[Bio] / FigKernelPackages / FIG.pm Repository:
ViewVC logotype

Diff of /FigKernelPackages/FIG.pm

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.334, Thu Aug 4 18:28:36 2005 UTC revision 1.335, Fri Aug 5 13:14:26 2005 UTC
# Line 306  Line 306 
306    
307  =head3 add_genome  =head3 add_genome
308    
309  C<< my $ok = $fig->add_genome($genomeF, $force); >>  C<< my $ok = $fig->add_genome($genomeF, $force, $skipnr); >>
310    
311  Add a new genome to the data store. A genome's data is kept in a directory  Add a new genome to the data store. A genome's data is kept in a directory
312  by itself, underneath the main organism directory. This method essentially  by itself, underneath the main organism directory. This method essentially
# Line 327  Line 327 
327  never do it, but I am in the situation where I need to move a genome from one machine  never do it, but I am in the situation where I need to move a genome from one machine
328  to another, and although I trust the genome I can't.  to another, and although I trust the genome I can't.
329    
330    =item skipnr
331    
332    We don't always want to add the pooteins into the nr database. For example wih a metagnome that has been called by blastx. This will just skip appending the proteins into the NR file.
333    
334  =item RETURN  =item RETURN
335    
336  Returns TRUE if successful, else FALSE.  Returns TRUE if successful, else FALSE.
# Line 336  Line 340 
340  =cut  =cut
341  #: Return Type $;  #: Return Type $;
342  sub add_genome {  sub add_genome {
343      my($self,$genomeF, $force) = @_;      my($self,$genomeF, $force, $skipnr) = @_;
344    
345      my $rc = 0;      my $rc = 0;
346    
# Line 378  Line 382 
382          &run("index_translations $genome");          &run("index_translations $genome");
383          my @tmp = `cut -f1 $FIG_Config::organisms/$genome/Features/peg/tbl`;          my @tmp = `cut -f1 $FIG_Config::organisms/$genome/Features/peg/tbl`;
384          chomp @tmp;          chomp @tmp;
385          &run("cat $FIG_Config::organisms/$genome/Features/peg/fasta >> $FIG_Config::data/Global/nr");          &run("cat $FIG_Config::organisms/$genome/Features/peg/fasta >> $FIG_Config::data/Global/nr") if (!$skipnr);
386          &enqueue_similarities(\@tmp);          &enqueue_similarities(\@tmp);
387      }      }
388      if ((-s "$FIG_Config::organisms/$genome/assigned_functions") ||      if ((-s "$FIG_Config::organisms/$genome/assigned_functions") ||

Legend:
Removed from v.1.334  
changed lines
  Added in v.1.335

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3