# Last edited on 2008-06-14 02:14:11 by stolfi

# ----------------------------------------------------------------------
# dbd_digest_Reese

function process_gene(arg,   i)
{
  # Processes the "/gene" (gene identifier) entry.
  # Saves it into the global variable {gene}.
  
  if (gene != "") { data_error(("more than one \"/gene\" entry")); }
  
  # Get complete argument, remove "/gene=\"\""
  while ((arg !~ /[\"] *$/) && getline) 
    { doc = ( doc $0 "\n") ;
      arg = ( arg $0 );
    }
  gsub(/[\/]gene *[=] *[\"]/, "", arg);
  gsub(/[\"] *$/, "", arg);
  # Remove all spaces:
  gsub(/[ ]/, "", arg);
  
  printf "gene = %s\n", arg > "/dev/stderr";
  
  # Save in global variables:
  gene = arg;
}




    { # Write the gene's translation
      nama = 0;
      phase = 0;
      for (k = 1; k <= cds_nranges; k++)
        { ini = get_ini(cds_range[k]);
          fin = get_fin(cds_range[k]);
          for (i = ini; i <= fin; i++)
            { phase = (phase + 1) % 3;
              if (phase == 0) 
                { if ((nama > 0) && (nama % 60 == 0)) { printf "\n" > ama_file; }
                  nama++;
                  if (nama > length(translation)+1)
                    { data_error(("translation is too short")); }
                  else if (nama <= length(translation))
                    { amino = substr(translation, nama, 1);
                      printf "%s", amino > ama_file; 
                    }
		}
      	    }
        }
      if (nama > 0) { printf "\n" > ama_file; }
      if (nama != length(translation)+1) { data_error(("translation too long")); }
      if (phase != 0) { data_error(("CDS not multiple of 3")); }
      close(ama_file);
    }

# ----------------------------------------------------------------------