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Revision 1.1 - (download) (as text) (annotate)
Fri Mar 7 20:15:45 2008 UTC (11 years, 8 months ago) by bartels
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
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#!/vol/cee/bin/perl
#
#

=head1 NAME 

createTIGfamSrc -- convert TIGR HMM file to table format

=head1 SYNOPSIS

ccreateTIGfamSrc.pl /vol/biotools/share/tigrfams/TIGRFAMs_6.0_HMM.LIB

=head1 DESCRIPTION

Convert tigrfams input file (from TIGR server) to tabular format.
Our local instance is: /vol/biodb/tigrfams/

The file we use is: TIGRFAMs_6.0_HMM.LIB
Our local, extracted copy lives in: /vol/biotools/share/tigrfams/TIGRFAMs_6.0_HMM.LIB

Example of output format:

TIGR02992       ectoine_eutC: ectoine utilization protein EutC


=head1 AUTHOR

Folker Meyer

=cut

use strict;

my $infile=$ARGV[0]; 
my $line="";
my $datahash=();

open (INFILE, $infile) || die "could not open $infile";
while ($line = <INFILE>) {

chomp ($line);
#print "$line\n";

	if ($line =~ /ACC\s+(.*)/ ) {
		print "$1\t";
	 }

	if ($line =~ /DESC\s+(.*)/ ) {
		print "$1\t\n";
	}
}
close (INFILE);



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