restructure

git-svn-id: http://biopieces.googlecode.com/svn/trunk@23 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/INSTALL b/INSTALL
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0c9e09a0b2c04a02f3450e504890f6aa055e82f4 100644 (file)
--- a/INSTALL
+++ b/INSTALL
@@ -0,0 +1,7 @@
+Find installation instructions online at:
+
+http://code.google.com/p/biopieces/wiki/Installation
+
+
+
+Martin A. Hansen, June 2008

diff --git a/bp_bin/add_ident b/bp_bin/add_ident
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/add_ident
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/align_seq b/bp_bin/align_seq
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/align_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/analyze_bed b/bp_bin/analyze_bed
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/analyze_bed
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/analyze_seq b/bp_bin/analyze_seq
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/analyze_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/analyze_tags b/bp_bin/analyze_tags
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/analyze_tags
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/analyze_vals b/bp_bin/analyze_vals
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/analyze_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/blast_seq b/bp_bin/blast_seq
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/blast_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/blat_seq b/bp_bin/blat_seq
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/blat_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/calc_bit_scores b/bp_bin/calc_bit_scores
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/calc_bit_scores
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/complement_seq b/bp_bin/complement_seq
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/complement_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/complexity_seq b/bp_bin/complexity_seq
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/complexity_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/compute b/bp_bin/compute
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/compute
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/count_records b/bp_bin/count_records
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/count_records
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/count_vals b/bp_bin/count_vals
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/count_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/create_blast_db b/bp_bin/create_blast_db
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/create_blast_db
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/create_vmatch_index b/bp_bin/create_vmatch_index
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/create_vmatch_index
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/create_weight_matrix b/bp_bin/create_weight_matrix
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/create_weight_matrix
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/extract_seq b/bp_bin/extract_seq
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/extract_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/flip_tab b/bp_bin/flip_tab
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/flip_tab
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/fold_seq b/bp_bin/fold_seq
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/fold_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/get_genome_align b/bp_bin/get_genome_align
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/get_genome_align
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/get_genome_phastcons b/bp_bin/get_genome_phastcons
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/get_genome_phastcons
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/get_genome_seq b/bp_bin/get_genome_seq
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/get_genome_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/grab b/bp_bin/grab
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/grab
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/head_records b/bp_bin/head_records
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/head_records
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/invert_align b/bp_bin/invert_align
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/invert_align
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/length_seq b/bp_bin/length_seq
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/length_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/length_vals b/bp_bin/length_vals
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/length_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/list_biotools b/bp_bin/list_biotools
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/list_biotools
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/match_seq b/bp_bin/match_seq
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/match_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/max_vals b/bp_bin/max_vals
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/max_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/mean_vals b/bp_bin/mean_vals
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/mean_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/median_vals b/bp_bin/median_vals
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/median_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/merge_vals b/bp_bin/merge_vals
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/merge_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/min_vals b/bp_bin/min_vals
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/min_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/oligo_freq b/bp_bin/oligo_freq
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/oligo_freq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/patscan_seq b/bp_bin/patscan_seq
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/patscan_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/plot_chrdist b/bp_bin/plot_chrdist
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/plot_chrdist
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/plot_histogram b/bp_bin/plot_histogram
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/plot_histogram
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/plot_karyogram b/bp_bin/plot_karyogram
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/plot_karyogram
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/plot_lendist b/bp_bin/plot_lendist
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/plot_lendist
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/plot_matches b/bp_bin/plot_matches
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/plot_matches
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/plot_phastcons_profiles b/bp_bin/plot_phastcons_profiles
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/plot_phastcons_profiles
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/plot_seqlogo b/bp_bin/plot_seqlogo
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/plot_seqlogo
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/print_usage b/bp_bin/print_usage
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/print_usage
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/random_records b/bp_bin/random_records
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/random_records
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/read_2bit b/bp_bin/read_2bit
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/read_2bit
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/read_align b/bp_bin/read_align
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/read_align
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/read_bed b/bp_bin/read_bed
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/read_bed
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/read_blast_tab b/bp_bin/read_blast_tab
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/read_blast_tab
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/read_embl b/bp_bin/read_embl
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/read_embl
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/read_fasta b/bp_bin/read_fasta
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/read_fasta
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/read_gff b/bp_bin/read_gff
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/read_gff
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/read_mysql b/bp_bin/read_mysql
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/read_mysql
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/read_phastcons b/bp_bin/read_phastcons
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/read_phastcons
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/read_psl b/bp_bin/read_psl
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/read_psl
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/read_soft b/bp_bin/read_soft
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/read_soft
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/read_solexa b/bp_bin/read_solexa
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/read_solexa
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/read_solid b/bp_bin/read_solid
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/read_solid
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/read_stockholm b/bp_bin/read_stockholm
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/read_stockholm
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/read_tab b/bp_bin/read_tab
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/read_tab
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/remove_indels b/bp_bin/remove_indels
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/remove_indels
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/remove_keys b/bp_bin/remove_keys
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/remove_keys
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/rename_keys b/bp_bin/rename_keys
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/rename_keys
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/reverse_seq b/bp_bin/reverse_seq
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/reverse_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/shuffle_seq b/bp_bin/shuffle_seq
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/shuffle_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/sort_records b/bp_bin/sort_records
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/sort_records
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/split_bed b/bp_bin/split_bed
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/split_bed
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/split_seq b/bp_bin/split_seq
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/split_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/sum_vals b/bp_bin/sum_vals
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/sum_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/tile_seq b/bp_bin/tile_seq
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/tile_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/translate_seq b/bp_bin/translate_seq
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/translate_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/transliterate_seq b/bp_bin/transliterate_seq
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/transliterate_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/transliterate_vals b/bp_bin/transliterate_vals
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/transliterate_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/uniq_vals b/bp_bin/uniq_vals
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/uniq_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/upload_to_ucsc b/bp_bin/upload_to_ucsc
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/upload_to_ucsc
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/uppercase_seq b/bp_bin/uppercase_seq
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/uppercase_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/vmatch_seq b/bp_bin/vmatch_seq
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/vmatch_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/write_2bit b/bp_bin/write_2bit
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/write_2bit
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/write_align b/bp_bin/write_align
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/write_align
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/write_bed b/bp_bin/write_bed
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/write_bed
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/write_blast b/bp_bin/write_blast
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/write_blast
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/write_fasta b/bp_bin/write_fasta
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/write_fasta
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/write_psl b/bp_bin/write_psl
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/write_psl
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/write_solid b/bp_bin/write_solid
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/write_solid
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_bin/write_tab b/bp_bin/write_tab
new file mode 100755 (executable)
index 0000000..c8c800f
--- /dev/null
+++ b/bp_bin/write_tab
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::Biotools;

