-#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Generate a dotplot of matches in the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use warnings;
use strict;
+use Maasha::Biopieces;
+use Maasha::Plot;
+use Maasha::Filesys;
+use IPC::Open2;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $default, $terminals, $record, @data, $fh, $result, %data_hash, $tmp_dir );
+
+$default = "plot_matches";
+$terminals = "dumb,x11,aqua,post,svg";
+
+$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 => 'terminal', short => 't', type => 'string', mandatory => 'no', default => 'dumb', allowed => $terminals, disallowed => undef },
+ { long => 'direction', short => 'd', type => 'string', mandatory => 'no', default => 'both', allowed => 'both,forward,reverse', 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 ) )
+{
+ if ( defined $record->{ "Q_BEG" } and defined $record->{ "S_BEG" } and $record->{ "Q_END" } and $record->{ "S_END" } ) {
+ push @data, $record;
+ }
+
+ Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
+}
+
+$options->{ "xlabel" } ||= $data[ 0 ]->{ "Q_ID" };
+$options->{ "ylabel" } ||= $data[ 0 ]->{ "S_ID" };
+
+$tmp_dir = Maasha::Biopieces::get_tmpdir();
+
+$result = dotplot_matches( \@data, $options, $tmp_dir );
+
+$fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
+
+print $fh "$_\n" foreach @{ $result };
+
+close $fh;
+
+Maasha::Filesys::dir_remove( $tmp_dir );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+sub dotplot_matches
+{
+ # Martin A. Hansen, August 2007.
+
+ # Generates a dotplot from a list of matches using Gnuplot.
+
+ my ( $matches, # list of hashrefs.
+ $options, # options hash
+ $tmp_dir, # temporary directory
+ ) = @_;
+
+ # Returns list.
+
+ my ( $forward_file, $backward_file, $pid, $fh_forward, $fh_backward,
+ $fh_in, $fh_out, $cmd, $match, $line, @lines, $q_max, $s_max );
+
+ $forward_file = "$tmp_dir/match_f.tab";
+ $backward_file = "$tmp_dir/match_r.tab";
+
+ $fh_forward = Maasha::Filesys::file_write_open( $forward_file );
+ $fh_backward = Maasha::Filesys::file_write_open( $backward_file );
+
+ $q_max = 0;
+ $s_max = 0;
+
+ foreach $match ( @{ $matches } )
+ {
+ if ( $match->{ "DIR" } =~ /^f/ )
+ {
+ print $fh_forward join( "\t", $match->{ "Q_BEG" } + 1, $match->{ "S_BEG" } + 1 ), "\n";
+ print $fh_forward join( "\t", $match->{ "Q_END" } + 1, $match->{ "S_END" } + 1 ), "\n";
+ print $fh_forward "\n\n";
+ }
+ else
+ {
+ print $fh_backward join( "\t", $match->{ "Q_BEG" } + 1, $match->{ "S_END" } + 1 ), "\n";
+ print $fh_backward join( "\t", $match->{ "Q_END" } + 1, $match->{ "S_BEG" } + 1 ), "\n";
+ print $fh_backward "\n\n";
+ }
+
+ $q_max = $match->{ "Q_END" } if $match->{ "Q_END" } > $q_max;
+ $s_max = $match->{ "S_END" } if $match->{ "S_END" } > $s_max;
+ }
+
+ $q_max++;
+ $s_max++;
+
+ close $fh_forward;
+ close $fh_backward;
+
+ $cmd = "gnuplot";
+
+ $pid = open2( $fh_out, $fh_in, $cmd );
+
+ print $fh_in "set terminal $options->{ 'terminal' }\n";
+ print $fh_in "set xrange [1:$q_max]\n";
+ print $fh_in "set yrange [1:$s_max]\n";
+ print $fh_in "set title \"$options->{ 'title' }\"\n" if $options->{ "title" };
+ print $fh_in "set xlabel \"$options->{ 'xlabel' }\"\n" if $options->{ "xlabel" };
+ print $fh_in "set ylabel \"$options->{ 'ylabel' }\"\n" if $options->{ "ylabel" };
+ print $fh_in "unset key\n";
+
+ if ( $options->{ "terminal" } ne "dumb" )
+ {
+ print $fh_in "set style line 1 linetype 1 linecolor rgb \"green\" linewidth 2 pointtype 6 pointsize default\n";
+ print $fh_in "set style line 2 linetype 1 linecolor rgb \"red\" linewidth 2 pointtype 6 pointsize default\n";
+ }
+
+ print $fh_in "set xtics border out\n";
+ print $fh_in "set ytics border out\n";
+ print $fh_in "set grid\n";
+
+ if ( $options->{ "direction" } =~ /^b/ ) {
+ print $fh_in qq(plot "$forward_file" with lines ls 1, "$backward_file" with lines ls 2\n);
+ } elsif ( $options->{ "direction" } =~ /^f/ ) {
+ print $fh_in qq(plot "$forward_file" with lines ls 1\n);
+ } elsif ( $options->{ "direction" } =~ /^r/ ) {
+ print $fh_in qq(plot "$backward_file" with lines ls 2\n);
+ }
+
+ close $fh_in;
+
+ while ( $line = <$fh_out> )
+ {
+ chomp $line;
+
+ push @lines, $line;
+ }
+
+ close $fh_out;
+
+ waitpid $pid, 0;
+
+ unlink $forward_file;
+ unlink $backward_file;
+
+ return wantarray ? @lines : \@lines;
