From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Sat, 17 Oct 2009 10:58:15 +0000 (+0000)
Subject: renaming create_blast_db to create_blast_index
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=6dfdfff30637a46f706b95bd4b094bdbd76fe2ca;p=biopieces.git

renaming create_blast_db to create_blast_index

git-svn-id: http://biopieces.googlecode.com/svn/trunk@694 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/create_blast_db b/bp_bin/create_blast_db
deleted file mode 100755
index 6cbd2bf..0000000
--- a/bp_bin/create_blast_db
+++ /dev/null
@@ -1,119 +0,0 @@
-#!/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 BLAST database from sequences in stream for use with [blast_seq].
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-use warnings;
-use strict;
-use Maasha::Seq;
-use Maasha::Fasta;
-use Maasha::Biopieces;
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-my ( $options, $in, $out, $record, $tmp_dir, $file_tmp, $fh_tmp, $entry, $seq_type, $arg );
-
-$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 },
-    ]   
-);
-
-$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/$options->{ 'index_name' }";
-$fh_tmp   = Maasha::Filesys::file_write_open( $file_tmp );
-
-while ( $record = Maasha::Biopieces::get_record( $in ) ) 
-{
-    if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) )
-    {
-        $seq_type = Maasha::Seq::seq_guess_type( $record->{ 'SEQ' } ) if not $seq_type;
-
-        Maasha::Fasta::put_entry( $entry, $fh_tmp );
-    }
-
-    Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
-}
-
-close $fh_tmp;
-
-$arg = "-t $options->{ 'index_name' }";
-
-if ( $seq_type eq "protein" ) {
-    $arg .= " -p T";
-} else {
-    $arg .= " -p F";
-}
-
-$arg .= " -i $file_tmp";
-
-if ( $options->{ 'verbose' } )
-{
-    print STDERR "Running: formatdb $arg\n";
-
-    Maasha::Common::run( "formatdb", "$arg" );
-}
-else
-{
-    Maasha::Common::run( "formatdb", "$arg -l /dev/null" );
-}
-
-Maasha::Filesys::dir_create( $options->{ 'directory' } );
-
-unlink $file_tmp;
-
-system( "cp $tmp_dir/* $options->{ 'directory' }" );
-
-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/create_blast_index b/bp_bin/create_blast_index
new file mode 100755
index 0000000..6cbd2bf
--- /dev/null
+++ b/bp_bin/create_blast_index
@@ -0,0 +1,119 @@
+#!/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 BLAST database from sequences in stream for use with [blast_seq].
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Maasha::Seq;
+use Maasha::Fasta;
+use Maasha::Biopieces;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $tmp_dir, $file_tmp, $fh_tmp, $entry, $seq_type, $arg );
+
+$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 },
+    ]   
+);
+
+$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/$options->{ 'index_name' }";
+$fh_tmp   = Maasha::Filesys::file_write_open( $file_tmp );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+{
+    if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) )
+    {
+        $seq_type = Maasha::Seq::seq_guess_type( $record->{ 'SEQ' } ) if not $seq_type;
+
+        Maasha::Fasta::put_entry( $entry, $fh_tmp );
+    }
+
+    Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
+}
+
+close $fh_tmp;
+
+$arg = "-t $options->{ 'index_name' }";
+
+if ( $seq_type eq "protein" ) {
+    $arg .= " -p T";
+} else {
+    $arg .= " -p F";
+}
+
+$arg .= " -i $file_tmp";
+
+if ( $options->{ 'verbose' } )
+{
+    print STDERR "Running: formatdb $arg\n";
+
+    Maasha::Common::run( "formatdb", "$arg" );
+}
+else
+{
+    Maasha::Common::run( "formatdb", "$arg -l /dev/null" );
+}
+
+Maasha::Filesys::dir_create( $options->{ 'directory' } );
+
+unlink $file_tmp;
+
+system( "cp $tmp_dir/* $options->{ 'directory' }" );
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__