_bin/list_biopieces b/bp_bin/list_biopieces deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/list_biopieces +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/list_biopieces b/bp_bin/list_biopieces new file mode 120000 index 0000000..cb71814 --- /dev/null +++ b/bp_bin/list_biopieces @@ -0,0 +1 @@ +../code_perl/Maasha/bin/list_biopieces \ No newline at end of file diff --git a/bp_bin/list_genomes b/bp_bin/list_genomes deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/list_genomes +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/list_genomes b/bp_bin/list_genomes new file mode 120000 index 0000000..2ad4d09 --- /dev/null +++ b/bp_bin/list_genomes @@ -0,0 +1 @@ +../code_perl/Maasha/bin/list_genomes \ No newline at end of file diff --git a/bp_bin/match_seq b/bp_bin/match_seq deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/match_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/match_seq b/bp_bin/match_seq new file mode 120000 index 0000000..2843de1 --- /dev/null +++ b/bp_bin/match_seq @@ -0,0 +1 @@ +../code_perl/Maasha/bin/match_seq \ No newline at end of file diff --git a/bp_bin/max_vals b/bp_bin/max_vals deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/max_vals +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/max_vals b/bp_bin/max_vals new file mode 120000 index 0000000..0fd7620 --- /dev/null +++ b/bp_bin/max_vals @@ -0,0 +1 @@ +../code_perl/Maasha/bin/max_vals \ No newline at end of file diff --git a/bp_bin/mean_vals b/bp_bin/mean_vals deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/mean_vals +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/mean_vals b/bp_bin/mean_vals new file mode 120000 index 0000000..9d6fae5 --- /dev/null +++ b/bp_bin/mean_vals @@ -0,0 +1 @@ +../code_perl/Maasha/bin/mean_vals \ No newline at end of file diff --git a/bp_bin/median_vals b/bp_bin/median_vals deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/median_vals +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/median_vals b/bp_bin/median_vals new file mode 120000 index 0000000..dfcd775 --- /dev/null +++ b/bp_bin/median_vals @@ -0,0 +1 @@ +../code_perl/Maasha/bin/median_vals \ No newline at end of file diff --git a/bp_bin/merge_records b/bp_bin/merge_records deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/merge_records +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/merge_records b/bp_bin/merge_records new file mode 120000 index 0000000..04dfe6c --- /dev/null +++ b/bp_bin/merge_records @@ -0,0 +1 @@ +../code_perl/Maasha/bin/merge_records \ No newline at end of file diff --git a/bp_bin/merge_vals b/bp_bin/merge_vals deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/merge_vals +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/merge_vals b/bp_bin/merge_vals new file mode 120000 index 0000000..9da46f8 --- /dev/null +++ b/bp_bin/merge_vals @@ -0,0 +1 @@ +../code_perl/Maasha/bin/merge_vals \ No newline at end of file diff --git a/bp_bin/min_vals b/bp_bin/min_vals deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/min_vals +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/min_vals b/bp_bin/min_vals new file mode 120000 index 0000000..089e58b --- /dev/null +++ b/bp_bin/min_vals @@ -0,0 +1 @@ +../code_perl/Maasha/bin/min_vals \ No newline at end of file diff --git a/bp_bin/oligo_freq b/bp_bin/oligo_freq deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/oligo_freq +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/oligo_freq b/bp_bin/oligo_freq new file mode 120000 index 0000000..d2a9215 --- /dev/null +++ b/bp_bin/oligo_freq @@ -0,0 +1 @@ +../code_perl/Maasha/bin/oligo_freq \ No newline at end of file diff --git a/bp_bin/patscan_seq b/bp_bin/patscan_seq deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/patscan_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/patscan_seq b/bp_bin/patscan_seq new file mode 120000 index 0000000..45ff4a7 --- /dev/null +++ b/bp_bin/patscan_seq @@ -0,0 +1 @@ +../code_perl/Maasha/bin/patscan_seq \ No newline at end of file diff --git a/bp_bin/plot_chrdist b/bp_bin/plot_chrdist deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/plot_chrdist +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/plot_chrdist b/bp_bin/plot_chrdist new file mode 120000 index 0000000..e88eb45 --- /dev/null +++ b/bp_bin/plot_chrdist @@ -0,0 +1 @@ +../code_perl/Maasha/bin/plot_chrdist \ No newline at end of file diff --git a/bp_bin/plot_histogram b/bp_bin/plot_histogram deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/plot_histogram +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/plot_histogram b/bp_bin/plot_histogram new file mode 120000 index 0000000..034da4e --- /dev/null +++ b/bp_bin/plot_histogram @@ -0,0 +1 @@ +../code_perl/Maasha/bin/plot_histogram \ No newline at end of file diff --git a/bp_bin/plot_karyogram b/bp_bin/plot_karyogram deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/plot_karyogram +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/plot_karyogram b/bp_bin/plot_karyogram new file mode 120000 index 0000000..99aeeba --- /dev/null +++ b/bp_bin/plot_karyogram @@ -0,0 +1 @@ +../code_perl/Maasha/bin/plot_karyogram \ No newline at end of file diff --git a/bp_bin/plot_lendist b/bp_bin/plot_lendist deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/plot_lendist +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/plot_lendist