added read_ace

git-svn-id: http://biopieces.googlecode.com/svn/trunk@798 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/read_ace b/bp_bin/read_ace
new file mode 100755 (executable)
index 0000000..83b1244
--- /dev/null
+++ b/bp_bin/read_ace
@@ -0,0 +1,100 @@
+#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Read ACE entries from one or more files.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Maasha::Biopieces;
+use Maasha::Filesys;
+use Maasha::ACE;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $data_in, $num, $entries, $entry );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'data_in', short => 'i', type => 'files!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'num',     short => 'n', type => 'uint',   mandatory => 'no', default => undef, allowed => undef, disallowed => '0' },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) {
+    Maasha::Biopieces::put_record( $record, $out );
+}
+
+if ( $options->{ 'data_in' } )
+{
+    $data_in = Maasha::Filesys::files_read_open( $options->{ 'data_in' } );
+
+    $num = 1;
+
+    while ( $entries = Maasha::ACE::ace_entries_get( $data_in ) ) 
+    {
+        foreach $entry ( @{ $entries } )
+        {
+            Maasha::Biopieces::put_record( $entry, $out );
+
+            last if $options->{ "num" } and $num == $options->{ "num" };
+
+            $num++;
+        }
+
+        last if $options->{ "num" } and $num == $options->{ "num" };
+    }
+
+    close $data_in;
+}
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__

diff --git a/code_perl/Maasha/ACE.pm b/code_perl/Maasha/ACE.pm
new file mode 100644 (file)
index 0000000..b50f240
--- /dev/null
+++ b/code_perl/Maasha/ACE.pm
@@ -0,0 +1,213 @@
+package Maasha::ACE;
+
+# Copyright (C) 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+# Routines to parse ACE format.
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Data::Dumper;
+use Storable;
+use Maasha::Common;
+use Maasha::Filesys;
+use Maasha::KISS;
+use Maasha::Seq;
+use vars qw ( @ISA @EXPORT );
+
+
+@ISA = qw( Exporter );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+sub ace_entries_get
+{
+    # Martin A. Hansen, December 2009.
+    #
+    # Fetches the next contig from an ACE file.
+
+    my ( $fh,
+       ) = @_;
+
+    my ( $block, $line, @lines, $records );
+
+    local $/ = "\nCO ";
+
+    while ( $block = <$fh> )
+    {
+        chomp $block;
+
+        next if $block =~ /^AS/;
+
+        if ( defined $block )
+        {
+            @lines = split "\n", "CO $block";
+
+            $records = ace_entry_parse( \@lines );
+
+            return wantarray ? @{ $records } : $records;
+        }
+    }
+}
+
+
+sub ace_entry_parse
+{
+    # Martin A. Hansen, December 2009.
+
+    # Parses an ACE entry given as a list of lines and
+    # returns a list of hashref.
+
+    my ( $entry,  # list of lines
+       ) = @_;
+
+    # Returns a list.
