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revision 1.20, Mon Nov 22 20:06:09 2010 UTC revision 1.21, Mon Nov 29 22:25:34 2010 UTC
# Line 204  Line 204 
204  my $load2 = start(["FFB2_load_oligo_index", "$newD/setI", "$newD/setI.db"]);  my $load2 = start(["FFB2_load_oligo_index", "$newD/setI", "$newD/setI.db"]);
205  my $build = start(["build_prok_nonff_fasta", "$newD"],  ">", "$newD/extra_prok_seqs.fasta");  my $build = start(["build_prok_nonff_fasta", "$newD"],  ">", "$newD/extra_prok_seqs.fasta");
206    
207    #
208    # create merge files and use the -merge to create_binary_kmers
209    #
210    
211  #foreach my $i (7..12)  my %mergefile;
212  #{  foreach my $i (7..12)
213  #    &FIG::run("FFB2_create_binary_kmers -s 4,2 $newD/Merged/$i/merged.oligos $newD/Merged/$i/table.binary");  {
214  #}      my $mf = "$newD/KmerBuild/mergefile.$i";
215        $mergefile{$i} = $mf;
216        open(MF, ">", $mf) or die "Cannot write $mf: $!";
217    
218        for my $f (sort <$newD/Kmers/kmers.2.*/$i/good.oligos.gz>)
219        {
220            print MF "$f\t1\n";
221        }
222        for my $f (sort <$newD/Kmers/kmers.3.*/$i/good.oligos.gz>)
223        {
224            print MF "$f\t3\n";
225        }
226        print MF "$newD/PhyloSigs/$i/good.oligos.gz\t2\n";
227        close(MF);
228    }
229    
230    foreach my $i (7..12)
231    {
232        my $mf = $mergefile{$i};
233        &FIG::run("FFB2_create_binary_kmers -l $i -s 4,2,4 -merge $mf - $newD/Merged/$i/table.binary");
234    }
235    
236  system("FFB2_run_tests $newD");  system("FFB2_run_tests $newD");
237  system("FFB2_compare_tests $oldD $newD");  system("FFB2_compare_tests $oldD $newD");
# Line 234  Line 257 
257      &FIG::run("FFB2_update_FIGfams -ssfams $ssfam $override_arg $newD/families.2c $newD/family.functions $oldD");      &FIG::run("FFB2_update_FIGfams -ssfams $ssfam $override_arg $newD/families.2c $newD/family.functions $oldD");
258      &FIG::run("FFB2_get_oligos2 $newD/families.2c $newD/family.functions $newD/function.index $newD/KmerBuild $mchost $mcport");      &FIG::run("FFB2_get_oligos2 $newD/families.2c $newD/family.functions $newD/function.index $newD/KmerBuild $mchost $mcport");
259    
260        &FIG::run("FFB2_xy $newD/KmerBuild $newD/Kmers 7-12");
261    
262  #    &FIG::run("FFB2_update_FIGfams -f $ssfam $newD/families.2c $newD/family.functions $oldD");  #    &FIG::run("FFB2_update_FIGfams -f $ssfam $newD/families.2c $newD/family.functions $oldD");
263  #    &FIG::run("FFB2_get_oligos $newD/families.2c $newD/family.functions $newD/function.index $mchost $mcport |" .  #    &FIG::run("FFB2_get_oligos $newD/families.2c $newD/family.functions $newD/function.index $mchost $mcport |" .
264  #             "FFB2_usable_motifs $newD/Kmers");  #             "FFB2_usable_motifs $newD/Kmers");

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