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Revision 1.2 - (download) (as text) (annotate)
Mon Dec 5 18:56:37 2005 UTC (14 years, 2 months ago) by olson
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, caBIG-05Apr06-00, 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, caBIG-13Feb06-00, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
Changes since 1.1: +17 -0 lines
Add license words.

# -*- perl -*-
#
# 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.
#


# usage: fasta_to_phylip < ali.fasta > ali.phylip

while (defined($_ = <STDIN>) && ($_ !~ /^>/)) {}
$line_ln = 0; $j=0;
while ($_ && ($_ =~ /^>(\S+)/))
{
    $id = $1; $seq = "";
    while (defined($_ = <STDIN>) && ($_ !~ /^>/)) 
    {
	chop;
	$seq = $seq.$_;
    }
    $seq =~ s/\s//g;
    $seq =~ s/~/-/g;
    $seq =~ s/\./-/g;
    $seq =~ tr/a-z/A-Z/;

    if (length($seq) > $line_ln)
    {
	$line_ln = length($seq);
    }
    $ln = length($id);
    for ($i=0; $ln + $i < 10; $i++)
    {
	$id = $id." ";
    }
    $line[$j] = "$id $seq";
    $j++;
}

print "$j $line_ln\n";
for ($i=0; $i < $j; $i++)
{
    $ln = length($line[$i]) - 11;
    for ($k=0; ($k + $ln) < $line_ln; $k++)
    {
	$line[$i] = $line[$i]."-";
    }
    print "$line[$i]\n";
}

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