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revision 1.7, Fri Jan 21 14:57:40 2011 UTC revision 1.8, Thu Jun 30 13:10:02 2011 UTC
# Line 478  Line 478 
478          &log($tmpD, $msg)    if $ENV{VERBOSE};          &log($tmpD, $msg)    if $ENV{VERBOSE};
479      }      }
480    
481      $domain  = substr($domain, 0, 1) || $tmp;      $domain  = $domain  ? substr($domain, 0, 1) : $tmp;
482      $genus   = quotemeta($genus)     || q(Unknown);      $genus   = $genus   ? quotemeta($genus)     : q(Unknown);
483      $species = quotemeta($species)   || q(sp.);      $species = $species ? quotemeta($species)   : q(sp.);
484    
485      my $contigs_fh;      my $contigs_fh;
486      my $contigs_file = qq($tmpD/contigs);      my $contigs_file = qq($tmpD/contigs);
# Line 989  Line 989 
989      close(TMP);      close(TMP);
990      print STDERR (@out, qq(\n)) if $ENV{VERBOSE};      print STDERR (@out, qq(\n)) if $ENV{VERBOSE};
991    
992        if (@out) {
993      my ($closest, $genus, $species) = ($out[0] =~ m/^(\S+)\t\d+\t(\S+)\s+(\S+)/o);      my ($closest, $genus, $species) = ($out[0] =~ m/^(\S+)\t\d+\t(\S+)\s+(\S+)/o);
994      my $result = $sapO->genome_domain(-ids => [$closest]);      my $result = $sapO->genome_domain(-ids => [$closest]);
995      my $domain = $result->{$closest};      my $domain = $result->{$closest};
   
996      return ($domain, $genus, $species);      return ($domain, $genus, $species);
997  }  }
998    
999        return ();
1000    }
1001    
1002    
1003    
1004  sub correct_frameshifts {  sub correct_frameshifts {

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