diff --git a/bp_conf/bashrc b/bp_conf/bashrc
index 60b0b789f2f6e7b6ebbb43a29cc88725f7a4fe1c..0a57f06eaea9e2646bafd443cbaf7b8d20cd9bac 100644 (file)
--- a/bp_conf/bashrc
+++ b/bp_conf/bashrc
@@ -1,21 +1,46 @@
-# >>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<
+### >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
+### Stuff that enables biopieces.
 
-# Stuff that enables biotools.
+### Initially we need to configure the directories where biopieces are installed
+### and where the data (genomes and indexes) that the biopieces work on are installed.
+### Allso, it is possible to change the temporary directory from the system's tmp.
 
-export TOOLS_DIR="/Users/m.hansen/tools"      # Contains binaries for BLAST and Vmatch.
-export  INST_DIR="/Users/m.hansen/maasha"     # Contains scripts and modules.
-export  DATA_DIR="/Users/m.hansen/DATA"       # Contains genomic data etc.
-export   TMP_DIR="/Users/m.hansen/maasha/tmp" # Required temporary directory.
-export   LOG_DIR="/Users/m.hansen/maasha/log" # Log directory
+export BP_DIR="/Users/m.hansen/biopieces"         # Directory where biopieces are installed
+export BP_DATA="/Users/m.hansen/bio_piece_data"   # Contains genomic data etc.
+export BP_TMP="/tmp"                              # Required temporary directory.
 
