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README  view on Meta::CPAN

                             - (N) known_gap
                             - (O) other
                             - (P) predraft
                             - (U) unknown_gap
                             - (W) wgs_contig
                ident    => identifier of the component, if any,
                length   => length of the component,
                is_gap   => 1 if the line is some kind of gap, 0 if it
                            is covered by a component,
                gap_type => one of:
                     fragment: gap between two sequence contigs (also
                        called a "sequence gap"),
                     clone: a gap between two clones that do not overlap.
                     contig: a gap between clone contigs (also called a
                        "layout gap").
                     centromere: a gap inserted for the centromere.
                     short_arm: a gap inserted at the start of an
                        acrocentric chromosome.
                     heterochromatin: a gap inserted for an especially
                        large region of heterochromatic sequence (may also
                        include the centromere).

lib/Bio/AGP/LowLevel.pm  view on Meta::CPAN

                         - (N) known_gap
                         - (O) other
                         - (P) predraft
                         - (U) unknown_gap
                         - (W) wgs_contig
            ident    => identifier of the component, if any,
            length   => length of the component,
            is_gap   => 1 if the line is some kind of gap, 0 if it
                        is covered by a component,
            gap_type => one of:
                 fragment: gap between two sequence contigs (also
                    called a "sequence gap"),
                 clone: a gap between two clones that do not overlap.
  		 contig: a gap between clone contigs (also called a
  		    "layout gap").
  		 centromere: a gap inserted for the centromere.
  		 short_arm: a gap inserted at the start of an
  		    acrocentric chromosome.
  		 heterochromatin: a gap inserted for an especially
     		    large region of heterochromatic sequence (may also
  		    include the centromere).

lib/Bio/AGP/LowLevel.pm  view on Meta::CPAN

      my %descmap = qw/ U unknown_gap N known_gap /;
      $r{typedesc} = $descmap{$r{type}}
	or parse_error("unregistered type $r{type}");
      $r{is_gap}   = 1;

      my $gap_size_to_use = $opt{gap_length} || $r{length};

      $r{length} == $r{oend} - $r{ostart} + 1
	or parse_error("gap size of '$r{length}' does not agree with ostart, oend of ($r{ostart},$r{oend})");

      str_in($r{gap_type},qw/fragment clone contig centromere short_arm heterochromatin telomere repeat/)
	or parse_error("invalid gap type '$r{gap_type}'");

      str_in($r{linkage},qw/yes no/)
	or parse_error("linkage (column 8) should be 'yes' or 'no'\n");

      defined $empty && $empty eq ''
	or parse_error("9th column should be present and empty\n");

      push @records,\%r;