[Bioperl-guts-l] [14985] bioperl-live/trunk/t/hmmer.t: [bug 2632]

Christopher John Fields cjfields at dev.open-bio.org
Tue Nov 11 14:21:45 EST 2008


Revision: 14985
Author:   cjfields
Date:     2008-11-11 14:21:45 -0500 (Tue, 11 Nov 2008)

Log Message:
-----------
[bug 2632]
* added tests for plain ol' hmmer parsing

Modified Paths:
--------------
    bioperl-live/trunk/t/hmmer.t

Modified: bioperl-live/trunk/t/hmmer.t
===================================================================
--- bioperl-live/trunk/t/hmmer.t	2008-11-11 18:39:20 UTC (rev 14984)
+++ bioperl-live/trunk/t/hmmer.t	2008-11-11 19:21:45 UTC (rev 14985)
@@ -7,7 +7,7 @@
     use lib 't/lib';
     use BioperlTest;
     
-    test_begin(-tests => 144);
+    test_begin(-tests => 147);
 	
 	use_ok('Bio::SearchIO');
 	use_ok('Bio::Tools::HMMER::Domain');
@@ -266,5 +266,25 @@
 ok($res2);
 is($res2->number, 604);
 
-# now let's test the new Bio::SearchIO::hmmer (I believe this is in SearchIO.t)
+# bug revealed by bug 2632 - CS lines were already ignored, but we couldn't
+# parse alignments when HSPs weren't in simple order!!
+$searchio = Bio::SearchIO->new(-format => 'hmmer_pull', -file => test_input_file('hmmpfam_cs.out'), -verbose => 1);
+my $result = $searchio->next_result;
+my $hit = $result->next_hit;
+my $hsp = $hit->next_hsp;
+is $hsp->seq_str, "IPPLLAVGAVHHHLINKGLRQEASILV";
 
+# and another bug revealed: we don't always know the hit length, and
+# shouldn't complain about that with a warning
+is $hsp->hit->seqlength, 412;
+
+my $count = 0;
+while (my $hit = $result->next_hit) {
+    $count++;
+    next if $count < 6;
+    last if $count > 6;
+	my $hsp = $hit->next_hsp;
+    ok ! $hsp->hit->seqlength;
+    #*** not sure how to test for the lack of a warning though...
+}
+




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