fuckup

git-svn-id: http://biopieces.googlecode.com/svn/trunk@660 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/create_bwa_index b/bp_bin/create_bwa_index
new file mode 100755 (executable)
index 0000000..9ccb0e4
--- /dev/null
+++ b/bp_bin/create_bwa_index
@@ -0,0 +1,104 @@
+#!/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 BWA index from sequences in stream for use with [bwa_seq].
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Maasha::Common;
+use Maasha::Biopieces;
+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 => 'directory',  short => 'd', type => 'dir',    mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+        { long => 'index_name', short => 'i', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+    ]   
+);
+
+Maasha::Common::error( qq(Directory already exists: "$options->{ 'directory' }") ) if -d $options->{ 'directory' };
+
+Maasha::Filesys::dir_create_if_not_exists( $options->{ 'directory' } );
+
+$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_bwa_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::Filesys::dir_create_if_not_exists( $options->{ 'directory' } );
+
+if ( $options->{ 'verbose' } ) {
+    Maasha::Common::run( "bwa", "index -p $options->{ 'directory' }/$options->{ 'index_name' } $file_tmp" );
+} else {
+    Maasha::Common::run( "bwa", "index -p $options->{ 'directory' }/$options->{ 'index_name' } $file_tmp > /dev/null 2>&1" );
+}
+
+unlink $file_tmp;
+
+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/Bowtie.pm b/code_perl/Maasha/Bowtie.pm
deleted file mode 100644 (file)
index fce2fbf..0000000
--- a/code_perl/Maasha/Bowtie.pm
+++ /dev/null
@@ -1,69 +0,0 @@
-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;