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revision 1.27, Tue Jan 19 21:23:40 2010 UTC revision 1.28, Fri Feb 12 17:32:59 2010 UTC
# Line 209  Line 209 
209          {          {
210              $type = $2;              $type = $2;
211              $rna  = $3;              $rna  = $3;
212              &process_rna($id, $type, \$rna, $prefixR, \$idNr, $contigs, $fh_rna_tbl, $fh_rna_fasta);              &process_rna($id, $type, \$rna, $prefixR, \$idNr, $contigs, $fh_rna_tbl, $fh_rna_fasta, $fh_assigned_funcs, $fh_annotations);
213          }          }
214      }      }
215  }  }
# Line 606  Line 606 
606  }  }
607    
608  sub process_rna {  sub process_rna {
609      my ($contigID, $type, $rnaP, $prefix, $idNr, $contigs, $fh_tbl, $fh_dna) = @_;      my ($contigID, $type, $rnaP, $prefix, $idNr, $contigs, $fh_tbl, $fh_dna, $fh_func, $fh_annot) = @_;
610      my ($loc, @aliases, $func, $trans, $id, $precise, $DNA);      my ($loc, @aliases, $func, $trans, $id, $precise, $DNA);
611    
612      ($loc, $precise) = &get_loc($contigID,$rnaP);      ($loc, $precise) = &get_loc($contigID,$rnaP);
# Line 621  Line 621 
621                  warn qq(WARNING: could not get func $$rnaP\n) if $ENV{VERBOSE};                  warn qq(WARNING: could not get func $$rnaP\n) if $ENV{VERBOSE};
622              }              }
623              else {              else {
624                  print $fh_tbl qq($id\t$loc\t$func\n);                  print $fh_func   qq($id\t$func\n);
625                    print $fh_tbl    qq($id\t$loc\t\n);
626    
627                    &make_annotation($id, qq(Set function to\n$func\nInitial import.), $fh_annot);
628                  &FIG::display_id_and_seq($id,\$dna,$fh_dna);                  &FIG::display_id_and_seq($id,\$dna,$fh_dna);
629              }              }
630          }          }

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