b/bp_bin/plot_lendist new file mode 120000 index 0000000..66ddb3c --- /dev/null +++ b/bp_bin/plot_lendist @@ -0,0 +1 @@ +../code_perl/Maasha/bin/plot_lendist \ No newline at end of file diff --git a/bp_bin/plot_matches b/bp_bin/plot_matches deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/plot_matches +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/plot_matches b/bp_bin/plot_matches new file mode 120000 index 0000000..4c310f9 --- /dev/null +++ b/bp_bin/plot_matches @@ -0,0 +1 @@ +../code_perl/Maasha/bin/plot_matches \ No newline at end of file diff --git a/bp_bin/plot_phastcons_profiles b/bp_bin/plot_phastcons_profiles deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/plot_phastcons_profiles +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/plot_phastcons_profiles b/bp_bin/plot_phastcons_profiles new file mode 120000 index 0000000..70757b2 --- /dev/null +++ b/bp_bin/plot_phastcons_profiles @@ -0,0 +1 @@ +../code_perl/Maasha/bin/plot_phastcons_profiles \ No newline at end of file diff --git a/bp_bin/plot_seqlogo b/bp_bin/plot_seqlogo deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/plot_seqlogo +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/plot_seqlogo b/bp_bin/plot_seqlogo new file mode 120000 index 0000000..236f33c --- /dev/null +++ b/bp_bin/plot_seqlogo @@ -0,0 +1 @@ +../code_perl/Maasha/bin/plot_seqlogo \ No newline at end of file diff --git a/bp_bin/print_usage b/bp_bin/print_usage deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/print_usage +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/print_usage b/bp_bin/print_usage new file mode 120000 index 0000000..8b05295 --- /dev/null +++ b/bp_bin/print_usage @@ -0,0 +1 @@ +../code_perl/Maasha/bin/print_usage \ No newline at end of file diff --git a/bp_bin/random_records b/bp_bin/random_records deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/random_records +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/random_records b/bp_bin/random_records new file mode 120000 index 0000000..2640774 --- /dev/null +++ b/bp_bin/random_records @@ -0,0 +1 @@ +../code_perl/Maasha/bin/random_records \ No newline at end of file diff --git a/bp_bin/read_2bit b/bp_bin/read_2bit deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/read_2bit +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/read_2bit b/bp_bin/read_2bit new file mode 120000 index 0000000..9ddf362 --- /dev/null +++ b/bp_bin/read_2bit @@ -0,0 +1 @@ +../code_perl/Maasha/bin/read_2bit \ No newline at end of file diff --git a/bp_bin/read_bed b/bp_bin/read_bed deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/read_bed +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/read_bed b/bp_bin/read_bed new file mode 120000 index 0000000..a0b3227 --- /dev/null +++ b/bp_bin/read_bed @@ -0,0 +1 @@ +../code_perl/Maasha/bin/read_bed \ No newline at end of file diff --git a/bp_bin/read_blast_tab b/bp_bin/read_blast_tab deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/read_blast_tab +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/read_blast_tab b/bp_bin/read_blast_tab new file mode 120000 index 0000000..7041a55 --- /dev/null +++ b/bp_bin/read_blast_tab @@ -0,0 +1 @@ +../code_perl/Maasha/bin/read_blast_tab \ No newline at end of file diff --git a/bp_bin/read_embl b/bp_bin/read_embl deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/read_embl +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/read_embl b/bp_bin/read_embl new file mode 120000 index 0000000..c7bf9e6 --- /dev/null +++ b/bp_bin/read_embl @@ -0,0 +1 @@ +../code_perl/Maasha/bin/read_embl \ No newline at end of file diff --git a/bp_bin/read_fasta b/bp_bin/read_fasta deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/read_fasta +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/read_fasta b/bp_bin/read_fasta new file mode 120000 index 0000000..11935a9 --- /dev/null +++ b/bp_bin/read_fasta @@ -0,0 +1 @@ +../code_perl/Maasha/bin/read_fasta \ No newline at end of file diff --git a/bp_bin/read_fixedstep b/bp_bin/read_fixedstep deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/read_fixedstep +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/read_fixedstep b/bp_bin/read_fixedstep new file mode 120000 index 0000000..25baf02 --- /dev/null +++ b/bp_bin/read_fixedstep @@ -0,0 +1 @@ +../code_perl/Maasha/bin/read_fixedstep \ No newline at end of file diff --git a/bp_bin/read_gff b/bp_bin/read_gff deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/read_gff +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/read_gff b/bp_bin/read_gff new file mode 120000 index 0000000..879dad9 --- /dev/null +++ b/bp_bin/read_gff @@ -0,0 +1 @@ +../code_perl/Maasha/bin/read_gff \ No newline at end of file diff --git a/bp_bin/read_mysql b/bp_bin/read_mysql deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/read_mysql +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/read_mysql b/bp_bin/read_mysql new file mode 120000 index 0000000..6f3bbd1 --- /dev/null +++ b/bp_bin/read_mysql @@ -0,0 +1 @@ +../code_perl/Maasha/bin/read_mysql \ No newline at end of file diff --git a/bp_bin/read_phastcons b/bp_bin/read_phastcons deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/read_phastcons +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/read_phastcons b/bp_bin/read_phastcons new file mode 