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revision 1.1, Tue Apr 5 18:30:12 2005 UTC revision 1.2, Tue Apr 12 21:25:21 2005 UTC
# Line 1  Line 1 
1    
2  &make_sure("clustalw","protdist","clustal_to_fasta","fasta_to_phylip","trim_sequences");  &make_sure("clustalw","protdist","clustal_to_fasta","fasta_to_phylip","trim_sequences","fitch");
3    
4  $usage = "usage: make_phob_from_seqs Directory [-trim] < Seqs";  $usage = "usage: make_phob_from_seqs Directory [-trim] < Seqs";
5    
# Line 37  Line 37 
37  if ($trim)  if ($trim)
38  {  {
39      rename("$puD/seqs.fasta","$puD/seqs.untrimmed");      rename("$puD/seqs.fasta","$puD/seqs.untrimmed");
40      &run("trim_sequences < \"$puD/seqs.untrimmed\" > \"$puD/seqs.fasta\"");      &run("trim_sequences 1.0e-5 0.8 < \"$puD/seqs.untrimmed\" > \"$puD/seqs.fasta\"");
41  }  }
42    
43  chdir $puD;  chdir $puD;
# Line 51  Line 51 
51  open(PROTDIST,"| protdist > /dev/null") || die "could not open protdist";  open(PROTDIST,"| protdist > /dev/null") || die "could not open protdist";
52  print PROTDIST "Y\n";  print PROTDIST "Y\n";
53  close(PROTDIST);  close(PROTDIST);
54    &run("cp outfile distance.matrix");
55    rename("outfile","infile");
56    
57    open(FITCH,"| fitch > /dev/null") || die "could not open fitch";
58    print FITCH "Y\n";
59    close(FITCH);
60    rename("outtree","tree.dnd");
61    
 rename("outfile","distance.matrix");  
62  unlink("infile");  unlink("infile");
63    
64  if (! ((-s "distance.matrix") && (-s "aln.fasta") && (-s "tree.dnd")))  if (! ((-s "distance.matrix") && (-s "aln.fasta") && (-s "tree.dnd")))

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