Writer
Table of Contents
Classes
- BedFeatureWriter
- The inverse of BedFeatureReader. PlasmidFeature's 1-based inclusive coordinates are converted back
to BED's zero-based, half-open ones the same way the reader converted them in : chromStart =
start - 1, chromEnd = end. An origin-crossing feature (start > end) has no BED representation -
BedFeatureReader already rejects one coming in with a warning, and this writer rejects one going
out by throwing, for the same reason GffFeatureWriter does.
- GenbankWriter
- Covers the subset of the GenBank flat-file format GenbankPlasmidMapper reads back : LOCUS,
DEFINITION, ACCESSION, a FEATURES table (a synthetic "source 1..length" line plus one entry per
PlasmidFeature) and an ORIGIN sequence block. It does not attempt REFERENCE, COMMENT, VERSION, a
real division code or submission date - Plasmid carries none of those, and inventing plausible-
looking values for them would misrepresent the record rather than describe it. The LOCUS line
follows NCBI's fixed columns (see writeLocusLine()), except for a locus name longer than 16
characters, written in full rather than truncated.
- GffFeatureWriter
- The inverse of GffFeatureReader. Coordinates need no conversion : GFF3, like PlasmidFeature, is
1-based inclusive. An origin-crossing feature (start > end) is written the GFF3 way, with end =
its real end + the molecule length, which therefore has to be given ; a landmark line spanning
1..length and flagged Is_circular=true is then written too (or, when a feature read in as that
"region" landmark is among the features, that line is flagged instead), so GffFeatureReader can
fold the feature back. Without the length, such a feature is rejected by throwing.