From: martinahansen Date: Wed, 27 May 2009 03:52:20 +0000 (+0000) Subject: added 3 more X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=0309c14a327e5dc44d6216f7d94721e563502d7b;p=biopieces.git added 3 more git-svn-id: http://biopieces.googlecode.com/svn/trunk@421 74ccb610-7750-0410-82ae-013aeee3265d --- diff --git a/bp_bin/invert_align b/bp_bin/invert_align index fdf5bd2..413ab29 100755 --- a/bp_bin/invert_align +++ b/bp_bin/invert_align @@ -1,6 +1,96 @@ -#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + +# Inverts an alignment showing only non-mathing residues using the first sequence as reference. + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + -use warnings; use strict; +use Maasha::Biopieces; +use Maasha::Align; + +use constant { + SEQ_NAME => 0, + SEQ => 1, +}; + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, @entries ); + +$options = Maasha::Biopieces::parse_options( + [ + { long => 'soft', short => 's', type => 'flag', mandatory => 'no', default => undef, 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 ) ) +{ + if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) + { + push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ]; + } + else + { + Maasha::Biopieces::put_record( $record, $out ); + } +} + +Maasha::Align::align_invert( \@entries, $options->{ "soft" } ); + +map { Maasha::Biopieces::put_record( { SEQ_NAME => $_->[ SEQ_NAME ], SEQ => $_->[ SEQ ] }, $out ) } @entries; + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +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 ); +} + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +__END__ -use Maasha::BioRun; diff --git a/bp_bin/length_seq b/bp_bin/length_seq index fdf5bd2..2ca4b0f 100755 --- a/bp_bin/length_seq +++ b/bp_bin/length_seq @@ -1,6 +1,88 @@ -#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + +# Determines the length of all sequences in the stream as well as a total length. + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + -use warnings; use strict; +use Maasha::Biopieces; + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $total ); + +$options = Maasha::Biopieces::parse_options( + [ + { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'data_out', short => 'o', type => 'file', mandatory => 'no', default => undef, 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 ) ) +{ + if ( $record->{ "SEQ" } ) + { + $record->{ "SEQ_LEN" } = length $record->{ "SEQ" }; + $total += $record->{ "SEQ_LEN" }; + } + + Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" }; +} + +Maasha::Biopieces::put_record( { TOTAL_SEQ_LEN => $total }, $out ); + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +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 ); +} + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +__END__ -use Maasha::BioRun; diff --git a/bp_bin/length_vals b/bp_bin/length_vals index fdf5bd2..8bcb33e 100755 --- a/bp_bin/length_vals +++ b/bp_bin/length_vals @@ -1,6 +1,86 @@ -#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + +# Find the length of values in the stream for given keys. + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + -use warnings; use strict; +use Maasha::Biopieces; + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $key ); + +$options = Maasha::Biopieces::parse_options( + [ + { long => 'keys', short => 'k', type => 'list', mandatory => 'yes', default => undef, 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 ) ) +{ + foreach $key ( @{ $options->{ "keys" } } ) + { + if ( $record->{ $key } ) { + $record->{ $key . "_LEN" } = length $record->{ $key }; + } + } + + Maasha::Biopieces::put_record( $record, $out ); +} + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +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 ); +} + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +__END__ -use Maasha::BioRun; diff --git a/code_perl/Maasha/BioRun.pm b/code_perl/Maasha/BioRun.pm index d79617c..be8d882 100644 --- a/code_perl/Maasha/BioRun.pm +++ b/code_perl/Maasha/BioRun.pm @@ -130,7 +130,6 @@ sub run_script 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 "read_ucsc_config" ) { script_read_ucsc_config( $in, $out, $options ) } - elsif ( $script eq "length_seq" ) { script_length_seq( $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 ) } elsif ( $script eq "oligo_freq" ) { script_oligo_freq( $in, $out, $options ) } @@ -141,7 +140,6 @@ sub run_script elsif ( $script eq "get_genome_align" ) { script_get_genome_align( $in, $out, $options ) } elsif ( $script eq "get_genome_phastcons" ) { script_get_genome_phastcons( $in, $out, $options ) } elsif ( $script