120000 index 0000000..ce7d6ff --- /dev/null +++ b/bp_bin/read_phastcons @@ -0,0 +1 @@ +../code_perl/Maasha/bin/read_phastcons \ No newline at end of file diff --git a/bp_bin/read_psl b/bp_bin/read_psl deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/read_psl +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/read_psl b/bp_bin/read_psl new file mode 120000 index 0000000..9ea2e70 --- /dev/null +++ b/bp_bin/read_psl @@ -0,0 +1 @@ +../code_perl/Maasha/bin/read_psl \ No newline at end of file diff --git a/bp_bin/read_soft b/bp_bin/read_soft deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/read_soft +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/read_soft b/bp_bin/read_soft new file mode 120000 index 0000000..339b425 --- /dev/null +++ b/bp_bin/read_soft @@ -0,0 +1 @@ +../code_perl/Maasha/bin/read_soft \ No newline at end of file diff --git a/bp_bin/read_solexa b/bp_bin/read_solexa deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/read_solexa +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/read_solexa b/bp_bin/read_solexa new file mode 120000 index 0000000..a38e5d8 --- /dev/null +++ b/bp_bin/read_solexa @@ -0,0 +1 @@ +../code_perl/Maasha/bin/read_solexa \ No newline at end of file diff --git a/bp_bin/read_solid b/bp_bin/read_solid deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/read_solid +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/read_solid b/bp_bin/read_solid new file mode 120000 index 0000000..cf25cc4 --- /dev/null +++ b/bp_bin/read_solid @@ -0,0 +1 @@ +../code_perl/Maasha/bin/read_solid \ No newline at end of file diff --git a/bp_bin/read_stockholm b/bp_bin/read_stockholm deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/read_stockholm +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/read_stockholm b/bp_bin/read_stockholm new file mode 120000 index 0000000..e203eb4 --- /dev/null +++ b/bp_bin/read_stockholm @@ -0,0 +1 @@ +../code_perl/Maasha/bin/read_stockholm \ No newline at end of file diff --git a/bp_bin/read_tab b/bp_bin/read_tab deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/read_tab +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/read_tab b/bp_bin/read_tab new file mode 120000 index 0000000..05c6209 --- /dev/null +++ b/bp_bin/read_tab @@ -0,0 +1 @@ +../code_perl/Maasha/bin/read_tab \ No newline at end of file diff --git a/bp_bin/read_ucsc_config b/bp_bin/read_ucsc_config deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/read_ucsc_config +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/read_ucsc_config b/bp_bin/read_ucsc_config new file mode 120000 index 0000000..5247bd7 --- /dev/null +++ b/bp_bin/read_ucsc_config @@ -0,0 +1 @@ +../code_perl/Maasha/bin/read_ucsc_config \ No newline at end of file diff --git a/bp_bin/remove_adaptor b/bp_bin/remove_adaptor deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/remove_adaptor +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/remove_adaptor b/bp_bin/remove_adaptor new file mode 120000 index 0000000..639285c --- /dev/null +++ b/bp_bin/remove_adaptor @@ -0,0 +1 @@ +../code_perl/Maasha/bin/remove_adaptor \ No newline at end of file diff --git a/bp_bin/remove_indels b/bp_bin/remove_indels deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/remove_indels +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/remove_indels b/bp_bin/remove_indels new file mode 120000 index 0000000..52c84d9 --- /dev/null +++ b/bp_bin/remove_indels @@ -0,0 +1 @@ +../code_perl/Maasha/bin/remove_indels \ No newline at end of file diff --git a/bp_bin/remove_keys b/bp_bin/remove_keys deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/remove_keys +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/remove_keys b/bp_bin/remove_keys new file mode 120000 index 0000000..afb4076 --- /dev/null +++ b/bp_bin/remove_keys @@ -0,0 +1 @@ +../code_perl/Maasha/bin/remove_keys \ No newline at end of file diff --git a/bp_bin/remove_mysql_tables b/bp_bin/remove_mysql_tables deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/remove_mysql_tables +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/remove_mysql_tables b/bp_bin/remove_mysql_tables new file mode 120000 index 0000000..39a2428 --- /dev/null +++ b/bp_bin/remove_mysql_tables @@ -0,0 +1 @@ +../code_perl/Maasha/bin/remove_mysql_tables \ No newline at end of file diff --git a/bp_bin/remove_ucsc_tracks b/bp_bin/remove_ucsc_tracks deleted file mode 100644 index fdf5bd2..0000000 --- a/bp_bin/remove_ucsc_tracks +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/remove_ucsc_tracks b/bp_bin/remove_ucsc_tracks new file mode 120000 index 0000000..fa1f7ca --- /dev/null +++ b/bp_bin/remove_ucsc_tracks @@ -0,0 +1 @@ +../code_perl/Maasha/bin/remove_ucsc_tracks \ No newline at end of file diff --git a/bp_bin/rename_keys b/bp_bin/rename_keys deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/rename_keys +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/rename_keys b/bp_bin/rename_keys new file mode 120000 index 0000000..78541e1 --- /dev/null +++ b/bp_bin/rename_keys @@ -0,0 +1 @@ +../code_perl/Maasha/bin/rename_keys \ No newline at end of file diff --git a/bp_bin/reverse_seq b/bp_bin/reverse_seq deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/reverse_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/reverse_seq b/bp_bin/reverse_seq new file mode 120000 index 