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Revision 1.2 - (download) (as text) (annotate)
Thu Oct 28 13:13:54 2010 UTC (9 years, 5 months ago) by fangfang
Branch: MAIN
Changes since 1.1: +0 -1 lines
remove dependency

#
# This is a SAS Component
#

#
# Copyright (c) 2003-2006 University of Chicago and Fellowship
# for Interpretations of Genomes. All Rights Reserved.
#
# This file is part of the SEED Toolkit.
#
# The SEED Toolkit is free software. You can redistribute
# it and/or modify it under the terms of the SEED Toolkit
# Public License.
#
# You should have received a copy of the SEED Toolkit Public License
# along with this program; if not write to the University of Chicago
# at info@ci.uchicago.edu or the Fellowship for Interpretation of
# Genomes at veronika@thefig.info or download a copy from
# http://www.theseed.org/LICENSE.TXT.
#

BEGIN {
    unshift @INC, 
            qw(
              /home/fangfang/WB/
              );
}
# FIXME: dependency on old gjoalignandtree.pm and customized SeedUtils.pm in ~fangfang/WB

use strict;
use Data::Dumper;
use Carp;
use Getopt::Long;

=head1 svr_trim_ali

    svr_trim_ali [options] < ali.fa > trim.fa

This script takes a FASTA file of aligned sequences, trims the
alignment by running PSIBLAST against sequences themselves, and writes
the trimmed alignment to the standard output.

=cut

use SeedUtils;
use AlignTree;
use gjoalignment;
use gjoseqlib;

my $usage = "Usage: $0 [options] < ali.fa > trim.fa";

my $ali = gjoseqlib::read_fasta();

my $trim = AlignTree::trim_alignment($ali);

gjoseqlib::print_alignment_as_fasta($trim);    


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