added Bowtie.pm

git-svn-id: http://biopieces.googlecode.com/svn/trunk@586 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_perl/Maasha/Bowtie.pm b/code_perl/Maasha/Bowtie.pm
new file mode 100644 (file)
index 0000000..fce2fbf
--- /dev/null
+++ b/code_perl/Maasha/Bowtie.pm
@@ -0,0 +1,69 @@
+package Maasha::Bowtie;
+
+# Copyright (C) 2006-2009 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 for manipulation of bowtie indexes and results.
+
+# http://bowtie-bio.sourceforge.net/index.shtml
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Data::Dumper;
+use vars qw( @ISA @EXPORT );
+
+@ISA = qw( Exporter );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+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" );
+    }
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+1;