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revision 1.41, Wed Feb 28 22:33:17 2007 UTC revision 1.42, Sun Mar 18 17:25:19 2007 UTC
# Line 342  Line 342 
342      if ((! -s $kernel_file) && (! -s "$dir/built.ali") && (-s "$dir/PEGs.fasta"))      if ((! -s $kernel_file) && (! -s "$dir/built.ali") && (-s "$dir/PEGs.fasta"))
343      {      {
344          my $seqs    = &gjoseqlib::read_fasta("$dir/PEGs.fasta");          my $seqs    = &gjoseqlib::read_fasta("$dir/PEGs.fasta");
345          my $ali     = &PHOB::trimmed_aligned_kernel(seqs => $seqs, retrim => 1 );          my $ali     = &PHOB::trimmed_aligned_kernel(seqs => $seqs, retrim => 1, tmp => $FIG_Config::temp );
346          &gjoseqlib::print_alignment_as_fasta("$kernel_file",$ali);          &gjoseqlib::print_alignment_as_fasta("$kernel_file",$ali);
347      }      }
348    
# Line 693  Line 693 
693    
694      my $ln1 = length($seq);      my $ln1 = length($seq);
695      my $good = 0;      my $good = 0;
696        my $bad = 0;
697    
698      my $sims = [];      my $sims = [];
699      foreach $_ (@tmp)      foreach $_ (@tmp)
# Line 734  Line 735 
735                      my $bad_func = $bounds->[2] ? $fig->function_of($bounds->[2]) : "";                      my $bad_func = $bounds->[2] ? $fig->function_of($bounds->[2]) : "";
736                      if ($ENV{'DEBUG'}) { print STDERR "    no - $peg ",join(",",@$bounds)," $bad_func\n" }                      if ($ENV{'DEBUG'}) { print STDERR "    no - $peg ",join(",",@$bounds)," $bad_func\n" }
737                      ++$no;                      ++$no;
738                        if ($no > $yes) { $bad = 1 }
739                  }                  }
740              }              }
741          }          }
742      }      }
743        $good = ($good && (! $bad)) ? 1 : 0;
744      if ($ENV{'DEBUG'}) { print STDERR "        yes=$yes no=$no good=$good\n" }      if ($ENV{'DEBUG'}) { print STDERR "        yes=$yes no=$no good=$good\n" }
745      return ($good,$sims);      return ($good,$sims);
746  }  }

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