rewrote bioscript

git-svn-id: http://biopieces.googlecode.com/svn/trunk@514 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/bioscript b/bp_bin/bioscript
new file mode 100755 (executable)
index 0000000..efc8b93
--- /dev/null
+++ b/bp_bin/bioscript
@@ -0,0 +1,76 @@
+#!/usr/bin/env perl -w
+
+# 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Enable Perl scripting on the data stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use strict;
+use Maasha::Biopieces qw( get_record put_record );
+use Maasha::Common;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $r );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'eval', short => 'e', 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" } );
+
+print STDERR "eval: $options->{ 'eval' }\n" if $options->{ 'verbose' };
+
+eval "$options->{ 'eval' }";
+
+Maasha::Common::error( qq(Eval of "$options->{ 'eval' }" failed) ) if $@;
+
+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_conf/bashrc b/bp_conf/bashrc
index 473e0c5fc8e03023252c29371286bd877c74acd0..a8a89b135ccc92bf329e7c4812cae84bbe047c83 100644 (file)
--- a/bp_conf/bashrc
+++ b/bp_conf/bashrc
@@ -12,7 +12,7 @@ export BP_BIN="$BP_DIR/bp_bin"              # Directory with biopiece executable
 ### The following directories hold the biopiece libraries, modules, gems, etc - one per programming language.
 
 export BP_PERL="$BP_DIR/code_perl"          # Direcotry with Perl code.
-export BP_C="$BP_DIR/code_c"                # Direcotry with c code.
+export BP_C="$BP_DIR/code_c"                # Direcotry with C code.
 export BP_PYTHON="$BP_DIR/code_python"      # Direcotry with Pyton code.
 export BP_RUBY="$BP_DIR/code_ruby"          # Direcotry with Ruby code.
 
@@ -28,11 +28,6 @@ export PERL5LIB="$PERL5LIB:$BP_PERL"
 
 export RUBYLIB="$RUBYLIB:$BP_RUBY"
 
-### Alias allowing power scripting with biopieces.
-
-alias bioscript="perl -MMaasha::Biopieces=read_stream,get_record,put_record -e"
-
-
 ### >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<