added create_bowtie_index

git-svn-id: http://biopieces.googlecode.com/svn/trunk@584 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/bowtie_seq b/bp_bin/bowtie_seq
index aedf02ad3edce43918f4eb460846e9407060f98e..f7229f106fba9abe71105bd6adca0758237c9848 100755 (executable)
--- a/bp_bin/bowtie_seq
+++ b/bp_bin/bowtie_seq
@@ -42,18 +42,26 @@ my ( $options, $in, $out, $index, $tmp_dir, $tmp_in, $tmp_out, $fh_in, $fh_out,
 
 $options = Maasha::Biopieces::parse_options(
     [
-        { long => 'genome',      short => 'g', type => 'genome', mandatory => 'yes', default => undef, allowed => undef,     disallowed => undef },
-        { long => 'mismatches',  short => 'm', type => 'uint',   mandatory => 'no',  default => 0,     allowed => "0,1,2,3", disallowed => undef },
-        { long => 'max_hits',    short => 'h', type => 'uint',   mandatory => 'no',  default => undef, allowed => undef,     disallowed => 0     },
-        { long => 'seed_length', short => 's', type => 'uint',   mandatory => 'no',  default => 28,    allowed => undef,     disallowed => 0     },
-        { long => 'cpus',        short => 'c', type => 'uint',   mandatory => 'no',  default => 1,     allowed => undef,     disallowed => 0     },
+        { long => 'genome',      short => 'g', type => 'genome', mandatory => 'no', default => undef, allowed => undef,     disallowed => undef },
+        { long => 'index_name',  short => 'i', type => 'string', mandatory => 'no', default => undef, allowed => undef,     disallowed => undef },
+        { long => 'mismatches',  short => 'm', type => 'uint',   mandatory => 'no', default => 0,     allowed => "0,1,2,3", disallowed => undef },
+        { long => 'max_hits',    short => 'h', type => 'uint',   mandatory => 'no', default => undef, allowed => undef,     disallowed => 0     },
+        { long => 'seed_length', short => 's', type => 'uint',   mandatory => 'no', default => 28,    allowed => undef,     disallowed => 0     },
+        { long => 'cpus',        short => 'c', type => 'uint',   mandatory => 'no', default => 1,     allowed => undef,     disallowed => 0     },
     ]   
 );
 
+Maasha::Common::error( qq(both --index_hame and --genome specified) ) if     $options->{ "genome" } and     $options->{ "index_name" };
+Maasha::Common::error( qq(no --index_name or --genome specified) )    if not $options->{ "genome" } and not $options->{ "index_name" };
+
 $in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
 
-$index = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/bowtie/$options->{ 'genome' }";
+if ( defined $options->{ 'genome' } ) {
+    $index = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/bowtie/$options->{ 'genome' }";
+} elsif (defined $options->{ 'index_name' } ) {
+    $index = $options->{ 'index_name' };
+}
 
 $tmp_dir = Maasha::Biopieces::get_tmpdir();
 $tmp_in  = "$tmp_dir/bowtie.seq";

diff --git a/bp_bin/create_bowtie_index b/bp_bin/create_bowtie_index
new file mode 100755 (executable)
index 0000000..b8949ea
--- /dev/null
+++ b/bp_bin/create_bowtie_index
@@ -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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Create a Bowtie index from sequences in stream for use with [bowtie_seq].
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Maasha::Common;
+use Maasha::Biopieces;
+use Maasha::Bowtie;
+use Maasha::Filesys;
+use Maasha::Fasta;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $default, $formats, $options, $in, $out, $record, $tmp_dir, $file_tmp, $fh_tmp, $entry );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'no_stream',  short => 'x', type => 'flag',   mandatory => 'no',  default => undef, allowed => undef, disallowed => undef },
+        { long => 'index_name', short => 'i', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+    ]   
+);
+
+Maasha::Common::error( qw(directory already exists: "$options->{ 'index_name' }") ) if -d $options->{ 'index_name' };
+
+Maasha::Filesys::dir_create_if_not_exists( $options->{ 'index_name' } );
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$tmp_dir  = Maasha::Biopieces::get_tmpdir();
+$file_tmp = "$tmp_dir/create_bowtie_index.seq";
+$fh_tmp   = Maasha::Filesys::file_write_open( $file_tmp );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+{
+    if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) ) {
+        Maasha::Fasta::put_entry( $entry, $fh_tmp );
+    }
+
+    Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
+}
+
+close $fh_tmp;
+
+Maasha::Bowtie::bowtie_index( $file_tmp, $options->{ 'index_name' }, $options->{ 'index_name' }, $options->{ 'verbose' } );
+
+unlink $file_tmp;
+
+Maasha::Filesys::dir_remove( $tmp_dir );
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__

diff --git a/bp_bin/format_genome b/bp_bin/format_genome
index 9972bf547f20038b4862898c650923c39a7b8a1a..af7de5c4ca25f3e18f5a64eeb85baff16a554055 100755 (executable)
--- a/bp_bin/format_genome
+++ b/bp_bin/format_genome
@@ -30,6 +30,7 @@ use warnings;
 use strict;
 use Maasha::Fasta;
 use Maasha::Biopieces;
+use Maasha::Bowtie;
 use Maasha::NCBI;
 use Maasha::Match;
 use Maasha::UCSC;
@@ -115,7 +116,7 @@ foreach $format ( @{ $options->{ 'formats' } } )
     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 ) }
-    elsif ( $format =~ /^bowtie$/i )    { bowtie_index( "$fasta_dir/$genome.fna", "$dir/genomes/$genome/bowtie", $genome, $options->{ 'verbose' } ) }
+    elsif ( $format =~ /^bowtie$/i )    { Maasha::Bowtie::bowtie_index( "$fasta_dir/$genome.fna", "$dir/genomes/$genome/bowtie", $genome, $options->{ 'verbose' } ) }
     elsif ( $format =~ /^phastcons$/i ) { Maasha::UCSC::phastcons_index( "$genome.pp", $phastcons_dir ) }
 
     print STDERR qq(done.\n) if $options->{ 'verbose' };
@@ -127,31 +128,6 @@ Maasha::Biopieces::close_stream( $in );
 Maasha::Biopieces::close_stream( $out );
 
 
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-sub bowtie_index
-{
-    # Martin A. Hansen, July 2009.
-    
-    # Create a bowtie index for fast sequence mapping.
-
-    my ( $src_file,   # filename of source file
-         $dst_dir,    # destination dir to store index
-         $base_name,  # base name of index
-         $verbose,    # verbose flag
-       ) = @_;
-
-    Maasha::Filesys::dir_create_if_not_exists( $dst_dir );
-
-    if ( $verbose ) {
-        Maasha::Common::run( "bowtie-build", "$src_file $dst_dir/$base_name" );
-    } else {
-        Maasha::Common::run( "bowtie-build", "$src_file $dst_dir/$base_name > /dev/null 2>&1" );
-    }
-}
-
-
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<