+
+    my ( $i, $contig, $reads, $read_name, $read_seq, $record, @records );
+
+    $i = 0;
+
+    while ( $i < scalar @{ $entry } )
+    {
+        if ( $entry->[ $i ] =~ /^CO ([^ ]+) (\d+) (\d+) (\d+) (U|C)/ )
+        {
+            $contig->{ 'CONTIG_NAME' }       = $1;
+            $contig->{ 'CONTIG_BASES' }      = $2;
+            $contig->{ 'CONTIG_READS' }      = $3;
+            $contig->{ 'CONTIG_SEGMENT' }    = $4;
+            $contig->{ 'CONTIG_COMPLEMENT' } = $5;
+            $contig->{ 'CONTIG_SEQ' }        = "";
+
+            $i++;
+
+            while ( $entry->[ $i ] ne "" )
+            {
+                $contig->{ 'CONTIG_SEQ' } .= $entry->[ $i ];
+
+                $i++;
+            }
+        }
+        elsif ( $entry->[ $i ] =~ /^AF ([^ ]+) (U|C) (-?\d+)/ )
+        {
+            $reads->{ $1 }->{ 'AF_READ_COMPLEMENT' } = $2;
+            $reads->{ $1 }->{ 'AF_READ_BEG' }        = ( $3 - 1 );
+        }
+        elsif ( $entry->[ $i ] =~ /^BS (\d+) (\d+) (.+)/ )
+        {
+            # skip
+        }
+        elsif ( $entry->[ $i ] =~ /^RD ([^ ]+) (\d+) (\d+) (\d+)/ )
+        {
+            $read_name = $1;
+
+            $reads->{ $read_name }->{ 'RD_READ_LEN' }   = $2;
+            $reads->{ $read_name }->{ 'RD_READ_ITEMS' } = $3;
+            $reads->{ $read_name }->{ 'RD_READ_TAGS' }  = $4;
+
+            $read_seq   = "";
+
+            $i++;
+
+            while ( $entry->[ $i ] ne "" )
+            {
+                $read_seq .= $entry->[ $i ];
+
+                $i++;
+            }
+
+            $reads->{ $read_name }->{ 'RD_READ_SEQ' } = $read_seq;
+        }
+        elsif ( $entry->[ $i ] =~ /^QA (\d+) (\d+) (\d+) (\d+)/ )
+        {
+            $reads->{ $read_name }->{ 'QA_CLIP_BEG' }  = ( $1 - 1 );
+            $reads->{ $read_name }->{ 'QA_CLIP_END' }  = ( $2 - 1 );
+            $reads->{ $read_name }->{ 'QA_ALIGN_BEG' } = ( $3 - 1 );
+            $reads->{ $read_name }->{ 'QA_ALIGN_END' } = ( $4 - 1 );
+        }
+
+        $i++;
+    }
+
+    my ( $read, $s_seq, $q_seq, $len, $align );
+
+    foreach $read ( keys %{ $reads } )
+    {
+        $len   = $reads->{ $read }->{ 'QA_ALIGN_END' } - $reads->{ $read }->{ 'QA_ALIGN_BEG' } + 1;
+        $s_seq = substr $contig->{ 'CONTIG_SEQ' }, $reads->{ $read }->{ 'AF_READ_BEG' } + $reads->{ $read }->{ 'QA_ALIGN_BEG' }, $len;
+        $q_seq = substr $reads->{ $read }->{ 'RD_READ_SEQ' }, $reads->{ $read }->{ 'QA_ALIGN_BEG' }, $len;
+
+        $s_seq =~ tr/*/-/;
+        $q_seq =~ tr/*/-/;
+
+        if ( $reads->{ $read }->{ 'AF_READ_COMPLEMENT' } eq 'C' )
+        {
+            $record->{ 'STRAND' } = '-';
+
+            Maasha::Seq::dna_comp( \$s_seq );
+            Maasha::Seq::dna_comp( \$q_seq );
+        }
+        else
+        {
+            $record->{ 'STRAND' } = '+';
+        }
+
+       # print Dumper( $read, $reads->{ $read } );
+
+        $align = Maasha::KISS::kiss_align_enc( \$s_seq, \$q_seq, $reads->{ $read }->{ 'QA_ALIGN_BEG' } );
+
+        $record->{ 'S_ID' }  = $contig->{ 'CONTIG_NAME' };
+        $record->{ 'S_BEG' } = $reads->{ $read }->{ 'AF_READ_BEG' };
+        $record->{ 'S_END' } = $record->{ 'S_BEG' } + $len - 1;   # FIXME
+        $record->{ 'Q_ID' }  = $read;
+        $record->{ 'Q_ID' }  =~ s/\..+//;
+        $record->{ 'ALIGN' } = join ",", @{ $align };
+
+        if ( 0 )   # DEBUG
+        {
+            print "LEN: $len\n";
+            print "S_SEQ: $s_seq\n";
+            print "Q_SEQ: $q_seq\n\n";
+            print "READ: $read\n";
+            print Dumper( $reads->{ $read } );
+            print Dumper( $record );
+        }
+
+        if ( $record->{ 'S_BEG' } >= 0 ) # FIXME
+        {
+            push @records, Storable::dclone $record;
+        }
+    }
+
+    return wantarray ? @records : \@records;
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+1;