added get_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@669 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/format_genome b/bp_bin/format_genome
index 35aa8b3af7354de14d65ef00aa444ebed767e149..2907aa4a61419aa31573d882cd0d2af192da76a0 100755 (executable)
--- a/bp_bin/format_genome
+++ b/bp_bin/format_genome
@@ -109,11 +109,13 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
     Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
 }
 
+close $fh_out if $fh_out;
+
 foreach $format ( @{ $options->{ 'formats' } } )
 {
     print STDERR qq(Creating format: $format for $genome ... ) if $options->{ 'verbose' };
 
-    if    ( $format =~ /^fasta$/i )     { Maasha::Fasta::fasta_index( "$fasta_dir/$genome.fna", "$dir/genomes/$genome/fasta/$genome.index" ) }
+    if    ( $format =~ /^fasta$/i )     { Maasha::Fasta::fasta_index( "$fasta_dir/$genome.fna", $fasta_dir, "$genome.index" ) }
     elsif ( $format =~ /^blast$/i )     { Maasha::NCBI::blast_index( "$genome.fna", $fasta_dir, "$dir/genomes/$genome/blast", "dna", $genome ) }
     elsif ( $format =~ /^blat$/i )      { warn "BLAT FORMAT NOT IMPLEMENTED" }
     elsif ( $format =~ /^vmatch$/i )    { Maasha::Match::vmatch_index( "$genome.fna", $fasta_dir, "$dir/genomes/$genome/vmatch", $tmp_dir ) }
@@ -124,8 +126,6 @@ foreach $format ( @{ $options->{ 'formats' } } )
     print STDERR qq(done.\n) if $options->{ 'verbose' };
 }
 
-close $fh_out if $fh_out;
-
 Maasha::Biopieces::close_stream( $in );
 Maasha::Biopieces::close_stream( $out );
 

diff --git a/bp_bin/get_seq b/bp_bin/get_seq
new file mode 100755 (executable)
index 0000000..72c797e
--- /dev/null
+++ b/bp_bin/get_seq
@@ -0,0 +1,192 @@
+#!/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 an indexed sequence file.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Data::Dumper;
+use Maasha::Biopieces;
+use Maasha::Filesys;
+use Maasha::Fasta;
+use Maasha::Seq;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $index, $fh, $record, $index_beg, $index_len, $beg, $end, $len, $seq );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'index',    short => 'i', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+        { long => 'seq_name', short => 's', 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 },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+if ( $options->{ 'beg' } ) {
+    $options->{ 'beg' }--;
+} else {
+    $options->{ 'beg' } = 0;
+}
+
+$index = Maasha::Fasta::index_retrieve( $options->{ 'index' } . ".index" );
+
+if ( $index->{ 'FILE_SIZE' } != Maasha::Filesys::file_size( $options->{ 'index' } . ".seq" ) ) {
+    Maasha::Common::error( qq(Filesize mismatch: $options->{ 'index' }.seq != $index->{ 'FILE_SIZE' }) );
+}
+
+$fh = Maasha::Filesys::file_read_open( $options->{ 'index' } . ".seq" );
+
+
+if ( $options->{ 'seq_name' } and exists $index->{ $options->{ 'seq_name' } } )
+{
+    ( $index_beg, $index_len ) = @{ $index->{ $options->{ 'seq_name' } } };
+
+    $beg = $options->{ 'beg' };
+    $end = $options->{ 'end' };
+    $len = $options->{ 'len' };
+
+    $seq = seq_get( $fh, $index_beg, $index_len, $beg, $end, $len );
+
+    if ( $seq )
+    {
+        $record->{ 'SEQ_NAME' } = $options->{ 'seq_name' };
+        $record->{ 'SEQ' }      = $seq;
+        $record->{ 'SEQ_LEN' }  = length $record->{ 'SEQ' };
+
+        Maasha::Biopieces::put_record( $record, $out );
+    }
+}
+
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+    if ( exists $index->{ $record->{ 'SEQ_NAME' } } )
+    {
+        ( $index_beg, $index_len ) = @{ $index->{ $record->{ 'SEQ_NAME' } } };
+
+        $beg = $record->{ 'BEG' } || $options->{ 'beg' };
+        $end = $record->{ 'END' } || $options->{ 'end' };
+        $len = $record->{ 'LEN' } || $options->{ 'len' };
+
+        $seq = seq_get( $fh, $index_beg, $index_len, $beg, $end, $len );
+
+        if ( $seq )
+        {
+            $record->{ 'SEQ' }      = $seq;
+            $record->{ 'SEQ_LEN' }  = length $record->{ 'SEQ' };
+        }
+    }
+
+    Maasha::Biopieces::put_record( $record, $out );
+}
+
+close $fh;
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+sub seq_get
+{
+    # Martin A. Hansen, September 2009.
+    
+    # Adjust the index coordianates according to specified options,
+    # and retrieves the sequence thus specified. The sequence is
+    # returned.
+
+    my ( $fh,          # filehandle to sequence file
+         $index_beg,   # begin position of sequence entry
+         $index_len,   # length of sequence entry
+         $opt_beg,     # optional begin position - OPTIONAL
+         $opt_end,     # optional end position   - OPTIONAL
+         $opt_len,     # optional length         - OPTIONAL
+       ) = @_;
+
+    # Returns a string.
+
+    my ( $beg, $len, $seq );
+
+    $beg = $index_beg;
+    
+    if ( $opt_beg ) {
+        $beg += $opt_beg;
+    }
+
+    if ( $opt_len )
+    {
+        $len = $opt_len;
+    }
+    elsif ( $opt_end )
+    {
+        $len = $opt_end - $opt_beg;
+    }
+    else
+    {
+        $len = $index_len - $opt_beg;
+    }
+
+    if ( $len > $index_len - $opt_beg ) {
+        $len = $index_len - $opt_beg;
+    }
+
+    return if $beg > $index_beg + $index_len - 1 or $len <= 0;
+
+    $seq = Maasha::Filesys::file_read( $fh, $beg, $len );
+
+    return $seq;
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__

diff --git a/code_perl/Maasha/Filesys.pm b/code_perl/Maasha/Filesys.pm
index e8e40a703c762c58832b307e3f86e743dac83cc8..403306496955e9416fb6c1864f06dd0fb286b6a0 100644 (file)
--- a/code_perl/Maasha/Filesys.pm
+++ b/code_perl/Maasha/Filesys.pm
@@ -33,6 +33,7 @@ use warnings;
 use strict;
 use IO::File;
 use Storable;
+use Data::Dumper;
 use Maasha::Common;
 
 use Exporter;
@@ -302,7 +303,7 @@ sub file_size
 
     # returns integer
 
-    my $file_size = ( stat ( $path ) )[ 7 ];
+    my $file_size = -s $path;
 
     return $file_size;
 }