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Revision 1.1 - (download) (as text) (annotate)
Tue Apr 8 17:32:39 2008 UTC (11 years, 10 months ago) by olson
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
Script to map IDs in a SEED NR into forms acceptable to the indexed NCBI fasta processing code.

use strict;

my $usage = "map-nr-ids-to-ncbi-std nr-file out-file\n";

@ARGV == 2 or die $usage;

my $nr = shift;
my $new = shift;

open(IN, "<$nr") or die "Cannot open input nr file $nr: $!\n";

my($id, $id2, $seq);

open(O, ">$new") or die "cannot write $new: $!";

while (<IN>)
{
    if (($id, $id2) = /^>(\S+)\s*(.*)/)
    {
	if ($id =~ /^gi/)
	{
	    # gi's are ok.
	}
	elsif ($id =~ /^ref|sp|gb/)
	{
	    $id = "$id|";
	}
	elsif ($id =~ /\|/)
	{
	    $id = "gnl|$id";
	}
	else
	{
	    $id = "lcl|$id";
	}
	chomp $id2;
	print O ">$id $id2\n";
    }
    else
    {
	print O $_;
    }
}
close(IN);
close(O);

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