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+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;
-#!/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 chromosome distribution histogram.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use warnings;
use strict;
+use Maasha::Biopieces;
+use Maasha::Plot;
+use Maasha::Matrix;
+use Maasha::Filesys;
+use Maasha::UCSC;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $default, $terminals, $phastcons_file, $phastcons_index,
+ $index, $fh_phastcons, $record, $scores, $AoA, $plot, $fh, $tmp_dir );
+
+$default = "PhastCons Profiles";
+$terminals = "dumb,x11,aqua,post,svg";
+
+$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 => 'genome', short => 'g', type => 'genome', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+ { long => 'mean', short => 'm', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'median', short => 'M', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'flank', short => 'f', type => 'uint', mandatory => 'no', default => 0, 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( $options->{ "stream_out" } );
+
+$phastcons_file = Maasha::Config::genome_phastcons( $options->{ "genome" } );
+$phastcons_index = Maasha::Config::genome_phastcons_index( $options->{ "genome" } );
+
+$index = Maasha::UCSC::fixedstep_index_retrieve( $phastcons_index );
+$fh_phastcons = Maasha::Filesys::file_read_open( $phastcons_file );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+ if ( $record->{ "CHR" } and $record->{ "CHR_BEG" } and $record->{ "CHR_END" } )
+ {
+ $scores = Maasha::UCSC::fixedstep_index_lookup( $index, $fh_phastcons, $record->{ "CHR" },
+ $record->{ "CHR_BEG" },
+ $record->{ "CHR_END" },
+ $options->{ "flank" } );
+
+ push @{ $AoA }, [ @{ $scores } ];
+ }
+
+ Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
+}
+
+Maasha::UCSC::phastcons_normalize( $AoA );
+
+$AoA = [ [ Maasha::UCSC::phastcons_mean( $AoA ) ] ] if $options->{ "mean" };
+$AoA = [ [ Maasha::UCSC::phastcons_median( $AoA ) ] ] if $options->{ "median" };
+
+$AoA = Maasha::Matrix::matrix_flip( $AoA );
+
+$tmp_dir = Maasha::Biopieces::get_tmpdir();
+
+$plot = Maasha::Plot::lineplot_simple( $AoA, $options, $tmp_dir );
+
+$fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
+
+print $fh "$_\n" foreach @{ $plot };
+
+close $fh;
+
+Maasha::Filesys::dir_remove( $tmp_dir );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+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;
-#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Split the values of a key into new key/value pairs.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use warnings;
use strict;
+use Maasha::Biopieces;
+use Maasha::Plot;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, @entries, $logo, $fh );
+
+$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_NAME" } and $record->{ "SEQ" } ) {
+ push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
+ }
+
+ Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
+}
+
+$logo = Maasha::Plot::seq_logo( \@entries );
+
+$fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
+
+print $fh $logo;
+
+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;
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_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 "upload_to_ucsc" ) { script_upload_to_ucsc( $in, $out, $options ) }
close $in if defined $in;
data_out|o=s
);
}
- elsif ( $script eq "plot_seqlogo" )
- {
- @options = qw(
- no_stream|x
- data_out|o=s
- );
- }
- elsif ( $script eq "plot_phastcons_profiles" )
- {
- @options = qw(
- no_stream|x
- data_out|o=s
- genome|g=s
- mean|m
- median|M
- flank|f=s
- terminal|t=s
- title|T=s
- xlabel|X=s
- ylabel|Y=s
- );
- }
elsif ( $script eq "remove_mysql_tables" )
{
@options = qw(
no_stream|x
);
}
- elsif ( $script eq "plot_matches" )
- {
- @options = qw(
- no_stream|x
- data_out|o=s
- terminal|t=s
- title|T=s
- xlabel|X=s
- ylabel|Y=s
- direction|d=s
- );
- }
elsif ( $script eq "upload_to_ucsc" )
{
@options = qw(
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/ and not $options{ "genome" };
+ Maasha::Common::error( qq(no --genome specified) ) if $script =~ /get_genome_align|get_genome_phastcons/ and not $options{ "genome" };
if ( $script eq "upload_to_ucsc" )
{
}
-sub script_plot_seqlogo
-{
- # Martin A. Hansen, August 2007.
