[Bioperl-guts-l] [15038] bioperl-live/trunk/t/cross_match.t: remove redundant copy

Christopher John Fields cjfields at dev.open-bio.org
Thu Nov 27 23:51:15 EST 2008


Revision: 15038
Author:   cjfields
Date:     2008-11-27 23:51:15 -0500 (Thu, 27 Nov 2008)

Log Message:
-----------
remove redundant copy

Removed Paths:
-------------
    bioperl-live/trunk/t/cross_match.t

Deleted: bioperl-live/trunk/t/cross_match.t
===================================================================
--- bioperl-live/trunk/t/cross_match.t	2008-11-28 04:50:18 UTC (rev 15037)
+++ bioperl-live/trunk/t/cross_match.t	2008-11-28 04:51:15 UTC (rev 15038)
@@ -1,62 +0,0 @@
-# -*-Perl-*- Test Harness script for Bioperl
-# $Id: cross_match.t 11788 2007-12-03 23:37:59Z jason $
-
-use strict;
-
-BEGIN {
-	use lib 't/lib';
-    use BioperlTest;
-    
-    test_begin(-tests => 15);
-	
-	use_ok('Bio::SearchIO');
-}
-
-my ($searchio, $result,$iter,$hit,$hsp);
-
-# The cross_match SearchIO parser is not event-based; it directly adds
-# information to the relevant Bio::Search objects as the report is parsed.
-# The parser currently misses much information present in the report. Also,
-# methods expected to work somehow don't (hsp->length('hsp'), for instance).
-# Unsure if this parses non-alignment-based cross-match reports accurately
-# (see bioperl-live/t/data/consed_project/edit_dir/test_project.screen.out for
-# an example).
-
-# Note lots of ResultI/HitI/HSPI methods not tested yet!
-
-$searchio = Bio::SearchIO->new('-format' => 'cross_match',
-				  '-file'   => test_input_file('testdata.crossmatch'));
-
-$result = $searchio->next_result;
-
-is($result->algorithm, 'cross_match');
-is($result->algorithm_version, '0.990329');
-
-my @valid = ( [ 'msx1_ens2', 0]);
-my $count = 0;
-while( $hit = $result->next_hit ) {
-    my $d = shift @valid;
-
-    is($hit->name, shift @$d);
-    is($hit->length, shift @$d);
-
-    if( $count == 0 ) {
-        my $hsps_left = 1;
-        while( my $hsp = $hit->next_hsp ) {
-            is($hsp->query->start, 19);
-            is($hsp->query->end, 603);
-            is($hsp->hit->start, 2824);
-            is($hsp->hit->end, 3409);
-            #is($hsp->length('hsp'), 820);  # shouldn't this work?
-            is($hsp->start('hit'), $hsp->hit->start);
-            is($hsp->end('query'), $hsp->query->end);
-            is($hsp->strand('sbjct'), $hsp->subject->strand);# alias for hit
-            is($hsp->gaps, 0);
-            $hsps_left--;
-        }
-        is($hsps_left, 0);
-    }
-    last if( $count++ > @valid );
-}
-
-is(@valid, 0);




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