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Revision 1.2 - (download) (as text) (annotate)
Fri Mar 16 20:51:25 2007 UTC (13 years ago) by olson
Branch: 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, HEAD
Changes since 1.1: +0 -1 lines
initial tweaks

#!/usr/bin/perl -w

# get some fasta sequences from a file

use strict;
use Rob;

my $us=<<EOF;
$0

-f fasta file
-n needed sequences, one per line

EOF

my ($faf, $nf);

while (@ARGV) {
 my $t=shift;
 if ($t eq "-f") {$faf=shift}
 elsif ($t eq "-n") {$nf=shift}
}

die $us unless ($faf && $nf);

my $fasta = Rob->read_fasta($faf);
open(IN, $nf) || die "Can't opne $nf";
while (<IN>) {
 chomp;
 if ($fasta->{$_}) {
  $fasta->{$_} =~ s/\s+//g;
  print ">$_\n", $fasta->{$_}, "\n";
 } else {
  print STDERR "No sequence for $_\n";
 }
}




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