more read_ tools migrated

[biopieces.git] / bp_bin / read_embl

diff --git a/bp_bin/read_embl b/bp_bin/read_embl
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..e0ba8b76b98acb61a0d60e6d4a091a63625db64b 100755 (executable)
--- a/bp_bin/read_embl
+++ b/bp_bin/read_embl
@@ -1,6 +1,134 @@
-#!/usr/bin/env perl
+#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Read EMBL entries from one or more files.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
 
-use warnings;
 use strict;
+use Maasha::Biopieces;
+use Maasha::Filesys;
+use Maasha::EMBL;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, %options2, $file, $data_in, $num, $entry, $record );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'data_in', short => 'i', type => 'files!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'num',     short => 'n', type => 'uint',   mandatory => 'no', default => undef, allowed => undef, disallowed => '0' },
+        { long => 'keys',    short => 'k', type => 'list',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'feats',   short => 'f', type => 'list',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'quals',   short => 'q', type => 'list',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+map { $options2{ "keys" }{ $_ } = 1 }  @{ $options->{ "keys" } };
+map { $options2{ "feats" }{ $_ } = 1 } @{ $options->{ "feats" } };
+map { $options2{ "quals" }{ $_ } = 1 } @{ $options->{ "quals" } };
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) {
+    Maasha::Biopieces::put_record( $record, $out );
+}
+
+if ( $options->{ 'data_in' } )
+{
+    $data_in = Maasha::Filesys::files_read_open( $options->{ 'data_in' } );
+
+    $num = 1;
+
+    while ( $entry = Maasha::EMBL::get_embl_entry( $data_in ) ) 
+    {
+        $record = Maasha::EMBL::parse_embl_entry( $entry, \%options2 );
+
+        my ( $feat, $feat2, $qual, $qual_val, $record_copy );
+
+        $record_copy = dclone $record;
+
+        delete $record_copy->{ "FT" };
+
+        Maasha::Biopieces::put_record( $record_copy, $out );
+
+        delete $record_copy->{ "SEQ" };
+
+        foreach $feat ( keys %{ $record->{ "FT" } } )
+        {
+            $record_copy->{ "FEAT_TYPE" } = $feat;
+
+            foreach $feat2 ( @{ $record->{ "FT" }->{ $feat } } )
+            {
+                foreach $qual ( keys %{ $feat2 } )
+                {
+                    $qual_val = join "; ", @{ $feat2->{ $qual } };
+
+                    $qual =~ s/^_//;
+                    $qual = uc $qual;
+
+                    $record_copy->{ $qual } = $qual_val;
+                }
+
+                Maasha::Biopieces::put_record( $record_copy, $out );
+            }
+        }
+
+        last if $options->{ "num" } and $num == $options->{ "num" };
+
+        $num++;
+    }
+
+    close $data_in;
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    $run_time_beg = Maasha::Biopieces::run_time();
+
+    Maasha::Biopieces::log_biopiece();
+}
+
+END
+{
+    Maasha::Biopieces::close_stream( $in );
+    Maasha::Biopieces::close_stream( $out );
+
+    $run_time_end = Maasha::Biopieces::run_time();
+
+    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
 
-use Maasha::BioRun;
+__END__