0000000..2ae4226 --- /dev/null +++ b/bp_bin/reverse_seq @@ -0,0 +1 @@ +../code_perl/Maasha/bin/reverse_seq \ No newline at end of file diff --git a/bp_bin/shuffle_seq b/bp_bin/shuffle_seq deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/shuffle_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/shuffle_seq b/bp_bin/shuffle_seq new file mode 120000 index 0000000..e9f42f1 --- /dev/null +++ b/bp_bin/shuffle_seq @@ -0,0 +1 @@ +../code_perl/Maasha/bin/shuffle_seq \ No newline at end of file diff --git a/bp_bin/soap_seq b/bp_bin/soap_seq deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/soap_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/soap_seq b/bp_bin/soap_seq new file mode 120000 index 0000000..7920fbc --- /dev/null +++ b/bp_bin/soap_seq @@ -0,0 +1 @@ +../code_perl/Maasha/bin/soap_seq \ No newline at end of file diff --git a/bp_bin/sort_records b/bp_bin/sort_records deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/sort_records +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/sort_records b/bp_bin/sort_records new file mode 120000 index 0000000..6ff6dd3 --- /dev/null +++ b/bp_bin/sort_records @@ -0,0 +1 @@ +../code_perl/Maasha/bin/sort_records \ No newline at end of file diff --git a/bp_bin/split_bed b/bp_bin/split_bed deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/split_bed +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/split_bed b/bp_bin/split_bed new file mode 120000 index 0000000..89c5725 --- /dev/null +++ b/bp_bin/split_bed @@ -0,0 +1 @@ +../code_perl/Maasha/bin/split_bed \ No newline at end of file diff --git a/bp_bin/split_seq b/bp_bin/split_seq deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/split_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/split_seq b/bp_bin/split_seq new file mode 120000 index 0000000..a428a1e --- /dev/null +++ b/bp_bin/split_seq @@ -0,0 +1 @@ +../code_perl/Maasha/bin/split_seq \ No newline at end of file diff --git a/bp_bin/sum_vals b/bp_bin/sum_vals deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/sum_vals +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/sum_vals b/bp_bin/sum_vals new file mode 120000 index 0000000..4193a49 --- /dev/null +++ b/bp_bin/sum_vals @@ -0,0 +1 @@ +../code_perl/Maasha/bin/sum_vals \ No newline at end of file diff --git a/bp_bin/tile_seq b/bp_bin/tile_seq deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/tile_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/tile_seq b/bp_bin/tile_seq new file mode 120000 index 0000000..f026ddd --- /dev/null +++ b/bp_bin/tile_seq @@ -0,0 +1 @@ +../code_perl/Maasha/bin/tile_seq \ No newline at end of file diff --git a/bp_bin/translate_seq b/bp_bin/translate_seq deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/translate_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/translate_seq b/bp_bin/translate_seq new file mode 120000 index 0000000..3e8ae5e --- /dev/null +++ b/bp_bin/translate_seq @@ -0,0 +1 @@ +../code_perl/Maasha/bin/translate_seq \ No newline at end of file diff --git a/bp_bin/transliterate_seq b/bp_bin/transliterate_seq deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/transliterate_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/transliterate_seq b/bp_bin/transliterate_seq new file mode 120000 index 0000000..ce6ea54 --- /dev/null +++ b/bp_bin/transliterate_seq @@ -0,0 +1 @@ +../code_perl/Maasha/bin/transliterate_seq \ No newline at end of file diff --git a/bp_bin/transliterate_vals b/bp_bin/transliterate_vals deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/transliterate_vals +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/transliterate_vals b/bp_bin/transliterate_vals new file mode 120000 index 0000000..bf8d8e2 --- /dev/null +++ b/bp_bin/transliterate_vals @@ -0,0 +1 @@ +../code_perl/Maasha/bin/transliterate_vals \ No newline at end of file diff --git a/bp_bin/uniq_vals b/bp_bin/uniq_vals deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/uniq_vals +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/uniq_vals b/bp_bin/uniq_vals new file mode 120000 index 0000000..fb3bafc --- /dev/null +++ b/bp_bin/uniq_vals @@ -0,0 +1 @@ +../code_perl/Maasha/bin/uniq_vals \ No newline at end of file diff --git a/bp_bin/upload_to_ucsc b/bp_bin/upload_to_ucsc deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/upload_to_ucsc +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/upload_to_ucsc b/bp_bin/upload_to_ucsc new file mode 120000 index 0000000..e97a1eb --- /dev/null +++ b/bp_bin/upload_to_ucsc @@ -0,0 +1 @@ +../code_perl/Maasha/bin/upload_to_ucsc \ No newline at end of file diff --git a/bp_bin/uppercase_seq b/bp_bin/uppercase_seq deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/uppercase_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/uppercase_seq b/bp_bin/uppercase_seq new file mode 120000 index 0000000..d149da2 --- /dev/null +++ b/bp_bin/uppercase_seq @@ -0,0 +1 @@ +../code_perl/Maasha/bin/uppercase_seq \ No newline at end of file diff --git a/bp_bin/vmatch_seq b/bp_bin/vmatch_seq deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/vmatch_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/vmatch_seq b/bp_bin/vmatch_seq new file mode 120000 index 0000000..f98275c --- /dev/null +++ b/bp_bin/vmatch_seq @@ -0,0 +1 @@ +../code_perl/Maasha/bin/vmatch_seq \ No newline at end of file diff --git a/bp_bin/write_2bit