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revision 1.1, Fri Dec 15 00:09:52 2006 UTC revision 1.2, Fri Dec 15 00:46:54 2006 UTC
# Line 24  Line 24 
24  # end of tool_hdr  # end of tool_hdr
25  ########################################################################  ########################################################################
26    
27    
28  use FIG;  use FIG;
29  use InsertIntoTree;  use InsertIntoTree;
30  use strict;  use strict;
# Line 31  Line 32 
32  use gjoseqlib;  use gjoseqlib;
33  use gjonewicklib;  use gjonewicklib;
34    
35  my $usage = "usage: insert_into_a_tree Alignment Tree [TreeProg] > new.tree\n";  my $usage = "usage: insert_into_a_tree [-c CheckPointFile] Alignment Tree [TreeProg] > new.tree\n";
36    
37    my $check_point = undef;
38    while ($ARGV[0] =~ /^-/)
39    {
40        my $flag = shift @ARGV;
41        if ( $flag =~ /^-c/ )
42        {
43            $check_point = shift @ARGV;
44        }
45        else
46        {
47            die "Error: invalid flag $flag\n$usage"
48        }
49    }
50    
51  my($aliF,$treeF);  my($aliF,$treeF);
52  (  (
# Line 45  Line 60 
60  my $ali  = &gjoseqlib::read_fasta($aliF);  my $ali  = &gjoseqlib::read_fasta($aliF);
61  my $tree = &gjonewicklib::parse_newick_tree_str(join("",`cat $treeF`));  my $tree = &gjonewicklib::parse_newick_tree_str(join("",`cat $treeF`));
62    
63  my $new_tree = &InsertIntoTree::update_old_tree_using_new_ali($ali,$tree,$tree_prog);  my $new_tree = &InsertIntoTree::update_old_tree_using_new_ali( align => $ali,
64                                                                   tree => $tree,
65                                                                   tree_prog => $tree_prog,
66                                                                   check_point => $check_point
67                                                                 );
68  &gjonewicklib::writeNewickTree($new_tree);  &gjonewicklib::writeNewickTree($new_tree);
69    

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