eq "tile_seq" ) { script_tile_seq( $in, $out, $options ) } - elsif ( $script eq "invert_align" ) { script_invert_align( $in, $out, $options ) } elsif ( $script eq "patscan_seq" ) { script_patscan_seq( $in, $out, $options ) } elsif ( $script eq "soap_seq" ) { script_soap_seq( $in, $out, $options ) } elsif ( $script eq "match_seq" ) { script_match_seq( $in, $out, $options ) } @@ -167,7 +165,6 @@ sub run_script elsif ( $script eq "plot_matches" ) { script_plot_matches( $in, $out, $options ) } elsif ( $script eq "plot_seqlogo" ) { script_plot_seqlogo( $in, $out, $options ) } elsif ( $script eq "plot_phastcons_profiles" ) { script_plot_phastcons_profiles( $in, $out, $options ) } - elsif ( $script eq "length_vals" ) { script_length_vals( $in, $out, $options ) } elsif ( $script eq "sum_vals" ) { script_sum_vals( $in, $out, $options ) } elsif ( $script eq "mean_vals" ) { script_mean_vals( $in, $out, $options ) } elsif ( $script eq "median_vals" ) { script_median_vals( $in, $out, $options ) } @@ -317,13 +314,6 @@ sub get_options num|n=s ); } - elsif ( $script eq "length_seq" ) - { - @options = qw( - no_stream|x - data_out|o=s - ); - } elsif ( $script eq "oligo_freq" ) { @options = qw( @@ -383,12 +373,6 @@ sub get_options supress_indels|s ); } - elsif ( $script eq "invert_align" ) - { - @options = qw( - soft|s - ); - } elsif ( $script eq "patscan_seq" ) { @options = qw( @@ -620,12 +604,6 @@ sub get_options direction|d=s ); } - elsif ( $script eq "length_vals" ) - { - @options = qw( - keys|k=s - ); - } elsif ( $script eq "sum_vals" ) { @options = qw( @@ -791,7 +769,7 @@ sub get_options Maasha::Common::error( qq(both --in_file and --genome specified) ) if $script eq "soap_seq" and $options{ "genome" } and $options{ "in_file" }; Maasha::Common::error( qq(no --genome specified) ) if $script =~ /get_genome_align|get_genome_phastcons|plot_phastcons_profiles|plot_karyogram/ and not $options{ "genome" }; Maasha::Common::error( qq(no --key specified) ) if $script =~ /plot_lendist|plot_histogram/ and not $options{ "key" }; - Maasha::Common::error( qq(no --keys speficied) ) if $script =~ /sort_records|sum_vals|mean_vals|median_vals|length_vals/ and not $options{ "keys" }; + Maasha::Common::error( qq(no --keys speficied) ) if $script =~ /sort_records|sum_vals|mean_vals|median_vals/ and not $options{ "keys" }; if ( $script eq "upload_to_ucsc" ) { @@ -1620,36 +1598,6 @@ sub script_read_ucsc_config } -sub script_length_seq -{ - # Martin A. Hansen, August 2007. - - # Determine the length of sequences in stream. - - my ( $in, # handle to in stream - $out, # handle to out stream - $options, # options hash - ) = @_; - - # Returns nothing. - - my ( $record, $total ); - - while ( $record = Maasha::Biopieces::get_record( $in ) ) - { - if ( $record->{ "SEQ" } ) - { - $record->{ "SEQ_LEN" } = length $record->{ "SEQ" }; - $total += $record->{ "SEQ_LEN" }; - } - - Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" }; - } - - Maasha::Biopieces::put_record( { TOTAL_SEQ_LEN => $total }, $out ); -} - - sub script_complexity_seq { # Martin A. Hansen, May 2008. @@ -2054,40 +2002,6 @@ sub script_tile_seq } -sub script_invert_align -{ - # Martin A. Hansen, February 2008. - - # Inverts an alignment showing only non-mathing residues - # using the first sequence as reference. - - my ( $in, # handle to in stream - $out, # handle to out stream - $options, # options hash - ) = @_; - - # Returns nothing. - - my ( $record, @entries ); - - while ( $record = Maasha::Biopieces::get_record( $in ) ) - { - if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) - { - push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ]; - } - else - { - Maasha::Biopieces::put_record( $record, $out ); - } - } - - Maasha::Align::align_invert( \@entries, $options->{ "soft" } ); - - map { Maasha::Biopieces::put_record( { SEQ_NAME => $_->[ SEQ_NAME ], SEQ => $_->[ SEQ ] }, $out ) } @entries; -} - - sub script_patscan_seq { # Martin A. Hansen, August 2007. @@ -3387,35 +3301,6 @@ sub script_plot_matches } -sub script_length_vals -{ - # Martin A. Hansen, August 2007. - - # Determine the length of the value for given keys. - - my ( $in, # handle to in stream - $out, # handle to out stream - $options, # options hash - ) = @_; - - # Returns nothing. - - my ( $record, $key ); - - while ( $record = Maasha::Biopieces::get_record( $in ) ) - { - foreach $key ( @{ $options->{ "keys" } } ) - { - if ( $record->{ $key } ) { - $record->{ $key . "_LEN" } = length $record->{ $key }; - } - } - - Maasha::Biopieces::put_record( $record, $out ); - } -} - - sub script_sum_vals { # Martin A. Hansen, August 2007.