[Bioperl-guts-l] bioperl-live/t SearchIO.t,1.86,1.87

Jason Stajich jason at pub.open-bio.org
Thu Jun 9 10:30:31 EDT 2005


Update of /home/repository/bioperl/bioperl-live/t
In directory pub.open-bio.org:/tmp/cvs-serv28207/t

Modified Files:
	SearchIO.t 
Log Message:
Bernd Brandt bug that webblast NCBI 2.2.10 does not have ':' after Query/Subject in alignment.  Tests and bugfix


Index: SearchIO.t
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/t/SearchIO.t,v
retrieving revision 1.86
retrieving revision 1.87
diff -C2 -d -r1.86 -r1.87
*** SearchIO.t	7 Sep 2004 17:47:30 -0000	1.86
--- SearchIO.t	9 Jun 2005 14:30:29 -0000	1.87
***************
*** 23,27 ****
      }
      use vars qw($NTESTS);
!     $NTESTS = 1216;
      $LASTXMLTEST = 63;
      $error = 0;
--- 23,27 ----
      }
      use vars qw($NTESTS);
!     $NTESTS = 1223;
      $LASTXMLTEST = 63;
      $error = 0;
***************
*** 1642,1646 ****
  $searchio = Bio::SearchIO->new(-format => 'blast',
  			       -file   => Bio::Root::IO->catfile
! 			       ((qw(t data brassica_ATH.WUBLASTN) )));
  ok($result = $searchio->next_result);
  ok($hit = $result->next_hit);
--- 1642,1646 ----
  $searchio = Bio::SearchIO->new(-format => 'blast',
  			       -file   => Bio::Root::IO->catfile
! 			       (qw(t data brassica_ATH.WUBLASTN) ));
  ok($result = $searchio->next_result);
  ok($hit = $result->next_hit);
***************
*** 1650,1653 ****
--- 1650,1669 ----
  ok($hsp->hit->strand, 1);
  ok($hsp->hsp_group, '1');
+ 
+ 
+ 
+ ## Web blast result parsing
+ 
+ $searchio = Bio::SearchIO->new(-format => 'blast',
+ 			       -file   => Bio::Root::IO->catfile
+ 			       (qw(t data catalase-webblast.BLASTP)));
+ ok($result = $searchio->next_result);
+ ok($hit = $result->next_hit);
+ ok($hit->name, 'gi|40747822|gb|EAA66978.1|', 'full hit name');
+ ok($hit->accession, 'EAA66978', 'hit accession');
+ ok($hsp = $hit->next_hsp);
+ ok($hsp->query->start, 1, 'query start');
+ ok($hsp->query->end, 528, 'query start');
+ 
  
  # some utilities



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