fixed seq qual length check

[biopieces.git] / bp_bin / analyze_tags

diff --git a/bp_bin/analyze_tags b/bp_bin/analyze_tags
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..181beb501b13b3b72b01a73e128144051419547c 100755 (executable)
--- a/bp_bin/analyze_tags
+++ b/bp_bin/analyze_tags
@@ -1,6 +1,100 @@
 #!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Analyze sequence tags in sequence or BED records from the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
 use warnings;
 use strict;
+use Maasha::Biopieces;
+use Maasha::Seq;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, %len_hash, %clone_hash, $clones, $key, $tag_record );
+
+$options = Maasha::Biopieces::parse_options();
+
+$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->{ "SEQ_NAME" } and $record->{ "SEQ" } )
+    {
+        if ( $record->{ "SEQ_NAME" } =~ /_(\d+)$/ )
+        {
+            $clones = $1;
+
+            $len_hash{ length( $record->{ "SEQ" } ) }++;
+            $clone_hash{ length( $record->{ "SEQ" } ) } += $clones;
+        }
+    }
+    elsif ( $record->{ "Q_ID" } and $record->{ "BED_LEN" } )
+    {
+        if ( $record->{ "Q_ID" } =~ /_(\d+)$/ )
+        {
+            $clones = $1;
+
+            $len_hash{ $record->{ "BED_LEN" } }++;
+            $clone_hash{ $record->{ "BED_LEN" } } += $clones;
+        }
+    }
+}
+
+foreach $key ( sort { $a <=> $b } keys %len_hash )
+{
+    $tag_record->{ "TAG_LEN" }    = $key;
+    $tag_record->{ "TAG_COUNT" }  = $len_hash{ $key };
+    $tag_record->{ "TAG_CLONES" } = $clone_hash{ $key };
+
+    Maasha::Biopieces::put_record( $tag_record, $out );
+}
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
 
-use Maasha::BioRun;
+__END__