[Bioperl-guts-l] bioperl commit

Brian Osborne bosborne at pub.open-bio.org
Fri Jul 23 20:52:37 EDT 2004


bosborne
Fri Jul 23 20:52:37 EDT 2004
Update of /home/repository/bioperl/bioperl-live
In directory pub.open-bio.org:/tmp/cvs-serv20291

Modified Files:
	FAQ 
Log Message:
Remove 7

bioperl-live FAQ,1.47,1.48
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/FAQ,v
retrieving revision 1.47
retrieving revision 1.48
diff -u -r1.47 -r1.48
--- /home/repository/bioperl/bioperl-live/FAQ	2004/06/02 19:32:21	1.47
+++ /home/repository/bioperl/bioperl-live/FAQ	2004/07/24 00:52:37	1.48
@@ -67,8 +67,7 @@
 	 according to Blast?
    Q3.6: How do I tell BLAST to search multiple database using
 	 Bio::Tools::Run::StandAloneBlast?
-   Q3.7: Does SearchIO parse the HTML output file that BLAST can create?
-   Q3.8: Can I get domain number from hmmpfam or hmmsearch output? E.g.
+   Q3.7: Can I get domain number from hmmpfam or hmmsearch output? E.g.
 		   SH2_5: domain 2 of 2, from 349 to 432: score 104.4, E =
 	 1.9e-26
 
@@ -588,34 +587,7 @@
 		   $factory->blastall($seqobj);
 
 
-   Q3.7: Does SearchIO parse the HTML output file that BLAST can create?
-
-      A: Yes, with a twist. You can modify SearchIO's _readline() method
-	 such that it reads in the HTML and strips it of tags using the
-	 StripHTML module:
-
-	 
-		   use Bio::SearchIO;
-		   use Bio::SearchIO::blast;
-		   use HTML::Strip;
-		   
-		   my $hs = new HTML::Strip;
-		   
-		   # replace the blast parser's _readline method with one
-	 that
-		   # auto-strips HTML:
-		   
-		   sub Bio::SearchIO::blast::_readline {
-		     my ($self, @args) = @_;
-		     return $hs->parse($self->SUPER::_readline(@args));
-		   }
-		   
-		   $io = new Bio::SearchIO(-file => "etc.bls", -format =>
-	 "blast");
-		   # etc ...
-
-
-   Q3.8: Can I get domain number from hmmpfam or hmmsearch output? E.g.
+   Q3.7: Can I get domain number from hmmpfam or hmmsearch output? E.g.
 		   SH2_5: domain 2 of 2, from 349 to 432: score 104.4, E =
 	 1.9e-26
 



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