#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Extract subsequences from a genome sequence.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
use warnings;
use strict;
+use Data::Dumper;
+use Maasha::Biopieces;
+use Maasha::Filesys;
+use Maasha::Fasta;
+use Maasha::Seq;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $genome_file, $index_file, $fh, $genome,
+ $beg, $end, $len, $index_beg, $index_len, @begs, @lens, $index, $seq, $i );
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'genome', short => 'g', type => 'genome', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+ { long => 'chr', short => 'c', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'beg', short => 'b', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 },
+ { long => 'end', short => 'e', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 },
+ { long => 'len', short => 'l', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 },
+ { long => 'flank', short => 'f', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef },
+ { long => 'mask', short => 'm', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'splice', short => 's', 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" } );
+
+if ( $options->{ "genome" } )
+{
+ $genome = $options->{ "genome" };
+
+ $genome_file = "$ENV{ 'BP_DATA' }/genomes/$genome/fasta/$genome.fna";
+ $index_file = "$ENV{ 'BP_DATA' }/genomes/$genome/fasta/$genome.index";
+
+ $fh = Maasha::Filesys::file_read_open( $genome_file );
+ $index = Maasha::Fasta::index_retrieve( $index_file );
+
+ if ( defined $options->{ "chr" } and exists $index->{ $options->{ "chr" } } and defined $options->{ "beg" } and ( defined $options->{ "end" } or defined $options->{ "len" } ) )
+ {
+ ( $index_beg, $index_len ) = @{ $index->{ $options->{ "chr" } } };
+
+ $beg = $index_beg + $options->{ "beg" } - 1;
+
+ if ( $options->{ "len" } ) {
+ $len = $options->{ "len" };
+ } elsif ( $options->{ "end" } ) {
+ $len = ( $options->{ "end" } - $options->{ "beg" } + 1 );
+ }
+
+ $beg -= $options->{ "flank" };
+ $len += 2 * $options->{ "flank" };
+
+ if ( $beg <= $index_beg )
+ {
+ $len -= $index_beg - $beg;
+ $beg = $index_beg;
+ }
+
+ if ( $beg + $len > $index_beg + $index_len ) {
+ $len = $index_beg + $index_len - $beg;
+ }
+
+ next if $beg > $index_beg + $index_len;
+
+ $record->{ "CHR" } = $options->{ "chr" };
+ $record->{ "CHR_BEG" } = $beg - $index_beg;
+ $record->{ "CHR_END" } = $record->{ "CHR_BEG" } + $len - 1;
+
+ $record->{ "SEQ" } = Maasha::Filesys::file_read( $fh, $beg, $len );
+ $record->{ "SEQ_LEN" } = $len;
+
+ Maasha::Biopieces::put_record( $record, $out );
+ }
+}
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+ if ( $options->{ "genome" } and not $record->{ "SEQ" } )
+ {
+ if ( $record->{ "REC_TYPE" } eq "BED" and exists $index->{ $record->{ "CHR" } } )
+ {
+ ( $index_beg, $index_len ) = @{ $index->{ $record->{ "CHR" } } };
+
+ $beg = $record->{ "CHR_BEG" } + $index_beg;
+ $len = $record->{ "CHR_END" } - $record->{ "CHR_BEG" } + 1;
+ }
+ elsif ( $record->{ "REC_TYPE" } eq "PSL" and exists $index->{ $record->{ "S_ID" } } )
+ {
+ ( $index_beg, $index_len ) = @{ $index->{ $record->{ "S_ID" } } };
+
+ $beg = $record->{ "S_BEG" } + $index_beg;
+ $len = $record->{ "S_END" } - $record->{ "S_BEG" } + 1;
+ }
+ elsif ( $record->{ "REC_TYPE" } eq "VMATCH" and exists $index->{ $record->{ "S_ID" } } )
+ {
+ ( $index_beg, $index_len ) = @{ $index->{ $record->{ "S_ID" } } };
+
+ $beg = $record->{ "S_BEG" } + $index_beg;
+ $len = $record->{ "S_END" } - $record->{ "S_BEG" } + 1;
+ }
+ elsif ( $record->{ "REC_TYPE" } eq "BLAST" and exists $index->{ $record->{ "S_ID" } } )
+ {
+ ( $index_beg, $index_len ) = @{ $index->{ $record->{ "S_ID" } } };
+
+ $beg = $record->{ "S_BEG" } + $index_beg;
+ $len = $record->{ "S_END" } - $record->{ "S_BEG" } + 1;
+ }
+
+ $beg -= $options->{ "flank" };
+ $len += 2 * $options->{ "flank" };
+
+ if ( $beg <= $index_beg )
+ {
+ $len -= $index_beg - $beg;
+ $beg = $index_beg;
+ }
+
+ $len = $index_beg + $index_len - $beg if $beg + $len > $index_beg + $index_len;
+
+ next if $beg > $index_beg + $index_len;
+
+ $record->{ "CHR_BEG" } = $beg - $index_beg;
+ $record->{ "CHR_END" } = $record->{ "CHR_BEG" } + $len - 1;
+
+ $record->{ "SEQ" } = Maasha::Filesys::file_read( $fh, $beg, $len );
+
+ if ( $record->{ "STRAND" } and $record->{ "STRAND" } eq "-" )
+ {
+ Maasha::Seq::dna_comp( \$record->{ "SEQ" } );
+ $record->{ "SEQ" } = reverse $record->{ "SEQ" };
+ }
+
+ if ( $options->{ "mask" } )
+ {
+ if ( $record->{ "BLOCK_COUNT" } > 1 ) # uppercase hit block segments and lowercase the rest.
+ {
+ $record->{ "SEQ" } = lc $record->{ "SEQ" };
+
+ @begs = split ",", $record->{ "Q_BEGS" };
+ @lens = split ",", $record->{ "BLOCK_LENS" };
+
+ for ( $i = 0; $i < @begs; $i++ ) {
+ substr $record->{ "SEQ" }, $begs[ $i ], $lens[ $i ], uc substr $record->{ "SEQ" }, $begs[ $i ], $lens[ $i ];
+ }
+ }
+ }
+ elsif ( $options->{ "splice" } )
+ {
+ if ( $record->{ "BLOCK_COUNT" } > 1 ) # splice block sequences
+ {
+ $seq = "";
+ @begs = split ",", $record->{ "Q_BEGS" };
+ @lens = split ",", $record->{ "BLOCK_LENS" };
+
+ for ( $i = 0; $i < @begs; $i++ ) {
+ $seq .= substr $record->{ "SEQ" }, $begs[ $i ], $lens[ $i ];
+ }
+
+ $record->{ "SEQ" } = $seq;
+ }
+ }
+
+ $record->{ "SEQ_LEN" } = length $record->{ "SEQ" };
+ }
+
+ Maasha::Biopieces::put_record( $record, $out );
+}
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+ Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+ Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use Maasha::BioRun;
+__END__
projects / biopieces.git / blobdiff