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Revision 1.1 - (download) (as text) (annotate)
Mon Nov 16 21:52:21 2009 UTC (10 years ago) by overbeek
Branch: MAIN
new scripts for updating FIGfams and Kmer tables

########################################################################

use FIG;

my $usage = "usage: FFB2_build_updated_FF OldReleaseDir NewReleaseDir";

my($oldD,$newD);

(
 ($oldD = shift @ARGV) && (-d $oldD) &&
 ($newD = shift @ARGV)
)
    || die $usage;

mkdir($newD,0777) || die "You have an existing $newD; remove it and try again";
&FIG::run("FFB2_update_FIGfams $newD/families.2c $newD/family.functions $oldD");
&FIG::run("FFB2_get_oligos $newD/families.2c $newD/family.functions 2> $newD/function.index |" .
	  "sort -T . | FFB2_usable_motifs $newD/Kmers");

&FIG::run("FFB2_get_prots $newD/ProtsByGenomeSet $newD/setI");
&FIG::run("FFB2_get_prot_gs_oligos $newD/ProtsByGenomeSet 12 | sort -T . | FFB2_usable_motifs $newD/PhyloSigs");
mkdir("$newD/Merged",0777) || die "could not make $newD/Merged: $!";
foreach my $i (7..12)
{
    mkdir("$newD/Merged/$i",0777) || die "could not make $newD/Merged/$i: $!";
    &FIG::run("FFB2_merge_oligos $newD/Kmers/$i/good.oligos $newD/PhyloSigs/$i/good.oligos > $newD/Merged/$i/merged.oligos");
}
&FIG::run("FFB2_load_oligo_index $newD/function.index $newD/FRI.db");
&FIG::run("FFB2_load_oligo_index $newD/setI $newD/setI.db");

&FIG::run("FFB2_create_binary_kmers -s 4,2 $newD/Merged/$i/merged.oligos $newD/Merged/$i/table.binary");

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