[Bioperl-guts-l] [14988] bioperl-live/trunk/t/hmmer.t: corrected test to test the hmmer parser, not the hmmer_pull parser; test passes but generates big warning

Chris Fields cjfields at illinois.edu
Tue Nov 11 14:47:17 EST 2008


Thanks, my bad.  I'll look into the warning.

On Nov 11, 2008, at 1:45 PM, Senduran Balasubramaniam wrote:

> Revision: 14988
> Author:   sendu
> Date:     2008-11-11 14:45:12 -0500 (Tue, 11 Nov 2008)
>
> Log Message:
> -----------
> corrected test to test the hmmer parser, not the hmmer_pull parser;  
> test passes but generates big warning
>
> Modified Paths:
> --------------
>    bioperl-live/trunk/t/hmmer.t
>
> Modified: bioperl-live/trunk/t/hmmer.t
> ===================================================================
> --- bioperl-live/trunk/t/hmmer.t	2008-11-11 19:44:15 UTC (rev 14987)
> +++ bioperl-live/trunk/t/hmmer.t	2008-11-11 19:45:12 UTC (rev 14988)
> @@ -7,7 +7,7 @@
>     use lib 't/lib';
>     use BioperlTest;
>
> -    test_begin(-tests => 147);
> +    test_begin(-tests => 145);
> 	
> 	use_ok('Bio::SearchIO');
> 	use_ok('Bio::Tools::HMMER::Domain');
> @@ -266,25 +266,9 @@
> ok($res2);
> is($res2->number, 604);
>
> -# bug revealed by bug 2632 - CS lines were already ignored, but we  
> couldn't
> -# parse alignments when HSPs weren't in simple order!!
> -$searchio = Bio::SearchIO->new(-format => 'hmmer_pull', -file =>  
> test_input_file('hmmpfam_cs.out'), -verbose => 1);
> +# test for bug 2632 - CS lines should get ignored without breaking  
> the parser
> +$searchio = Bio::SearchIO->new(-format => 'hmmer', -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...
> -}
> -
> +is $hsp->seq_str, 'CGV- 
> GFIADVNNVANHKIVVQALEALTCMEHRGACSADRDSGDGAGITTAIPWNLFQKSLQNQNIKFEQnDSVGVGMLFLPAHKLKES--KLIIETVLKEENLEIIGWRLVPTVQEVLGKQAYLNKPHVEQVFCKSSNLSKDRLEQQLFLVRKKIEKYIGINGKDwaheFYICSLSCYTIVYKGMMRSAVLGQFYQDLYHSEYTSSFAIYHRRFSTNTMPKWPLAQPMR---------FVSHNGEINTLLGNLNWMQSREPLLQSKVWKDRIHELKPITNKDNSDSANLDAAVELLIASGRSPEEALMILVPEAFQNQPDFA-NNTEISDFYEYYSGLQEPWDGPALVVFTNGKV-IGATLDRNGL-RPARYVIT----KDNLVIVSSES';
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign






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