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Revision 1.1.1.1 - (download) (as text) (annotate) (vendor branch)
Mon Feb 19 17:15:26 2007 UTC (12 years, 9 months 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

# a quick gbk2fasta script that will put locus/definition on the ID line and DNA sequence

use strict;

my ($print, $locus, $def);

while (<>)
{
 if (/^LOCUS\s+(\S+)/) {$locus=$1; next}
 if (/^DEFINITION\s+(.*)/) {$def=$1; chomp($def)}
 if (/ORIGIN/)
 {
  if ($locus && $def) 
  {
   print ">$locus $def\n";
   $print=1;
   next;
  }
  else
  {
   print STDERR "No locus or definition we have |$locus| and |$def|\n";
   $print=2;
  }
  next;
 }
 if (m#^//#) {($locus, $def, $print)=(undef, undef, undef)}
 if ($print && $print ==2)
 {
  print STDERR "Next line is:\n$_";
  undef $print;
  next;
 }
 if ($print) 
 {
  chomp;
  s/\d//g;
  s/\s//g;
  print "$_\n";
 }
} 
 

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