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revision 1.60, Sun Sep 16 14:54:22 2007 UTC revision 1.61, Thu Oct 4 00:58:56 2007 UTC
# Line 70  Line 70 
70      my($class,$fig,$fam_id,$fam_data) = @_;      my($class,$fig,$fam_id,$fam_data) = @_;
71    
72      ($fam_id =~ /^FIG\d{6}$/) || confess "invalid family id: $fam_id";      ($fam_id =~ /^FIG\d{6}$/) || confess "invalid family id: $fam_id";
73        if ($ENV{'VERBOSE'})  { print STDERR "building FigFam for $fam_id\n"; }
74      my $fam = {};      my $fam = {};
75      $fam->{id}  = $fam_id;      $fam->{id}  = $fam_id;
76      $fam->{fig} = $fig;      $fam->{fig} = $fig;
# Line 107  Line 107 
107              return undef;              return undef;
108          }          }
109      }      }
110        if ($ENV{'VERBOSE'})  { print STDERR "PEGs built\n"; }
111    
112      if ((! -s "$dir/function") && (! -s "$dir/built"))      if ((! -s "$dir/function") && (! -s "$dir/built"))
113      {      {
# Line 119  Line 120 
120      chomp $func;      chomp $func;
121      close(FUNC);      close(FUNC);
122      $fam->{function} = $func;      $fam->{function} = $func;
123        if ($ENV{'VERBOSE'})  { print STDERR "function=$func\n"; }
124    
125      my($peg,$pegs);      my($peg,$pegs);
126      my $pegsL = [      my $pegsL = [
# Line 128  Line 130 
130                   map { $_ =~ /^\S+\t(\S+)/; $1 }                   map { $_ =~ /^\S+\t(\S+)/; $1 }
131                   `cat \"$dir/PEGs\"`                   `cat \"$dir/PEGs\"`
132                  ];                  ];
133        if ($ENV{'VERBOSE'}) { print STDERR &Dumper($pegsL) }
134      if (@$pegsL < 2)      if (@$pegsL < 2)
135      {      {
136          if (-w $dir) {          if (-w $dir) {
# Line 181  Line 183 
183    
184      if ((! -s "$dir/built") && ((! -s "$dir/PEGs.fasta.pin") || ((-M "$dir/PEGs.fasta.pin") > (-M "$dir/PEGs.fasta"))))      if ((! -s "$dir/built") && ((! -s "$dir/PEGs.fasta.pin") || ((-M "$dir/PEGs.fasta.pin") > (-M "$dir/PEGs.fasta"))))
185      {      {
186          &FIG::run("$FIG_Config::ext_bin/formatdb -i \"$dir/PEGs.fasta\" -p");          &FIG::run("$FIG_Config::ext_bin/formatdb -i \"$dir/PEGs.fasta\" -p T");
187      }      }
188    
189      if ((! -s "$dir/bounds.sims") && (! -s "$dir/built"))      if ((! -s "$dir/bounds.sims") && (! -s "$dir/built"))
# Line 194  Line 196 
196          {          {
197              $n = ((@$pegsL - $i) > 50) ? $i+49 : (@$pegsL - 1);              $n = ((@$pegsL - $i) > 50) ? $i+49 : (@$pegsL - 1);
198              $req = [@$pegsL[$i..$n]];              $req = [@$pegsL[$i..$n]];
199                if ($ENV{'DEBUG'}) { print STDERR "requesting sims for ",&Dumper($req); }
200              @sims = sort { ($a->id1 cmp $b->id1)  } $fig->sims($req,50000,1.0e-10,"fig");              @sims = sort { ($a->id1 cmp $b->id1)  } $fig->sims($req,50000,1.0e-10,"fig");
201              if (@sims == 0) { print STDERR "no similarities returned for ",join(",",@$req),"\n"; }              if (@sims == 0) { print STDERR "no similarities returned for ",join(",",@$req),"\n"; }
202    

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