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revision 1.2, Mon Nov 16 21:56:22 2009 UTC revision 1.5, Thu Apr 1 19:28:40 2010 UTC
# Line 12  Line 12 
12  )  )
13      || die $usage;      || die $usage;
14    
15    my $sort_args = "-T $FIG_Config::temp -S 4G";
16    
17  mkdir($newD,0777) || die "You have an existing $newD; remove it and try again";  mkdir($newD,0777) || die "You have an existing $newD; remove it and try again";
18  &FIG::run("FFB2_update_FIGfams $newD/families.2c $newD/family.functions $oldD");  &FIG::run("FFB2_update_FIGfams $newD/families.2c $newD/family.functions $oldD");
19  &FIG::run("FFB2_get_oligos $newD/families.2c $newD/family.functions 2> $newD/function.index |" .  &FIG::run("FFB2_get_oligos $newD/families.2c $newD/family.functions 2> $newD/function.index |" .
20            "sort -T . | FFB2_usable_motifs $newD/Kmers");            "sort $sort_args | FFB2_usable_motifs $newD/Kmers");
21    
22  &FIG::run("FFB2_get_prots $newD/ProtsByGenomeSet $newD/setI");  &FIG::run("FFB2_get_prots $newD/ProtsByGenomeSet $newD/setI");
23  &FIG::run("FFB2_get_prot_gs_oligos $newD/ProtsByGenomeSet 12 | sort -T . | FFB2_usable_motifs $newD/PhyloSigs");  &FIG::run("FFB2_get_prot_gs_oligos $newD/ProtsByGenomeSet 12 | sort $sort_args | FFB2_usable_motifs $newD/PhyloSigs");
24  mkdir("$newD/Merged",0777) || die "could not make $newD/Merged: $!";  mkdir("$newD/Merged",0777) || die "could not make $newD/Merged: $!";
25  foreach my $i (7..12)  foreach my $i (7..12)
26  {  {
# Line 32  Line 34 
34  {  {
35      &FIG::run("FFB2_create_binary_kmers -s 4,2 $newD/Merged/$i/merged.oligos $newD/Merged/$i/table.binary");      &FIG::run("FFB2_create_binary_kmers -s 4,2 $newD/Merged/$i/merged.oligos $newD/Merged/$i/table.binary");
36  }  }
37    
38    &FIG::run("FFB2_run_tests $newD");
39    &FIG::run("FFB2_compare_tests $oldD $newD");
40    &FIG::run("build_prok_nonff_fasta $newD > $newD/extra_prok_seqs.fasta");
41    &FIG::run("formatdb -p T -i $newD/extra_prok_seqs.fasta");

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