From: martinahansen Date: Fri, 29 May 2009 09:56:36 +0000 (+0000) Subject: migrated plot_karyogram X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=f2b1b113e4ca24d303bad1579fd4b382c828359a;p=biopieces.git migrated plot_karyogram git-svn-id: http://biopieces.googlecode.com/svn/trunk@450 74ccb610-7750-0410-82ae-013aeee3265d --- diff --git a/bp_bin/plot_karyogram b/bp_bin/plot_karyogram index fdf5bd2..5e6c015 100755 --- a/bp_bin/plot_karyogram +++ b/bp_bin/plot_karyogram @@ -1,6 +1,99 @@ -#!/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 karyogram with positions indicated according to records in the stream. + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + -use warnings; use strict; +use Maasha::Biopieces; +use Maasha::Plot; + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, @data, $fh, $result, %data_hash ); + +$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 => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'genome', short => 'g', type => 'string', mandatory => 'yes', default => undef, allowed => 'hg18,mm9', disallowed => undef }, + { long => 'feat_color', short => 'f', type => 'string', mandatory => 'no', default => 'black', allowed => undef, disallowed => undef }, + ] +); + +$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } ); +$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } ); + +$options->{ "genome" } ||= "human"; +$options->{ "feat_color" } ||= "black"; + +while ( $record = Maasha::Biopieces::get_record( $in ) ) +{ + if ( $record->{ "CHR" } and $record->{ "CHR_BEG" } and $record->{ "CHR_END" } ) + { + push @{ $data_hash{ $record->{ "CHR" } } }, [ $record->{ "CHR_BEG" }, $record->{ "CHR_END" }, $options->{ "feat_color" } ]; + } + + Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" }; +} + +$result = Maasha::Plot::karyogram( \%data_hash, $options ); + +$fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } ); + +print $fh $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 be5975b..c063bc2 100644 --- a/code_perl/Maasha/BioRun.pm +++ b/code_perl/Maasha/BioRun.pm @@ -144,7 +144,6 @@ sub run_script 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_karyogram" ) { script_plot_karyogram( $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 ) } @@ -432,15 +431,6 @@ sub get_options key|k=s ); } - elsif ( $script eq "plot_karyogram" ) - { - @options = qw( - no_stream|x - data_out|o=s - genome|g=s - feat_color|f=s - ); - } elsif ( $script eq "plot_matches" ) { @options = qw( @@ -572,7 +562,7 @@ sub get_options Maasha::Common::error( qq(no --database specified) ) if $script eq "remove_ucsc_tracks" and not $options{ "database" }; 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|plot_karyogram/ and not $options{ "genome" }; + 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" ) @@ -2127,44 +2117,6 @@ sub script_plot_lendist } -sub script_plot_karyogram -{ - # Martin A. Hansen, August 2007. - - # Plot hits on karyogram. - - my ( $in, # handle to in stream - $out, # handle to out stream - $options, # options hash - ) = @_; - - # Returns nothing. - - my ( %options, $record, @data, $fh, $result, %data_hash ); - - $options->{ "genome" } ||= "human"; - $options->{ "feat_color" } ||= "black"; - - while ( $record = Maasha::Biopieces::get_record( $in ) ) - { - if ( $record->{ "CHR" } and $record->{ "CHR_BEG" } and $record->{ "CHR_END" } ) - { - push @{ $data_hash{ $record->{ "CHR" } } }, [ $record->{ "CHR_BEG" }, $record->{ "CHR_END" }, $options->{ "feat_color" } ]; - } - - Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" }; - } - - $result = Maasha::Plot::karyogram( \%data_hash, \%options ); - - $fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } ); - - print $fh $result; - - close $fh; -} - - sub script_plot_matches { # Martin A. Hansen, August 2007. diff --git a/code_perl/Maasha/Plot.pm b/code_perl/Maasha/Plot.pm index 07673c1..88992c5 100644 --- a/code_perl/Maasha/Plot.pm +++ b/code_perl/Maasha/Plot.pm @@ -437,15 +437,13 @@ sub karyogram my ( $karyo_file, $svg, $features, $karyo ); - if ( $options->{ "genome" } eq "human" ) + if ( $options->{ "genome" } eq "hg18" ) { - $karyo_file = "/Users/m.hansen/maasha/perl_scripts/biopieces/karyo_data/human_cytobands.txt"; -# $karyo_file = "/home/m.hansen/maasha/perl_scripts/biopieces/karyo_data/human_cytobands.txt"; + $karyo_file = $ENV{ 'BP_DIR' } . "/bp_data/human_cytobands.txt"; } - else + elsif( $options->{ "genome" } eq "mm9" ) { - $karyo_file = "/Users/m.hansen/maasha/perl_scripts/biopieces/karyo_data/mouse_cytobands.txt"; - # $karyo_file = "/home/m.hansen/maasha/perl_scripts/biopieces/karyo_data/mouse_cytobands.txt"; + $karyo_file = $ENV{ 'BP_DIR' } . "/bp_data/mouse_cytobands.txt"; } $karyo = parse_karyo_data( $karyo_file ); @@ -604,10 +602,10 @@ sub chromosome_layout map { $_->[ 0 ] *= $factor; $_->[ 1 ] *= $factor } @{ $feat_list->{ $feat } }; } - @list = sort { $A = $a; $B = $b; $A =~ s/chr//; $B =~ s/chr//; $A <=> $B } keys %{ $karyo_list }; +# @list = sort { $A = $a; $B = $b; $A =~ s/chr//; $B =~ s/chr//; $A <=> $B } keys %{ $karyo_list }; - splice @list, 0, 2; - push @list, "chrX", "chrY"; +# splice @list, 0, 2; +# push @list, "chrX", "chrY"; $i = 0;