b/bp_bin/write_2bit deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/write_2bit +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/write_2bit b/bp_bin/write_2bit new file mode 120000 index 0000000..3b58b31 --- /dev/null +++ b/bp_bin/write_2bit @@ -0,0 +1 @@ +../code_perl/Maasha/bin/write_2bit \ No newline at end of file diff --git a/bp_bin/write_align b/bp_bin/write_align deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/write_align +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/write_align b/bp_bin/write_align new file mode 120000 index 0000000..15fd96a --- /dev/null +++ b/bp_bin/write_align @@ -0,0 +1 @@ +../code_perl/Maasha/bin/write_align \ No newline at end of file diff --git a/bp_bin/write_bed b/bp_bin/write_bed deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/write_bed +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/write_bed b/bp_bin/write_bed new file mode 120000 index 0000000..38a4411 --- /dev/null +++ b/bp_bin/write_bed @@ -0,0 +1 @@ +../code_perl/Maasha/bin/write_bed \ No newline at end of file diff --git a/bp_bin/write_blast b/bp_bin/write_blast deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/write_blast +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/write_blast b/bp_bin/write_blast new file mode 120000 index 0000000..e84bd5c --- /dev/null +++ b/bp_bin/write_blast @@ -0,0 +1 @@ +../code_perl/Maasha/bin/write_blast \ No newline at end of file diff --git a/bp_bin/write_fasta b/bp_bin/write_fasta deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/write_fasta +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/write_fasta b/bp_bin/write_fasta new file mode 120000 index 0000000..d7afcfb --- /dev/null +++ b/bp_bin/write_fasta @@ -0,0 +1 @@ +../code_perl/Maasha/bin/write_fasta \ No newline at end of file diff --git a/bp_bin/write_fixedstep b/bp_bin/write_fixedstep deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/write_fixedstep +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/write_fixedstep b/bp_bin/write_fixedstep new file mode 120000 index 0000000..67f50bb --- /dev/null +++ b/bp_bin/write_fixedstep @@ -0,0 +1 @@ +../code_perl/Maasha/bin/write_fixedstep \ No newline at end of file diff --git a/bp_bin/write_psl b/bp_bin/write_psl deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/write_psl +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/write_psl b/bp_bin/write_psl new file mode 120000 index 0000000..edf73ff --- /dev/null +++ b/bp_bin/write_psl @@ -0,0 +1 @@ +../code_perl/Maasha/bin/write_psl \ No newline at end of file diff --git a/bp_bin/write_solid b/bp_bin/write_solid deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/write_solid +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/write_solid b/bp_bin/write_solid new file mode 120000 index 0000000..48c24a4 --- /dev/null +++ b/bp_bin/write_solid @@ -0,0 +1 @@ +../code_perl/Maasha/bin/write_solid \ No newline at end of file diff --git a/bp_bin/write_tab b/bp_bin/write_tab deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/write_tab +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/write_tab b/bp_bin/write_tab new file mode 120000 index 0000000..1a45ade --- /dev/null +++ b/bp_bin/write_tab @@ -0,0 +1 @@ +../code_perl/Maasha/bin/write_tab \ No newline at end of file diff --git a/bp_bin/write_ucsc_config b/bp_bin/write_ucsc_config deleted file mode 100755 index fdf5bd2..0000000 --- a/bp_bin/write_ucsc_config +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; diff --git a/bp_bin/write_ucsc_config b/bp_bin/write_ucsc_config new file mode 120000 index 0000000..d25e997 --- /dev/null +++ b/bp_bin/write_ucsc_config @@ -0,0 +1 @@ +../code_perl/Maasha/bin/write_ucsc_config \ No newline at end of file diff --git a/code_perl/Maasha/bin/add_ident b/code_perl/Maasha/bin/add_ident new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/add_ident @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/align_seq b/code_perl/Maasha/bin/align_seq new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/align_seq @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/analyze_bed b/code_perl/Maasha/bin/analyze_bed new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/analyze_bed @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/analyze_seq b/code_perl/Maasha/bin/analyze_seq new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/analyze_seq @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/analyze_tags b/code_perl/Maasha/bin/analyze_tags new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/analyze_tags @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/analyze_vals b/code_perl/Maasha/bin/analyze_vals new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/analyze_vals @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/assemble_tag_contigs b/code_perl/Maasha/bin/assemble_tag_contigs new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/assemble_tag_contigs @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/blast_seq b/code_perl/Maasha/bin/blast_seq new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/blast_seq @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/blat_seq b/code_perl/Maasha/bin/blat_seq new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/blat_seq @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/calc_bit_scores