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revision 1.17, Fri Oct 29 17:10:34 2010 UTC revision 1.18, Mon Nov 22 17:41:30 2010 UTC
# Line 6  Line 6 
6  use Cache::Memcached::Fast;  use Cache::Memcached::Fast;
7  use Getopt::Long;  use Getopt::Long;
8    
9  my $usage = "usage: FFB2_build_updated_FF [--skipotu] OldReleaseDir NewReleaseDir memcache-host memcache-port [ssfam]";  my $usage = "usage: FFB2_build_updated_FF [--override fn-override-file] [--skipotu] OldReleaseDir NewReleaseDir memcache-host memcache-port [ssfam]";
10    
11  my $skip_otu;  my $skip_otu;
12    my $override_file;
13    
14  my $rc = GetOptions("skipotu" => \$skip_otu);  my $rc = GetOptions("skipotu" => \$skip_otu,
15                        "override=s" => \$override_file);
16    
17  $rc or die $usage;  $rc or die $usage;
18    
# Line 124  Line 126 
126    
127      my @files = map { $_->[2] } @handles;      my @files = map { $_->[2] } @handles;
128      print STDERR "Merging phylo @files\n";      print STDERR "Merging phylo @files\n";
129      &FIG::run("sort -S 2G -m @files | FFB2_usable_motifs $newD/PhyloSigs 7-12");  
130        #
131        # The Debian sort on the mac pro's does bad things with
132        # large merges. Use the latest one there, built in a local dir.
133        my @sort;
134        if (-x "/scratch/olson/coreutils/bin/sort")
135        {
136            my $n = @files;
137            $n++;
138            @sort = ("/scratch/olson/coreutils/bin/sort", "--batch-size=$n", "-m", @files);
139        }
140        else
141        {
142            @sort = ("sort", "-S", "2G", "-m", @files);
143        }
144    
145    
146        &FIG::run("@sort | FFB2_usable_motifs $newD/PhyloSigs 7-12");
147    
148      #&FIG::run("FFB2_get_prots $newD/ProtsByGenomeSet $newD/setI");      #&FIG::run("FFB2_get_prots $newD/ProtsByGenomeSet $newD/setI");
149      #&FIG::run("FFB2_get_prot_gs_oligos $newD/ProtsByGenomeSet 12 | sort $sort_args | FFB2_usable_motifs $newD/PhyloSigs");      #&FIG::run("FFB2_get_prot_gs_oligos $newD/ProtsByGenomeSet 12 | sort $sort_args | FFB2_usable_motifs $newD/PhyloSigs");
# Line 139  Line 158 
158      }      }
159  }  }
160    
161    die "We're at the merge\n";
162    
163  mkdir("$newD/Merged",0777) || die "could not make $newD/Merged: $!";  mkdir("$newD/Merged",0777) || die "could not make $newD/Merged: $!";
164    
# Line 189  Line 209 
209    
210  sub figfam_processing  sub figfam_processing
211  {  {
212      &FIG::run("FFB2_update_FIGfams -f $ssfam $newD/families.2c $newD/family.functions $oldD");      my $override_arg = "";
213      &FIG::run("FFB2_get_oligos $newD/families.2c $newD/family.functions $newD/function.index $mchost $mcport |" .      if (defined($override_file))
214                "FFB2_usable_motifs $newD/Kmers");      {
215            $override_arg = "--override $override_file";
216        }
217        &FIG::run("FFB2_update_FIGfams -ssfams $ssfam $override_arg $newD/families.2c $newD/family.functions $oldD");
218        &FIG::run("FFB2_get_oligos2 $newD/families.2c $newD/family.functions $newD/function.index $newD/KmerBuild $mchost $mcport");
219    
220    #    &FIG::run("FFB2_update_FIGfams -f $ssfam $newD/families.2c $newD/family.functions $oldD");
221    #    &FIG::run("FFB2_get_oligos $newD/families.2c $newD/family.functions $newD/function.index $mchost $mcport |" .
222    #             "FFB2_usable_motifs $newD/Kmers");
223    
224  }  }
225    
226    

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