[Bioperl-guts-l] [14786] bioperl-live/trunk/Bio/SearchIO/blasttable.pm: Previous changes killed RemoteBlast again; make a little more bulletproof

[Christopher John Fields]

Revision: 14786
Author:   cjfields
Date:     2008-08-05 18:00:00 -0400 (Tue, 05 Aug 2008)

Log Message:
-----------
Previous changes killed RemoteBlast again; make a little more bulletproof

Modified Paths:
--------------
    bioperl-live/trunk/Bio/SearchIO/blasttable.pm

Modified: bioperl-live/trunk/Bio/SearchIO/blasttable.pm
===================================================================
--- bioperl-live/trunk/Bio/SearchIO/blasttable.pm	2008-08-05 01:17:28 UTC (rev 14785)
+++ bioperl-live/trunk/Bio/SearchIO/blasttable.pm	2008-08-05 22:00:00 UTC (rev 14786)
@@ -162,8 +162,6 @@
    local $_;
    my ($alg, $ver);
    while( defined ($_ = $self->_readline) ) {
-      # skip any HTML cruft (e.g. from RemoteBlast)
-      next if (m{^<\/?PRE>});
 	  # WU-BLAST -mformat 3 only
 	  if(m{^#\s((?:\S+?)?BLAST[NPX])\s(\d+\.\d+.+\d{4}\])}) {
             ($alg, $ver) = ($1, $2);
@@ -183,6 +181,7 @@
        next if /^#/ || /^\s*$/;
 
 	  my @fields = split;
+      next if @fields == 1;
 	  my ($qname,$hname, $percent_id, $hsp_len, $mismatches,$gapsm,
 	      $qstart,$qend,$hstart,$hend,$evalue,$bits);
 	  # WU-BLAST-specific
@@ -207,9 +206,6 @@
 	      # we need total gaps in the alignment
 	      $gapsm=$qgaps+$sgaps;
 	  }
-	  else {
-            $self->throw("Unknown BLAST tabular format");
-      }
 
        # Remember Jim's code is 0 based
        if( defined $lastquery &&