From afbdacf13f1672d85575067efade87beb51d2904 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Tue, 2 Jun 2009 16:48:32 +0000 Subject: [PATCH] remove bin dir git-svn-id: http://biopieces.googlecode.com/svn/trunk@468 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/read_solid | 121 ++++++++++++++++++- code_perl/Maasha/BioRun.pm | 75 ------------ 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 - 100 files changed, 118 insertions(+), 666 deletions(-) delete mode 100755 code_perl/Maasha/bin/add_ident delete mode 100755 code_perl/Maasha/bin/align_seq delete mode 100755 code_perl/Maasha/bin/analyze_bed delete mode 100755 code_perl/Maasha/bin/analyze_seq delete mode 100755 code_perl/Maasha/bin/analyze_tags delete mode 100755 code_perl/Maasha/bin/analyze_vals delete mode 100755 code_perl/Maasha/bin/assemble_tag_contigs delete mode 100755 code_perl/Maasha/bin/blast_seq delete mode 100755 code_perl/Maasha/bin/blat_seq delete mode 100755 code_perl/Maasha/bin/calc_bit_scores delete mode 100755 code_perl/Maasha/bin/calc_fixedstep delete mode 100755 code_perl/Maasha/bin/complement_seq delete mode 100755 code_perl/Maasha/bin/complexity_seq delete mode 100755 code_perl/Maasha/bin/compute delete mode 100755 code_perl/Maasha/bin/count_records delete mode 100755 code_perl/Maasha/bin/count_vals delete mode 100755 code_perl/Maasha/bin/create_blast_db delete mode 100755 code_perl/Maasha/bin/create_vmatch_index delete mode 100755 code_perl/Maasha/bin/create_weight_matrix delete mode 100755 code_perl/Maasha/bin/extract_seq delete mode 100755 code_perl/Maasha/bin/flip_tab delete mode 100755 code_perl/Maasha/bin/fold_seq delete mode 100755 code_perl/Maasha/bin/format_genome delete mode 100755 code_perl/Maasha/bin/get_genome_align delete mode 100755 code_perl/Maasha/bin/get_genome_phastcons delete mode 100755 code_perl/Maasha/bin/get_genome_seq delete mode 100755 code_perl/Maasha/bin/grab delete mode 100755 code_perl/Maasha/bin/head_records delete mode 100755 code_perl/Maasha/bin/invert_align delete mode 100755 code_perl/Maasha/bin/length_seq delete mode 100755 code_perl/Maasha/bin/length_vals delete mode 100755 code_perl/Maasha/bin/list_biopieces delete mode 100755 code_perl/Maasha/bin/list_genomes delete mode 100755 code_perl/Maasha/bin/match_seq delete mode 100755 code_perl/Maasha/bin/max_vals delete mode 100755 code_perl/Maasha/bin/mean_vals delete mode 100755 code_perl/Maasha/bin/median_vals delete mode 100755 code_perl/Maasha/bin/merge_records delete mode 100755 code_perl/Maasha/bin/merge_vals delete mode 100755 code_perl/Maasha/bin/min_vals delete mode 100755 code_perl/Maasha/bin/oligo_freq delete mode 100755 code_perl/Maasha/bin/patscan_seq delete mode 100755 code_perl/Maasha/bin/plot_chrdist delete mode 100755 code_perl/Maasha/bin/plot_histogram delete mode 100755 code_perl/Maasha/bin/plot_karyogram delete mode 100755 code_perl/Maasha/bin/plot_lendist delete mode 100755 code_perl/Maasha/bin/plot_matches delete mode 100755 code_perl/Maasha/bin/plot_phastcons_profiles delete mode 100755 code_perl/Maasha/bin/plot_seqlogo delete mode 100755 code_perl/Maasha/bin/print_usage delete mode 100755 code_perl/Maasha/bin/random_records delete mode 100755 code_perl/Maasha/bin/read_2bit delete mode 100755 code_perl/Maasha/bin/read_bed delete mode 100755 code_perl/Maasha/bin/read_blast_tab delete mode 100755 code_perl/Maasha/bin/read_embl delete mode 100755 code_perl/Maasha/bin/read_fasta delete mode 100755 code_perl/Maasha/bin/read_fixedstep delete mode 100755 code_perl/Maasha/bin/read_gff delete mode 100755 code_perl/Maasha/bin/read_mysql delete mode 100755 code_perl/Maasha/bin/read_phastcons delete mode 100755 code_perl/Maasha/bin/read_psl delete mode 100755 code_perl/Maasha/bin/read_soft delete mode 100755 code_perl/Maasha/bin/read_solexa delete mode 100755 code_perl/Maasha/bin/read_solid delete mode 100755 code_perl/Maasha/bin/read_stockholm delete mode 100755 code_perl/Maasha/bin/read_tab delete mode 100755 code_perl/Maasha/bin/read_ucsc_config delete mode 100755 code_perl/Maasha/bin/remove_adaptor delete mode 100755 code_perl/Maasha/bin/remove_indels delete mode 100755 code_perl/Maasha/bin/remove_keys delete mode 100755 code_perl/Maasha/bin/remove_mysql_tables delete mode 100644 code_perl/Maasha/bin/remove_ucsc_tracks delete mode 100755 code_perl/Maasha/bin/rename_keys delete mode 100755 code_perl/Maasha/bin/reverse_seq delete mode 100755 code_perl/Maasha/bin/shuffle_seq delete mode 100755 code_perl/Maasha/bin/soap_seq delete mode 100755 code_perl/Maasha/bin/sort_records