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Revision 1.2 - (download) (as text) (annotate)
Wed Oct 20 01:04:35 2010 UTC (9 years ago) by gdpusch
Branch: MAIN
CVS Tags: mgrast_dev_08112011, mgrast_dev_08022011, rast_rel_2014_0912, myrast_rel40, mgrast_dev_05262011, mgrast_dev_04082011, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_06072011, rast_rel_2014_0729, mgrast_dev_02212011, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2011_0119, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, mgrast_dev_04012011, myrast_33, rast_rel_2011_0928, mgrast_dev_04052011, mgrast_dev_02222011, mgrast_dev_10262011, HEAD
Changes since 1.1: +5 -4 lines
Fixed incorrect function names.

# This is a SAS component
#
use gjoseqlib;
use gjoalignment;
use strict;

my $usage = "usage: svr_align_using_muscle [Seqs Alignment]";

my($seqs,$ali);
if (@ARGV > 1)
{
    my $seqs = &gjoseqlib::read_fasta($ARGV[0]);
    my $ali  = &gjoalignment::align_with_muscle($seqs);
    &gjoseqlib::print_alignment_as_fasta($ali,0,$ARGV[1]);
}
else
{
    my $seqs = &gjoseqlib::read_fasta();
    my $ali  = &gjoalignment::align_with_muscle($seqs);
    &gjoseqlib::print_alignment_as_fasta($ali);
}

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