From ee61a2a4055ef203ea89e75548f775a7b3a98638 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Fri, 29 May 2009 10:04:43 +0000 Subject: [PATCH] migrated plot_lendist git-svn-id: http://biopieces.googlecode.com/svn/trunk@453 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/plot_lendist | 106 +++++++++++++++++++++++++++++++++++-- code_perl/Maasha/BioRun.pm | 54 ------------------- 2 files changed, 103 insertions(+), 57 deletions(-) diff --git a/bp_bin/plot_lendist b/bp_bin/plot_lendist index fdf5bd2..0197aca 100755 --- a/bp_bin/plot_lendist +++ b/bp_bin/plot_lendist @@ -1,6 +1,106 @@ -#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + +# Plot a length distribution histogram. + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + -use warnings; use strict; +use Maasha::Biopieces; +use Maasha::Plot; +use Maasha::Calc; + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +my ( $run_time_beg, $run_time_end, $options, $in, $out, $default, $terminals, $record, %data_hash, $max, @data_list, $i, $result, $fh ); + +$default = "Length Distribution"; +$terminals = "dumb,x11,aqua,post,svg"; + +$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 }, + { long => 'key', short => 'k', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef }, + { long => 'terminal', short => 't', type => 'string', mandatory => 'no', default => 'dumb', allowed => $terminals, disallowed => undef }, + { long => 'title', short => 'T', type => 'string', mandatory => 'no', default => $default, allowed => undef, disallowed => undef }, + { long => 'xlabel', short => 'X', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'ylabel', short => 'Y', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + ] +); + +$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } ); +$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } ); + +while ( $record = Maasha::Biopieces::get_record( $in ) ) +{ + $data_hash{ $record->{ $options->{ "key" } } }++ if defined $record->{ $options->{ "key" } }; + + Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" }; +} + +$max = Maasha::Calc::list_max( [ keys %data_hash ] ); + +for ( $i = 0; $i < $max; $i++ ) { + push @data_list, [ $i, $data_hash{ $i } || 0 ]; +} + +$result = Maasha::Plot::histogram_lendist( \@data_list, $options ); + +$fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } ); + +print $fh "$_\n" foreach @{ $result }; + +close $fh; + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +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 c063bc2..d5f4e1f 100644 --- a/code_perl/Maasha/BioRun.pm +++ b/code_perl/Maasha/BioRun.pm @@ -143,7 +143,6 @@ sub run_script elsif ( $script eq "write_ucsc_config" ) { script_write_ucsc_config( $in, $out, $options ) } elsif ( $script eq "remove_mysql_tables" ) { script_remove_mysql_tables( $in, $out, $options ) } elsif ( $script eq "remove_ucsc_tracks" ) { script_remove_ucsc_tracks( $in, $out, $options ) } - elsif ( $script eq "plot_lendist" ) { script_plot_lendist( $in, $out, $options ) } 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 ) } @@ -419,18 +418,6 @@ sub get_options no_stream|x ); } - elsif ( $script eq "plot_lendist" ) - { - @options = qw( - no_stream|x - data_out|o=s - terminal|t=s - title|T=s - xlabel|X=s - ylabel|Y=s - key|k=s - ); - } elsif ( $script eq "plot_matches" ) { @options = qw( @@ -563,7 +550,6 @@ sub get_options Maasha::Common::error( qq(no --in_file or --genome specified) ) if $script eq "soap_seq" and not $options{ "genome" } and not $options{ "in_file" }; 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/ and not $options{ "genome" }; - Maasha::Common::error( qq(no --key specified) ) if $script =~ /plot_lendist/ and not $options{ "key" }; if ( $script eq "upload_to_ucsc" ) { @@ -2077,46 +2063,6 @@ sub script_remove_ucsc_tracks } -sub script_plot_lendist -{ - # Martin A. Hansen, August 2007. - - # Plot length distribution using GNU plot. - - my ( $in, # handle to in stream - $out, # handle to out stream - $options, # options hash - ) = @_; - - # Returns nothing. - - my ( $record, %data_hash, $max, @data_list, $i, $result, $fh ); - - $options->{ "title" } ||= "Length Distribution"; - - while ( $record = Maasha::Biopieces::get_record( $in ) ) - { - $data_hash{ $record->{ $options->{ "key" } } }++ if defined $record->{ $options->{ "key" } }; - - Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" }; - } - - $max = Maasha::Calc::list_max( [ keys %data_hash ] ); - - for ( $i = 0; $i < $max; $i++ ) { - push @data_list, [ $i, $data_hash{ $i } || 0 ]; - } - - $result = Maasha::Plot::histogram_lendist( \@data_list, $options ); - - $fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } ); - - print $fh "$_\n" foreach @{ $result }; - - close $fh; -} - - sub script_plot_matches { # Martin A. Hansen, August 2007. -- 2.39.2