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Revision 1.1 - (download) (as text) (annotate)
Sat May 12 20:12:56 2007 UTC (12 years, 9 months ago) by overbeek
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, rast_rel_2008_06_18, myrast_rel40, rast_rel_2008_06_16, mgrast_dev_05262011, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, rast_rel_2008_04_23, mgrast_dev_06072011, rast_rel_2008_09_30, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, mgrast_dev_02212011, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, rast_rel_2009_02_05, rast_rel_2011_0119, mgrast_rel_2008_0625, 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, rast_rel_2008_10_09, mgrast_dev_04012011, rast_release_2008_09_29, mgrast_rel_2008_0806, mgrast_rel_2008_0923, mgrast_rel_2008_0919, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, mgrast_rel_2008_0917, rast_rel_2008_10_29, mgrast_dev_04052011, mgrast_dev_02222011, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
add utilities for computing alignments

use gjoseqlib;

# usage: order_seqs_on_length AllSeqs CoreAli

(
 ($seqsF   = shift @ARGV)
)
    || die "usage: order_seqs_on_length seqs.fasta [ali.fasta]";

my %seen;
my $seqs = &gjoseqlib::read_fasta($seqsF);
if ($aliF = shift @ARGV)
{
    my $ali  = &gjoseqlib::read_fasta($aliF);
    %seen = map { $_->[0] => 1 } @$ali;
}
my %seq_lns = map { $_->[0] => length($_->[2]) } @$seqs;
my @seqs = sort { $seq_lns{$b->[0]} <=> $seq_lns{$a->[0]} } grep { ! $seen{$_->[0]} } @$seqs;
&gjoseqlib::print_alignment_as_fasta(\@seqs);


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