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Annotation of /FigKernelScripts/FFB2_build_updated_FF.pl

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1 : overbeek 1.1 ########################################################################
2 :    
3 :     use FIG;
4 :    
5 :     my $usage = "usage: FFB2_build_updated_FF OldReleaseDir NewReleaseDir";
6 :    
7 :     my($oldD,$newD);
8 :    
9 :     (
10 :     ($oldD = shift @ARGV) && (-d $oldD) &&
11 :     ($newD = shift @ARGV)
12 :     )
13 :     || die $usage;
14 :    
15 : olson 1.3 my $sort_args = "-T $FIG_Config::temp -S 4G";
16 :    
17 : overbeek 1.1 mkdir($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");
19 :     &FIG::run("FFB2_get_oligos $newD/families.2c $newD/family.functions 2> $newD/function.index |" .
20 : olson 1.3 "sort $sort_args | FFB2_usable_motifs $newD/Kmers");
21 : overbeek 1.1
22 :     &FIG::run("FFB2_get_prots $newD/ProtsByGenomeSet $newD/setI");
23 : olson 1.3 &FIG::run("FFB2_get_prot_gs_oligos $newD/ProtsByGenomeSet 12 | sort $sort_args | FFB2_usable_motifs $newD/PhyloSigs");
24 : overbeek 1.1 mkdir("$newD/Merged",0777) || die "could not make $newD/Merged: $!";
25 :     foreach my $i (7..12)
26 :     {
27 :     mkdir("$newD/Merged/$i",0777) || die "could not make $newD/Merged/$i: $!";
28 :     &FIG::run("FFB2_merge_oligos $newD/Kmers/$i/good.oligos $newD/PhyloSigs/$i/good.oligos > $newD/Merged/$i/merged.oligos");
29 :     }
30 :     &FIG::run("FFB2_load_oligo_index $newD/function.index $newD/FRI.db");
31 :     &FIG::run("FFB2_load_oligo_index $newD/setI $newD/setI.db");
32 :    
33 : olson 1.2 foreach my $i (7..12)
34 :     {
35 :     &FIG::run("FFB2_create_binary_kmers -s 4,2 $newD/Merged/$i/merged.oligos $newD/Merged/$i/table.binary");
36 :     }
37 : olson 1.5
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 : overbeek 1.4 &FIG::run("formatdb -p T -i $newD/extra_prok_seqs.fasta");
42 : overbeek 1.6
43 :     &FIG::run("FFB2_make_FF_index $newD $newD/fam.func.index $newD/FamFuncBlastD");

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