diff variant_effect_predictor/Bio/SearchIO/chadosxpr.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/SearchIO/chadosxpr.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,78 @@
+# $Id: chadosxpr.pm,v 1.2 2002/12/05 13:46:35 heikki Exp $
+#
+# BioPerl module for Bio::SearchIO::chadosxpr
+#
+# Chris Mungall <[e-mail]>
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::SearchIO::chadosxpr - chadosxpr sequence input/output stream
+
+=head1 SYNOPSIS
+
+It is probably best not to use this object directly, but
+rather go through the SearchIO handler system. Go:
+
+    $stream = Bio::SearchIO->new(-file => $filename, -format => 'chadosxpr');
+
+    while ( my $seq = $stream->next_seq() ) {
+	# do something with $seq
+    }
+
+=head1 DESCRIPTION
+
+This object can transform Bio::Search objects to and from chadosxpr flat
+file databases. CURRENTLY ONLY TO
+
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this
+and other Bioperl modules. Send your comments and suggestions preferably
+ to one of the Bioperl mailing lists.
+Your participation is much appreciated.
+
+  [e-mail]                  - General discussion
+  http://www.bioperl.org/MailList.shtml  - About the mailing lists
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+ the bugs and their resolution.
+ Bug reports can be submitted via email or the web:
+
+  [e-mail]
+  http://bio.perl.org/bioperl-bugs/
+
+=head1 AUTHOR - Chris Mungall
+
+Email [e-mail]
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
+
+=cut
+
+# Let the code begin...
+
+package Bio::SearchIO::chadosxpr;
+use Bio::SearchIO::chado;
+use vars qw(@ISA);
+use strict;
+
+use Data::Stag::SxprWriter;
+
+@ISA = qw(Bio::SearchIO::chado);
+
+sub default_handler_class {
+    return "Data::Stag::SxprWriter";
+} 
+
+1;