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Mon Feb 19 17:15:26 2007 UTC (13 years ago) by olson
Branch: x, MAIN
CVS Tags: mgrast_dev_08112011, mgrast_dev_08022011, mgrast_dev_05262011, mgrast_dev_04082011, mgrast_version_3_2, mgrast_dev_12152011, mgrast_dev_06072011, mgrast_rel_2008_0806, mgrast_dev_10262011, mgrast_dev_02212011, mgrast_rel_2008_0923, mgrast_release_3_0, mgrast_dev_03252011, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, 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, mgrast_dev_04012011, mgrast_rel_2008_0919, mgrast_rel_2008_1110, myrast_33, mgrast_rel_2008_0917, mgrast_dev_04052011, mgrast_dev_02222011, y, HEAD
Changes since 1.1: +0 -0 lines
Initial import

#!/usr/bin/perl -w

# create a fasta file from some directory

use strict;

my $usage=<<EOF;
-d list of source directories
-e list of directories to exclude
-o output file


my (@inc, @exc, $output);
my $exc;
while (@ARGV) {
 my $t=shift @ARGV;
 if ($t eq "-d") {$exc=1;next}
 elsif ($t eq "-e") {$exc=2;next}
 elsif ($t eq "-o") {$output=shift @ARGV; next}
 if ($exc==1) {push @inc, $t}
 elsif ($exc==2) {push @exc, $t}

die $usage unless ($inc[0] && $output);

my $all=0; my $kept=0;
foreach my $dir (@inc) {
 opendir(DIR, $dir) || die "Can't open $dir";
 while (my $f=readdir(DIR)) {
  next if ($f =~ /^\./);
  my $keep=1; 
  foreach my $e (@exc) {
   if (-e "$e/$f") {undef $keep; last}
  next unless ($keep);
  `cat $dir/$f >> $output`;

print STDERR "Looked through $all files and kept $kept of them\n";


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