b/code_perl/Maasha/bin/calc_bit_scores new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/calc_bit_scores @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/calc_fixedstep b/code_perl/Maasha/bin/calc_fixedstep new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/calc_fixedstep @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/complement_seq b/code_perl/Maasha/bin/complement_seq new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/complement_seq @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/complexity_seq b/code_perl/Maasha/bin/complexity_seq new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/complexity_seq @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/compute b/code_perl/Maasha/bin/compute new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/compute @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/count_records b/code_perl/Maasha/bin/count_records new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/count_records @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/count_vals b/code_perl/Maasha/bin/count_vals new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/count_vals @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/create_blast_db b/code_perl/Maasha/bin/create_blast_db new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/create_blast_db @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/create_vmatch_index b/code_perl/Maasha/bin/create_vmatch_index new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/create_vmatch_index @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/create_weight_matrix b/code_perl/Maasha/bin/create_weight_matrix new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/create_weight_matrix @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/extract_seq b/code_perl/Maasha/bin/extract_seq new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/extract_seq @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/flip_tab b/code_perl/Maasha/bin/flip_tab new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/flip_tab @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/fold_seq b/code_perl/Maasha/bin/fold_seq new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/fold_seq @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/format_genome b/code_perl/Maasha/bin/format_genome new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/format_genome @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/get_genome_align b/code_perl/Maasha/bin/get_genome_align new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/get_genome_align @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/get_genome_phastcons b/code_perl/Maasha/bin/get_genome_phastcons new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/get_genome_phastcons @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/get_genome_seq b/code_perl/Maasha/bin/get_genome_seq new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/get_genome_seq @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/grab b/code_perl/Maasha/bin/grab new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/grab @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/head_records b/code_perl/Maasha/bin/head_records new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/head_records @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/invert_align b/code_perl/Maasha/bin/invert_align new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/invert_align @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/length_seq b/code_perl/Maasha/bin/length_seq new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/length_seq @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/length_vals b/code_perl/Maasha/bin/length_vals new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/length_vals @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/list_biopieces b/code_perl/Maasha/bin/list_biopieces new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/list_biopieces @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/list_genomes b/code_perl/Maasha/bin/list_genomes new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/list_genomes @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/match_seq b/code_perl/Maasha/bin/match_seq new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/match_seq @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/max_vals b/code_perl/Maasha/bin/max_vals new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/max_vals @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/mean_vals b/code_perl/Maasha/bin/mean_vals new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/mean_vals @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/median_vals b/code_perl/Maasha/bin/median_vals new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/median_vals @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/merge_records b/code_perl/Maasha/bin/merge_records new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/merge_records @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/merge_vals b/code_perl/Maasha/bin/merge_vals new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/merge_vals @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/min_vals b/code_perl/Maasha/bin/min_vals new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/min_vals @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/oligo_freq