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Revision 1.1 - (download) (as text) (annotate)
Mon Feb 12 00:20:58 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 last round of phylogeny tools

$usage = "usage: trimmed_kernel_alignment [-r] [-d MinDiff] [-c MinFracInCol] [-i MinInfo] Sequences > TrimmedAlignment";

use gjoseqlib;
use PHOB;

my $min_iden_diff = 0.7;   # 2 members of the same representative's group have at most 70% identity
my $min_inf  = 2;          # minimum information content of bounding columns
my $retrim = 0;            # default is no "retrim"
my $min_hits = 0.7;        # bounding column must have 70% of the sequences an entries by default

while ($ARGV[0] =~ /^-/)
{
    $_ = shift @ARGV;
    if ($_ =~ s/^-r//)    { $retrim = 1 }
    elsif ($_ =~ s/^-d//) { $min_iden_diff = ($_ || shift @ARGV) }
    elsif ($_ =~ s/^-i//) { $min_inf = ($_ || shift @ARGV) }
    elsif ($_ =~ s/^-c//) { $min_hits = ($_ || shift @ARGV) }
    else                  { die "Bad Flag: $_" }
}

(
 ($seqF = shift @ARGV)
)
    || die $usage;

$seqs    = &gjoseqlib::read_fasta($seqF);
$trimmed = &PHOB::kernel_of_trimmed_seqs(seqs => $seqs,  
			    min_hits => $min_incol, 
			    min_inf => $min_inf,
			    min_iden_diff => $min_iden_diff
			   );
$ali     = &PHOB::align_seqs(seqs => $trimmed);
if ($retrim)
{
    $retrimmed = &PHOB::retrim_seqs(seqs => $seqs,  
				    ali => $ali,
				    );
    $ali     = &PHOB::align_seqs(seqs => $retrimmed);
}
&gjoseqlib::print_alignment_as_fasta($ali);

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