-export     PATH="$PATH:$TOOLS_DIR/blast-2.2.17/bin:$TOOLS_DIR/vmatch.distribution"
-export     PATH="$INST_DIR/bin/:$INST_DIR/perl/bin:$INST_DIR/perl_scripts/:$INST_DIR/biotools:$PATH"  
-export PERL5LIB="$PERL5LIB:$INST_DIR/perl_modules"
 
-# Alias allowing power scripting with biotools
+### The below bin directory should hold biopiece executables - regardsles of programming language.
 
-alias bioscript="perl -MMaasha::Biotools=read_stream,get_record,put_record -e"
+export BP_BIN="$BP_DIR/bp_bin"              # Directory with biopiece executables.
 
 
-# >>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<
+### The following directories hold the biopiece libraries, modules, gems, etc - one per programming language.
+
+export BP_PERL="$BP_DIR/code_perl"          # Direcotry with Perl code.
+export BP_C="$BP_DIR/code_c"                # Direcotry with c code.
+export BP_PYTHON="$BP_DIR/code_python"      # Direcotry with Pyton code.
+export BP_RUBY="$BP_DIR/code_ruby"          # Direcotry with Ruby code.
+
+
+### For the Perl modules they may be contributed by different developers, so we define a variable for each.
+
+export BP_PERL_LIBS="$BP_PERL/Maasha"                 # Perl modules from the developer Maasha.
+# export BP_PERL_LIBS="$BP_PERL_LIBS:$BP_PERL/<new>"  # Perl modules from a new developer.
+
+
+### Here we add the biopiece variable to the existing PATH and PERL5LIB variables.
+
+export PATH="$PATH:$BP_BIN"  
+export PERL5LIB="$PERL5LIB:$BP_PERL_LIBS"
+
+### Alias allowing power scripting with biopieces.
+
+alias bioscript="perl -MMaasha::Biopieces=read_stream,get_record,put_record -e"
+
+
+### >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+### Martin A. Hansen, June 2008