delete mode 100755 code_perl/Maasha/bin/split_bed delete mode 100755 code_perl/Maasha/bin/split_seq delete mode 100755 code_perl/Maasha/bin/sum_vals delete mode 100755 code_perl/Maasha/bin/tile_seq delete mode 100755 code_perl/Maasha/bin/translate_seq delete mode 100755 code_perl/Maasha/bin/transliterate_seq delete mode 100755 code_perl/Maasha/bin/transliterate_vals delete mode 100755 code_perl/Maasha/bin/uniq_vals delete mode 100755 code_perl/Maasha/bin/upload_to_ucsc delete mode 100755 code_perl/Maasha/bin/uppercase_seq delete mode 100755 code_perl/Maasha/bin/vmatch_seq delete mode 100755 code_perl/Maasha/bin/write_2bit delete mode 100755 code_perl/Maasha/bin/write_align delete mode 100755 code_perl/Maasha/bin/write_bed delete mode 100755 code_perl/Maasha/bin/write_blast delete mode 100755 code_perl/Maasha/bin/write_fasta delete mode 100755 code_perl/Maasha/bin/write_fixedstep delete mode 100755 code_perl/Maasha/bin/write_psl delete mode 100755 code_perl/Maasha/bin/write_solid delete mode 100755 code_perl/Maasha/bin/write_tab delete mode 100755 code_perl/Maasha/bin/write_ucsc_config diff --git a/bp_bin/read_solid b/bp_bin/read_solid index fdf5bd2..2d6ccf9 100755 --- a/bp_bin/read_solid +++ b/bp_bin/read_solid @@ -1,6 +1,121 @@ -#!/usr/bin/env perl +#!/usr/bin/env perl -w + +# Copyright (C) 2007-2009 Martin A. Hansen. + +# This program is free software; you can redistribute it and/or +# modify it under the terms of the GNU General Public License +# as published by the Free Software Foundation; either version 2 +# of the License, or (at your option) any later version. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. + +# You should have received a copy of the GNU General Public License +# along with this program; if not, write to the Free Software +# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. + +# http://www.gnu.org/copyleft/gpl.html + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + +# Read SOLID entries from one or more files. + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + -use warnings; use strict; +use Maasha::Biopieces; +use Maasha::Filesys; +use Maasha::Solid; +use Maasha::Calc; + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $data_in, $num, $entry, $i, + $seq_name, $seq_cs, $line, $seq_qual, @scores, @seqs ); + +$options = Maasha::Biopieces::parse_options( + [ + { long => 'data_in', short => 'i', type => 'files!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'num', short => 'n', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => '0' }, + { long => 'quality', short => 'q', type => 'uint', mandatory => 'no', default => 20, allowed => undef, disallowed => undef }, + ] +); + +$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } ); +$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } ); + +while ( $record = Maasha::Biopieces::get_record( $in ) ) { + Maasha::Biopieces::put_record( $record, $out ); +} + +if ( $options->{ 'data_in' } ) +{ + $data_in = Maasha::Filesys::files_read_open( $options->{ 'data_in' } ); + + $num = 1; + + while ( $line = <$data_in> ) + { + chomp $line; + + ( $seq_name, $seq_cs, $seq_qual ) = split /\t/, $line; + + @scores = split /,/, $seq_qual; + @seqs = split //, Maasha::Solid::color_space2seq( $seq_cs ); + + for ( $i = 0; $i < @seqs; $i++ ) { + $seqs[ $i ] = lc $seqs[ $i ] if $scores[ $i ] < $options->{ "quality" }; + } + + $record = { + REC_TYPE => 'SOLID', + SEQ_NAME => $seq_name, + SEQ_CS => $seq_cs, + SEQ_QUAL => join( ";", @scores ), + SEQ_LEN => length $seq_cs, + SEQ => join( "", @seqs ), + SCORE_MEAN => sprintf( "%.2f", Maasha::Calc::mean( \@scores ) ), + }; + + Maasha::Biopieces::put_record( $record, $out ); + + last if $options->{ "num" } and $num == $options->{ "num" }; + + $num++; + } + + close $data_in; +} + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +BEGIN +{ + $run_time_beg = Maasha::Biopieces::run_time(); + + Maasha::Biopieces::log_biopiece(); +} + +END +{ + Maasha::Biopieces::close_stream( $in ); + Maasha::Biopieces::close_stream( $out ); + + $run_time_end = Maasha::Biopieces::run_time(); + + Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options ); +} + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + -use Maasha::BioRun; +__END__ diff --git a/code_perl/Maasha/BioRun.pm b/code_perl/Maasha/BioRun.pm index dbc5e8b..3f4fb1c 100644 --- a/code_perl/Maasha/BioRun.pm +++ b/code_perl/Maasha/BioRun.pm @@ -113,7 +113,6 @@ sub run_script if ( $script eq "print_usage" ) { script_print_usage( $in, $out, $options ) } elsif ( $script eq "read_stockholm" ) { script_read_stockholm( $in, $out, $options ) } elsif ( $script eq "read_phastcons" ) { script_read_phastcons( $in, $out, $options ) } - elsif ( $script eq "read_solid" ) { script_read_solid( $in, $out, $options ) } elsif ( $script eq "read_mysql" ) { script_read_mysql( $in, $out, $options ) } elsif ( $script eq "uppercase_seq" ) { script_uppercase_seq( $in, $out, $options ) } elsif ( $script eq "complexity_seq" ) { script_complexity_seq( $in, $out, $options ) } @@ -170,14 +169,6 @@ sub get_options gap|g=s ); } - elsif ( $script eq "read_solid" ) - { - @options = qw( - data_in|i=s - num|n=s - quality|q=s - ); - } elsif ( $script eq "read_mysql" ) { @options = qw( @@ -532,72 +523,6 @@ sub script_read_phastcons } -sub script_read_solid -{ - # Martin A. Hansen, April 2008. - - # Read Solid sequence from file. - - my ( $in, # handle to in stream - $out, # handle to out stream - $options, # options hash - ) = @_; - - # Returns nothing. - - my ( $record, $file, $data_in, $line, $num, $seq_name, $seq_cs, $seq_qual, @scores, @seqs, $i ); - - $options->{ "quality" } ||= 15; - - while ( $record = Maasha::Biopieces::get_record( $in ) ) { - Maasha::Biopieces::put_record( $record, $out ); - } - - $num = 1; - - foreach $file ( @{ $options->{ "files" } } ) - { - $data_in = Maasha::Common::read_open( $file ); - - while ( $line = <$data_in> ) - { - chomp $line; - - ( $seq_name, $seq_cs, $seq_qual ) = split /\t/, $line; - - @scores = split /,/, $seq_qual; - @seqs = split //, Maasha::Solid::color_space2seq( $seq_cs ); - - for ( $i = 0; $i < @seqs; $i++ ) { - $seqs[ $i ] = lc $seqs[ $i ] if $scores[ $i ] < $options->{ "quality" }; - } - - $record = { - REC_TYPE => 'SOLID', - SEQ_NAME => $seq_name, - SEQ_CS => $seq_cs, - SEQ_QUAL => join( ";", @scores ), - SEQ_LEN => length $seq_cs, - SEQ => join( "", @seqs ), - SCORE_MEAN => sprintf( "%.2f", Maasha::Calc::mean( \@scores ) ), - }; - - Maasha::Biopieces::put_record( $record, $out ); - - goto NUM if $options->{ "num" } and $num == $options->{ "num" }; - - $num++; - } - - close $data_in; - } - - NUM: - - close $data_in if $data_in; -} - - sub script_read_mysql { # Martin A. Hansen, May 2008. diff --git a/code_perl/Maasha/bin/add_ident b/code_perl/Maasha/bin/add_ident deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/add_ident +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/align_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/analyze_bed +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/analyze_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/analyze_tags +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/analyze_vals +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/assemble_tag_contigs +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/blast_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/blat_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/calc_bit_scores +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/calc_fixedstep +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/complement_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/complexity_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/compute +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/count_records +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/count_vals +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/create_blast_db +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/create_vmatch_index +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/create_weight_matrix +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/extract_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/flip_tab +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/fold_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/format_genome +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/get_genome_align +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/get_genome_phastcons +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/get_genome_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/grab +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/head_records +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/invert_align +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/length_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/length_vals +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/list_biopieces +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/list_genomes +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/match_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/max_vals +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/mean_vals +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/median_vals +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/merge_records +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/merge_vals +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/min_vals +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/oligo_freq +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/patscan_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/plot_chrdist +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/plot_histogram +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/plot_karyogram +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/plot_lendist +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/plot_matches +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/plot_phastcons_profiles +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/plot_seqlogo +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/print_usage +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/random_records +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/read_2bit +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/read_bed +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/read_blast_tab +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/read_embl +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/read_fasta +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/read_fixedstep +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/read_gff +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/read_mysql +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/read_phastcons +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/read_psl +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/read_soft +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/read_solexa +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/read_solid +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/read_stockholm +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/read_tab +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/read_ucsc_config +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/remove_adaptor +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/remove_indels +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/remove_keys +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/remove_mysql_tables +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100644 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/remove_ucsc_tracks +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/rename_keys +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/reverse_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/shuffle_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/soap_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/sort_records +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/split_bed +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/split_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/sum_vals +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/tile_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/translate_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/transliterate_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/transliterate_vals +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/uniq_vals +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/upload_to_ucsc +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/uppercase_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/vmatch_seq +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/write_2bit +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/write_align +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/write_bed +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/write_blast +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/write_fasta +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/write_fixedstep +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/write_psl +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/write_solid +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/write_tab +++ /dev/null @@ -1,6 +0,0 @@ -#!/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 deleted file mode 100755 index fdf5bd2..0000000 --- a/code_perl/Maasha/bin/write_ucsc_config +++ /dev/null @@ -1,6 +0,0 @@ -#!/usr/bin/env perl - -use warnings; -use strict; - -use Maasha::BioRun; -- 2.39.5