b/code_perl/Maasha/bin/oligo_freq new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/oligo_freq @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/patscan_seq b/code_perl/Maasha/bin/patscan_seq new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/patscan_seq @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/plot_chrdist b/code_perl/Maasha/bin/plot_chrdist new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/plot_chrdist @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/plot_histogram b/code_perl/Maasha/bin/plot_histogram new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/plot_histogram @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/plot_karyogram b/code_perl/Maasha/bin/plot_karyogram new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/plot_karyogram @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/plot_lendist b/code_perl/Maasha/bin/plot_lendist new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/plot_lendist @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/plot_matches b/code_perl/Maasha/bin/plot_matches new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/plot_matches @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/plot_phastcons_profiles b/code_perl/Maasha/bin/plot_phastcons_profiles new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/plot_phastcons_profiles @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/plot_seqlogo b/code_perl/Maasha/bin/plot_seqlogo new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/plot_seqlogo @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/print_usage b/code_perl/Maasha/bin/print_usage new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/print_usage @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/random_records b/code_perl/Maasha/bin/random_records new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/random_records @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/read_2bit b/code_perl/Maasha/bin/read_2bit new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/read_2bit @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/read_bed b/code_perl/Maasha/bin/read_bed new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/read_bed @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/read_blast_tab b/code_perl/Maasha/bin/read_blast_tab new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/read_blast_tab @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/read_embl b/code_perl/Maasha/bin/read_embl new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/read_embl @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/read_fasta b/code_perl/Maasha/bin/read_fasta new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/read_fasta @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/read_fixedstep b/code_perl/Maasha/bin/read_fixedstep new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/read_fixedstep @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/read_gff b/code_perl/Maasha/bin/read_gff new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/read_gff @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/read_mysql b/code_perl/Maasha/bin/read_mysql new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/read_mysql @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/read_phastcons b/code_perl/Maasha/bin/read_phastcons new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/read_phastcons @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/read_psl b/code_perl/Maasha/bin/read_psl new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/read_psl @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/read_soft b/code_perl/Maasha/bin/read_soft new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/read_soft @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/read_solexa b/code_perl/Maasha/bin/read_solexa new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/read_solexa @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/read_solid b/code_perl/Maasha/bin/read_solid new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/read_solid @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/read_stockholm b/code_perl/Maasha/bin/read_stockholm new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/read_stockholm @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/read_tab b/code_perl/Maasha/bin/read_tab new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/read_tab @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/read_ucsc_config b/code_perl/Maasha/bin/read_ucsc_config new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/read_ucsc_config @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/remove_adaptor b/code_perl/Maasha/bin/remove_adaptor new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/remove_adaptor @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/remove_indels b/code_perl/Maasha/bin/remove_indels new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/remove_indels @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/remove_keys b/code_perl/Maasha/bin/remove_keys new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/remove_keys @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/remove_mysql_tables b/code_perl/Maasha/bin/remove_mysql_tables new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/remove_mysql_tables @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/remove_ucsc_tracks b/code_perl/Maasha/bin/remove_ucsc_tracks new file mode 100644 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/remove_ucsc_tracks @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/rename_keys b/code_perl/Maasha/bin/rename_keys new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/rename_keys @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/reverse_seq b/code_perl/Maasha/bin/reverse_seq new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/reverse_seq @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/shuffle_seq b/code_perl/Maasha/bin/shuffle_seq new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/shuffle_seq @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/soap_seq b/code_perl/Maasha/bin/soap_seq new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/soap_seq @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/sort_records b/code_perl/Maasha/bin/sort_records new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/sort_records @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/split_bed b/code_perl/Maasha/bin/split_bed new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/split_bed @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/split_seq b/code_perl/Maasha/bin/split_seq new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/split_seq @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/sum_vals b/code_perl/Maasha/bin/sum_vals new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/sum_vals @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/tile_seq b/code_perl/Maasha/bin/tile_seq new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/tile_seq @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/translate_seq b/code_perl/Maasha/bin/translate_seq new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/translate_seq @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/transliterate_seq b/code_perl/Maasha/bin/transliterate_seq new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/transliterate_seq @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/transliterate_vals b/code_perl/Maasha/bin/transliterate_vals new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/transliterate_vals @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/uniq_vals b/code_perl/Maasha/bin/uniq_vals new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/uniq_vals @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/upload_to_ucsc b/code_perl/Maasha/bin/upload_to_ucsc new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/upload_to_ucsc @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/uppercase_seq b/code_perl/Maasha/bin/uppercase_seq new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/uppercase_seq @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/vmatch_seq b/code_perl/Maasha/bin/vmatch_seq new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/vmatch_seq @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/write_2bit b/code_perl/Maasha/bin/write_2bit new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/write_2bit @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/write_align b/code_perl/Maasha/bin/write_align new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/write_align @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/write_bed b/code_perl/Maasha/bin/write_bed new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/write_bed @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/write_blast b/code_perl/Maasha/bin/write_blast new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/write_blast @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/write_fasta b/code_perl/Maasha/bin/write_fasta new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/write_fasta @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/write_fixedstep b/code_perl/Maasha/bin/write_fixedstep new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/write_fixedstep @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/write_psl b/code_perl/Maasha/bin/write_psl new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/write_psl @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/write_solid b/code_perl/Maasha/bin/write_solid new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/write_solid @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/write_tab b/code_perl/Maasha/bin/write_tab new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/write_tab @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_perl/Maasha/bin/write_ucsc_config b/code_perl/Maasha/bin/write_ucsc_config new file mode 100755 index 0000000..fdf5bd2 --- /dev/null +++ b/code_perl/Maasha/bin/write_ucsc_config @@ -0,0 +1,6 @@ +#!/usr/bin/env perl + +use warnings; +use strict; + +use Maasha::BioRun; diff --git a/code_python/Cjung/Args.pyc b/code_python/Cjung/Args.pyc index 8b121787fa51f401453d056b37e17c49ecd4e740..4e8e789b3798ad76e1306bcf450f0d152744ab37 100644 GIT binary patch delta 2410 zcmb_d&u<%55T3W*UE6CrbsD#&O+!*}S~mp(L84WOA_T3HMrze=K`9m}GTBYKCGncw zjT%IXk&46t0jk~|2@V{3sYEXzapPXZ5%D*0K?nf{;QQV-35TLog0*)%@7K(H-^@IJ zcI@Mc;k!TAyszZfb4zmnDdP79yy^3|h9B(*j=X70+m--d=#I3VE!~y2D*?WbNKlmb zMQ)0`+Ad01lAt8lEQx;<6&58Z%S|QivIL%lWr;iqDl#2Zw+1zt<}?fqaHHa&LSyaf 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