3 # $Id: gs_aa_extract.pl,v 1.2 2008/03/09 00:11:50 cmzmasek Exp $
5 # This extracts the AA sequences from GENSCAN output files
6 # Copyright (C) 2008-2009 Christian M. Zmasek
8 # Created 2007-07-28 in Winterthur, Switzerland by CMZ
10 # Usage: gs_aa_extract.pl <genscan-output infile> <outfile>
14 if ( scalar( @ARGV ) != 2 ) {
15 print "\ngs_aa_extract.pl <genscan-output infile> <outfile>\n\n";
19 my $infile = $ARGV[ 0 ];
20 my $outfile = $ARGV[ 1 ];
23 die "\n$0: \"$outfile\" already exists.\n\n";
25 unless( ( -s $infile ) && ( -f $infile ) && ( -T $infile ) ) {
26 die "\n$0: cannot read from \"$infile\".\n\n";
29 open( IN, "$infile" ) || die "\n$0: Cannot open file \"$infile\": $!\n";
30 open( OUT, ">$outfile" ) || die "\n$0: Cannot create file \"$outfile\": $!\n";
35 while ( $line = <IN> ) {
36 if ( $line =~ /^>/ ) {
39 elsif ( $line =~ /^[A-Z]+$/ ) {
40 if ( length( $desc ) > 0 ) {