added plot_lines

git-svn-id: http://biopieces.googlecode.com/svn/trunk@839 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/cluster_seq b/bp_bin/cluster_seq
index 04fc8bb045ce40bee0589e752dc6d51a245c02c0..53d8f2c72ca6cce554d674ec4ad5eb2a2a17d185 100755 (executable)
--- a/bp_bin/cluster_seq
+++ b/bp_bin/cluster_seq
@@ -39,71 +39,77 @@ use Maasha::Filesys;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $options, $in, $out, $tmp_dir, $tmp_fh1, $tmp_fh2, $fh, $record, $entry, @args1, @args2, $arg_str1, $arg_str2, $clusters );
-
-$tmp_dir  = Maasha::Biopieces::get_tmpdir();
+my ( $options, $in, $out, $tmp_dir, $tmp_file, $tmp_fh, $record, $entry, @args, $arg_str, @fields, $line );
 
 $options = Maasha::Biopieces::parse_options(
     [
-        { long => 'identity',   short => 'i', type => 'float', mandatory => 'no', default => "0.9",    allowed => undef, disallowed => undef },
-        { long => 'word_size',  short => 'w', type => 'uint',  mandatory => 'no', default => 7,        allowed => undef, disallowed => 0 },
-        { long => 'fast_clust', short => 'f', type => 'flag',  mandatory => 'no', default => undef,    allowed => undef, disallowed => undef },
-
-        { long => 'tmp_dir',    short => 't', type => 'dir!',  mandatory => 'no', default => $tmp_dir, allowed => undef, disallowed => undef },
+        { long => 'identity', short => 'i', type => 'float', mandatory => 'no', default => "0.9", allowed => undef, disallowed => undef },
+        { long => 'library',  short => 'l', type => 'file!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'no_sort',  short => 'n', 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" } );
 
-$tmp_fh1  = Maasha::Filesys::file_write_open( "$tmp_dir/cluster.fasta" );
-$tmp_fh2  = Maasha::Filesys::file_write_open( "$tmp_dir/cluster.stream" );
+$tmp_dir  = Maasha::Biopieces::get_tmpdir();
+$tmp_file = "$tmp_dir/uclust.fasta";
+$tmp_fh   = Maasha::Filesys::file_write_open( $tmp_file );
 
 while ( $record = Maasha::Biopieces::get_record( $in ) )
 {
-    if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) )
-    {
-        Maasha::Fasta::put_entry( $entry, $tmp_fh1 );
+    if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) ) {
+        Maasha::Fasta::put_entry( $entry, $tmp_fh );
     }
 
-    Maasha::Biopieces::put_record( $record, $tmp_fh2 );
+    Maasha::Biopieces::put_record( $record, $out );
 }
 
-close $tmp_fh1;
-close $tmp_fh2;
-
-push @args1, "--sort $tmp_dir/cluster.fasta";
-push @args1, "--output $tmp_dir/cluster.fasta.sort";
-push @args1, "--tmpdir $options->{ 'tmp_dir' }";
-push @args1, "--quiet"          if not $options->{ 'verbose' };
-push @args1, "> /dev/null 2>&1" if not $options->{ 'verbose' };
+close $tmp_fh;
 
-push @args2, "--input $tmp_dir/cluster.fasta.sort";
-push @args2, "--id $options->{ 'identity' }";
-push @args2, "--tmpdir $options->{ 'tmp_dir' }";
-push @args2, "--uc $tmp_dir/cluster.uc";
-push @args2, "--quiet"          if not $options->{ 'verbose' };
-push @args2, "> /dev/null 2>&1" if not $options->{ 'verbose' };
+uclust_sort( $tmp_file, $tmp_dir, $options->{ 'verbose' } ) if not $options->{ 'no_sort' };
 
-$arg_str1 = join " ", @args1;
-$arg_str2 = join " ", @args2;
+push @args, "--input $tmp_file";
+push @args, "--id $options->{ 'identity' }";
+push @args, "--tmpdir $tmp_dir";
+push @args, "--uc $tmp_file.out";
+push @args, "--lib $options->{ 'library' }" if $options->{ 'library' };
+push @args, "--libonly"                     if $options->{ 'library' };
+push @args, "--quiet"                       if not $options->{ 'verbose' };
+push @args, "> /dev/null 2>&1"              if not $options->{ 'verbose' };
 
-Maasha::Common::run( "uclust", $arg_str1 );
-Maasha::Common::run( "uclust", $arg_str2 );
+$arg_str = join " ", @args;
 
-$clusters = parse_clusters( "$tmp_dir/cluster.uc" );
+Maasha::Common::run( "uclust", $arg_str );
 
-$tmp_fh2 = Maasha::Filesys::file_read_open( "$tmp_dir/cluster.stream" );
+$tmp_fh = Maasha::Filesys::file_read_open( "$tmp_file.out" ); 
 
