X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fsplit_bed;h=bd708a4d20a341c3f5515a6e3d6d99ebd42fc540;hb=5de6112b70b59420b245ce636a8b2e3c90acbe00;hp=89c57253da25b05ce1722b3a6e049cab715af5d6;hpb=f7e5c1b54c562cc1b25fe419cacd4da9ac01f129;p=biopieces.git

diff --git a/bp_bin/split_bed b/bp_bin/split_bed
deleted file mode 120000
index 89c5725..0000000
--- a/bp_bin/split_bed
+++ /dev/null
@@ -1 +0,0 @@
-../code_perl/Maasha/bin/split_bed
\ No newline at end of file
diff --git a/bp_bin/split_bed b/bp_bin/split_bed
new file mode 100755
index 0000000..bd708a4
--- /dev/null
+++ b/bp_bin/split_bed
@@ -0,0 +1,97 @@
+#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Split BED entries into overlapping windows.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Maasha::Biopieces;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $new_record, $i );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'window_size', short => 'w', type => 'uint', mandatory => 'no', default => 20, allowed => undef, disallowed => 0 },
+        { long => 'step_size',   short => 's', type => 'uint', mandatory => 'no', default => 1,  allowed => undef, disallowed => 0 },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+{
+    if ( $record->{ "CHR" } and $record->{ "CHR_BEG" } and $record->{ "CHR_END" } )
+    {
+        $record->{ "BED_LEN" } = $record->{ "CHR_END" } - $record->{ "CHR_BEG" } + 1;
+
+        for ( $i = 0; $i < $record->{ "BED_LEN" } - $options->{ "window_size" }; $i += $options->{ "step_size" } )
+        {
+            $new_record->{ "REC_TYPE" } = "BED";
+            $new_record->{ "CHR" }      = $record->{ "CHR" };
+            $new_record->{ "CHR_BEG" }  = $record->{ "CHR_BEG" } + $i;
+            $new_record->{ "CHR_END" }  = $record->{ "CHR_BEG" } + $i + $options->{ "window_size" };
+            $new_record->{ "BED_LEN" }  = $options->{ "window_size" };
+            $new_record->{ "Q_ID" }     = $record->{ "Q_ID" } . "_$i";
+            $new_record->{ "SCORE" }    = $record->{ "SCORE" };
+            $new_record->{ "STRAND" }   = $record->{ "STRAND" };
+
+            Maasha::Biopieces::put_record( $new_record, $out );
+        }
+    }
+    else
+    {
+        Maasha::Biopieces::put_record( $record, $out );
+    }
+}
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__