-
- # Calculates and writes a sequence logo for alignments.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, @entries, $logo, $fh );
-
- while ( $record = Maasha::Biopieces::get_record( $in ) )
- {
- if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) {
- push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ];
- }
-
- Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- $logo = Maasha::Plot::seq_logo( \@entries );
-
- $fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
-
- print $fh $logo;
-
- close $fh;
-}
-
-
-sub script_plot_phastcons_profiles
-{
- # Martin A. Hansen, January 2008.
-
- # Plots PhastCons profiles.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $phastcons_file, $phastcons_index, $index, $fh_phastcons, $record, $scores, $AoA, $plot, $fh );
-
- $options->{ "title" } ||= "PhastCons Profiles";
-
- $phastcons_file = Maasha::Config::genome_phastcons( $options->{ "genome" } );
- $phastcons_index = Maasha::Config::genome_phastcons_index( $options->{ "genome" } );
-
- $index = Maasha::UCSC::fixedstep_index_retrieve( $phastcons_index );
- $fh_phastcons = Maasha::Common::read_open( $phastcons_file );
-
- while ( $record = Maasha::Biopieces::get_record( $in ) )
- {
- if ( $record->{ "CHR" } and $record->{ "CHR_BEG" } and $record->{ "CHR_END" } )
- {
- $scores = Maasha::UCSC::fixedstep_index_lookup( $index, $fh_phastcons, $record->{ "CHR" },
- $record->{ "CHR_BEG" },
- $record->{ "CHR_END" },
- $options->{ "flank" } );
-
- push @{ $AoA }, [ @{ $scores } ];
- }
-
- Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- Maasha::UCSC::phastcons_normalize( $AoA );
-
- $AoA = [ [ Maasha::UCSC::phastcons_mean( $AoA ) ] ] if $options->{ "mean" };
- $AoA = [ [ Maasha::UCSC::phastcons_median( $AoA ) ] ] if $options->{ "median" };
-
- $AoA = Maasha::Matrix::matrix_flip( $AoA );
-
- $plot = Maasha::Plot::lineplot_simple( $AoA, $options, $BP_TMP );
-
- $fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
-
- print $fh "$_\n" foreach @{ $plot };
-
- close $fh;
-}
-
-
sub script_remove_mysql_tables
{
# Martin A. Hansen, November 2008.
}
-sub script_plot_matches
-{
- # Martin A. Hansen, August 2007.
-
- # Plot matches in 2D generating a dotplot.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $record, @data, $fh, $result, %data_hash );
-
- $options->{ "direction" } ||= "both";
-
- while ( $record = Maasha::Biopieces::get_record( $in ) )
- {
- if ( defined $record->{ "Q_BEG" } and defined $record->{ "S_BEG" } and $record->{ "Q_END" } and $record->{ "S_END" } ) {
- push @data, $record;
- }
-
- Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
- }
-
- $options->{ "title" } ||= "plot_matches";
- $options->{ "xlabel" } ||= $data[ 0 ]->{ "Q_ID" };
- $options->{ "ylabel" } ||= $data[ 0 ]->{ "S_ID" };
-
- $result = Maasha::Plot::dotplot_matches( \@data, $options, $BP_TMP );
-
- $fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
-
- print $fh "$_\n" foreach @{ $result };
-
- close $fh;
-}
-
-
sub script_upload_to_ucsc
{
# Martin A. Hansen, August 2007.
}
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DOTPLOT <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-sub dotplot_matches
-{
- # Martin A. Hansen, August 2007.