-while ( $record = Maasha::Biopieces::get_record( $tmp_fh2 ) )
+while ( $line = <$tmp_fh> )
 {
-    if ( exists $clusters->{ $record->{ 'SEQ_NAME' } } ) {
-        $record->{ 'CLUSTER' } = $clusters->{ $record->{ 'SEQ_NAME' } };
-    }
+    next if $line =~ /^#/;
+
+    chomp $line;
+
+    @fields = split "\t", $line;
+
+    $record = {
+        REC_TYPE => 'UCLUST',
+        TYPE     => $fields[ 0 ],
+        CLUSTER  => $fields[ 1 ],
+        SIZE     => $fields[ 2 ],
+        IDENT    => $fields[ 3 ],
+        STRAND   => $fields[ 4 ],
+        Q_BEG    => $fields[ 5 ],
+        S_BEG    => $fields[ 6 ],
+        CIGAR    => $fields[ 7 ],
+        SEQ_NAME => $fields[ 8 ],
+    };
 
     Maasha::Biopieces::put_record( $record, $out );
 }
 
+close $tmp_fh;
+
 Maasha::Biopieces::close_stream( $in );
 Maasha::Biopieces::close_stream( $out );
 
@@ -111,36 +117,33 @@ Maasha::Biopieces::close_stream( $out );
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-sub parse_clusters
+sub uclust_sort
 {
     # Martin A. Hansen, January 2010.
     
-    # Parses a uclust uc cluster file and returns a hash with
-    # sequence name as key and cluster number as value.
+    # Sorts a FASTA file according to sequence length
+    # - longest first -  using uclust.
 
-    my ( $file,   # cluster file
+    my ( $file,      # file to sort
+         $tmp_dir,   # temporary directory for sorting
+         $verbose,   # verbose flag  -  OPTIONAL
        ) = @_;
 
-    # Returns a hash.
-   
-    my ( $fh, $line, %clusters, $seq_name, $cluster );
-
-    $fh = Maasha::Filesys::file_read_open( $file );
-
-    while ( $line = <$fh> )
-    {
-        next if $line =~ /^#/;
-
-        chomp $line;
+    # Returns nothing.
+    
+    my ( @args, $arg_str );
 
-        ( undef, $cluster, undef, undef, undef, undef, undef, undef, $seq_name ) = split "\t", $line;
+    push @args, "--mergesort $file";
+    push @args, "--output $file.sort";
+    push @args, "--tmpdir $tmp_dir";
+    push @args, "--quiet"          if not $verbose;
+    push @args, "> /dev/null 2>&1" if not $verbose;
 
-        $clusters{ $seq_name } = $cluster;
-    }
+    $arg_str = join " ", @args;
 
-    close $fh;
+    Maasha::Common::run( "uclust", $arg_str );
 
-    return wantarray ? %clusters : \%clusters;
+    rename "$file.sort", $file;
 }
 
 

diff --git a/bp_bin/plot_lines b/bp_bin/plot_lines
new file mode 100755 (executable)
index 0000000..4b9c041
--- /dev/null
+++ b/bp_bin/plot_lines
@@ -0,0 +1,119 @@
+#!/usr/bin/env perl
+
+# 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 one or more lines.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Data::Dumper;
+use Maasha::Common;
+use Maasha::Biopieces;
+use Maasha::Plot;
+use Maasha::Matrix;
+use Maasha::Filesys;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $default, $terminals, $record, $AoA, $fh, $plot, $tmp_dir, $key, @list );
+
+$default   = "Lines";
+$terminals = "dumb,x11,aqua,post,svg";
+
+$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 => 'keys',       short => 'k', type => 'list',   mandatory => 'no', default => undef,    allowed => undef,      disallowed => undef },
+        { long => 'list',       short => 'l', type => 'string', mandatory => 'no', 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 },
+        { long => 'logscale_y', short => 'L', type => 'flag',   mandatory => 'no', default => undef,    allowed => undef,      disallowed => undef },
+    ]   
+);
+
+Maasha::Common::error( qq(neither 'keys' or 'list' specified - use one or the other) )    if not defined $options->{ 'keys' } and not defined $options->{ 'list' };
+Maasha::Common::error( qq(both 'keys' and 'list' specified - use only one or the other) ) if     defined $options->{ 'keys' } and     defined $options->{ 'list' };
+
+$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 $options->{ 'list' } and defined $record->{ $options->{ 'list' } } )
+    {
+        push @{ $AoA }, [ split ";", $record->{ $options->{ 'list' } } ];
+    }
+    elsif ( defined $options->{ 'keys' } )
+    {
+        undef @list;
+
+        map { push @list, $record->{ $_ } if defined $record->{ $_ }  } @{ $options->{ 'keys' } };
+
+        push @{ $AoA }, [ @list ] if scalar @list > 0;
+    }
+
+    Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
+}
+
+$AoA     = Maasha::Matrix::matrix_flip( $AoA ) if $options->{ 'list' };  # convert row to column
+
+$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::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__