diff --git a/bp_scripts/add_ident b/bp_scripts/add_ident
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/add_ident
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/align_seq b/bp_scripts/align_seq
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/align_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/analyze_bed b/bp_scripts/analyze_bed
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/analyze_bed
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/analyze_seq b/bp_scripts/analyze_seq
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/analyze_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/analyze_tags b/bp_scripts/analyze_tags
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/analyze_tags
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/analyze_vals b/bp_scripts/analyze_vals
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/analyze_vals
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/blast_seq b/bp_scripts/blast_seq
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/blast_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/blat_seq b/bp_scripts/blat_seq
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/blat_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/calc_bit_scores b/bp_scripts/calc_bit_scores
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/calc_bit_scores
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/complement_seq b/bp_scripts/complement_seq
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/complement_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/complexity_seq b/bp_scripts/complexity_seq
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/complexity_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/compute b/bp_scripts/compute
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/compute
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/count_records b/bp_scripts/count_records
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/count_records
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/count_vals b/bp_scripts/count_vals
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/count_vals
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/create_blast_db b/bp_scripts/create_blast_db
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/create_blast_db
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/create_vmatch_index b/bp_scripts/create_vmatch_index
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/create_vmatch_index
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/create_weight_matrix b/bp_scripts/create_weight_matrix
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/create_weight_matrix
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/extract_seq b/bp_scripts/extract_seq
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/extract_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/flip_tab b/bp_scripts/flip_tab
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/flip_tab
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/fold_seq b/bp_scripts/fold_seq
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/fold_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/get_genome_align b/bp_scripts/get_genome_align
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/get_genome_align
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/get_genome_phastcons b/bp_scripts/get_genome_phastcons
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/get_genome_phastcons
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/get_genome_seq b/bp_scripts/get_genome_seq
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/get_genome_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/grab b/bp_scripts/grab
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/grab
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/head_records b/bp_scripts/head_records
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/head_records
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/invert_align b/bp_scripts/invert_align
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/invert_align
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/length_seq b/bp_scripts/length_seq
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/length_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/length_vals b/bp_scripts/length_vals
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/length_vals
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/list_biotools b/bp_scripts/list_biotools
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/list_biotools
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/match_seq b/bp_scripts/match_seq
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/match_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/max_vals b/bp_scripts/max_vals
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/max_vals
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/mean_vals b/bp_scripts/mean_vals
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/mean_vals
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/median_vals b/bp_scripts/median_vals
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/median_vals
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/merge_vals b/bp_scripts/merge_vals
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/merge_vals
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/min_vals b/bp_scripts/min_vals
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/min_vals
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/oligo_freq b/bp_scripts/oligo_freq
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/oligo_freq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/patscan_seq b/bp_scripts/patscan_seq
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/patscan_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/plot_chrdist b/bp_scripts/plot_chrdist
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/plot_chrdist
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/plot_histogram b/bp_scripts/plot_histogram
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/plot_histogram
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/plot_karyogram b/bp_scripts/plot_karyogram
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/plot_karyogram
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/plot_lendist b/bp_scripts/plot_lendist
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/plot_lendist
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/plot_matches b/bp_scripts/plot_matches
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/plot_matches
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/plot_phastcons_profiles b/bp_scripts/plot_phastcons_profiles
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/plot_phastcons_profiles
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/plot_seqlogo b/bp_scripts/plot_seqlogo
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/plot_seqlogo
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/print_usage b/bp_scripts/print_usage
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/print_usage
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/random_records b/bp_scripts/random_records
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/random_records
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/read_2bit b/bp_scripts/read_2bit
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/read_2bit
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/read_align b/bp_scripts/read_align
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/read_align
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/read_bed b/bp_scripts/read_bed
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/read_bed
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/read_blast_tab b/bp_scripts/read_blast_tab
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/read_blast_tab
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/read_embl b/bp_scripts/read_embl
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/read_embl
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/read_fasta b/bp_scripts/read_fasta
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/read_fasta
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/read_gff b/bp_scripts/read_gff
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/read_gff
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/read_mysql b/bp_scripts/read_mysql
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/read_mysql
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/read_phastcons b/bp_scripts/read_phastcons
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/read_phastcons
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/read_psl b/bp_scripts/read_psl
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/read_psl
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/read_soft b/bp_scripts/read_soft
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/read_soft
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/read_solexa b/bp_scripts/read_solexa
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/read_solexa
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/read_solid b/bp_scripts/read_solid
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/read_solid
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/read_stockholm b/bp_scripts/read_stockholm
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/read_stockholm
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/read_tab b/bp_scripts/read_tab
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/read_tab
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/remove_indels b/bp_scripts/remove_indels
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/remove_indels
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/remove_keys b/bp_scripts/remove_keys
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/remove_keys
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/rename_keys b/bp_scripts/rename_keys
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/rename_keys
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/reverse_seq b/bp_scripts/reverse_seq
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/reverse_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/shuffle_seq b/bp_scripts/shuffle_seq
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/shuffle_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/sort_records b/bp_scripts/sort_records
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/sort_records
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/split_bed b/bp_scripts/split_bed
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/split_bed
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/split_seq b/bp_scripts/split_seq
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/split_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/sum_vals b/bp_scripts/sum_vals
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/sum_vals
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/tile_seq b/bp_scripts/tile_seq
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/tile_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/translate_seq b/bp_scripts/translate_seq
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/translate_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/transliterate_seq b/bp_scripts/transliterate_seq
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/transliterate_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/transliterate_vals b/bp_scripts/transliterate_vals
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/transliterate_vals
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/uniq_vals b/bp_scripts/uniq_vals
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/uniq_vals
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/upload_to_ucsc b/bp_scripts/upload_to_ucsc
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/upload_to_ucsc
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/uppercase_seq b/bp_scripts/uppercase_seq
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/uppercase_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/vmatch_seq b/bp_scripts/vmatch_seq
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/vmatch_seq
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/write_2bit b/bp_scripts/write_2bit
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/write_2bit
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/write_align b/bp_scripts/write_align
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/write_align
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/write_bed b/bp_scripts/write_bed
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/write_bed
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/write_blast b/bp_scripts/write_blast
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/write_blast
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/write_fasta b/bp_scripts/write_fasta
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/write_fasta
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/write_psl b/bp_scripts/write_psl
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/write_psl
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/write_solid b/bp_scripts/write_solid
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/write_solid
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;

diff --git a/bp_scripts/write_tab b/bp_scripts/write_tab
deleted file mode 100755 (executable)
index c8c800f..0000000
--- a/bp_scripts/write_tab
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/usr/bin/env perl
-
-use warnings;
-use strict;
-
-use Maasha::Biotools;