-
- # Generates a dotplot from a list of matches using Gnuplot.
-
- my ( $matches, # list of hashrefs.
- $options, # options hash
- $tmp_dir, # temporary directory
- ) = @_;
-
- # Returns list.
-
- my ( $forward_file, $backward_file, $pid, $fh_forward, $fh_backward,
- $fh_in, $fh_out, $cmd, $match, $line, @lines, $q_max, $s_max );
-
- $tmp_dir ||= $ENV{ 'BP_TMP' };
-
- $forward_file = "$tmp_dir/match_f.tab";
- $backward_file = "$tmp_dir/match_r.tab";
-
- $fh_forward = Maasha::Filesys::file_write_open( $forward_file );
- $fh_backward = Maasha::Filesys::file_write_open( $backward_file );
-
- $q_max = 0;
- $s_max = 0;
-
- foreach $match ( @{ $matches } )
- {
- if ( $match->{ "DIR" } =~ /^f/ )
- {
- print $fh_forward join( "\t", $match->{ "Q_BEG" } + 1, $match->{ "S_BEG" } + 1 ), "\n";
- print $fh_forward join( "\t", $match->{ "Q_END" } + 1, $match->{ "S_END" } + 1 ), "\n";
- print $fh_forward "\n\n";
- }
- else
- {
- print $fh_backward join( "\t", $match->{ "Q_BEG" } + 1, $match->{ "S_END" } + 1 ), "\n";
- print $fh_backward join( "\t", $match->{ "Q_END" } + 1, $match->{ "S_BEG" } + 1 ), "\n";
- print $fh_backward "\n\n";
- }
-
- $q_max = $match->{ "Q_END" } if $match->{ "Q_END" } > $q_max;
- $s_max = $match->{ "S_END" } if $match->{ "S_END" } > $s_max;
- }
-
- $q_max++;
- $s_max++;
-
- close $fh_forward;
- close $fh_backward;
-
- $options->{ "terminal" } ||= "dumb";
-
- $cmd = "gnuplot";
-
- $pid = open2( $fh_out, $fh_in, $cmd );
-
- print $fh_in "set terminal $options->{ 'terminal' }\n";
- print $fh_in "set xrange [1:$q_max]\n";
- print $fh_in "set yrange [1:$s_max]\n";
- print $fh_in "set title \"$options->{ 'title' }\"\n" if $options->{ "title" };
- print $fh_in "set xlabel \"$options->{ 'xlabel' }\"\n" if $options->{ "xlabel" };
- print $fh_in "set ylabel \"$options->{ 'ylabel' }\"\n" if $options->{ "ylabel" };
- print $fh_in "unset key\n";
-
- if ( $options->{ "terminal" } ne "dumb" )
- {
- print $fh_in "set style line 1 linetype 1 linecolor rgb \"green\" linewidth 2 pointtype 6 pointsize default\n";
- print $fh_in "set style line 2 linetype 1 linecolor rgb \"red\" linewidth 2 pointtype 6 pointsize default\n";
- }
-
- print $fh_in "set xtics border out\n";
- print $fh_in "set ytics border out\n";
- print $fh_in "set grid\n";
-
- if ( $options->{ "direction" } =~ /^b/ ) {
- print $fh_in qq(plot "$forward_file" with lines ls 1, "$backward_file" with lines ls 2\n);
- } elsif ( $options->{ "direction" } =~ /^f/ ) {
- print $fh_in qq(plot "$forward_file" with lines ls 1\n);
- } elsif ( $options->{ "direction" } =~ /^r/ ) {
- print $fh_in qq(plot "$backward_file" with lines ls 2\n);
- }
-
- close $fh_in;
-
- while ( $line = <$fh_out> )
- {
- chomp $line;
-
- push @lines, $line;
- }
-
- close $fh_out;
-
- waitpid $pid, 0;
-
- unlink $forward_file;
- unlink $backward_file;
-
- return wantarray ? @lines : \@lines;
-}
-
-
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> KARYOGRAM <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
projects / biopieces.git / commitdiff