Documentation

GffFeatureWriter
in package
implements GffFeatureWriterInterface

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.

GFF3 requires a phase on every CDS. A CDS whose phase is unknown is written with phase 0, i.e. as starting on a complete codon, the usual assumption for a complete CDS ; any other type gets ".".

A feature read in FROM a GFF3 file carries its original "type" column in getMetadata()["gffType"] ; that exact term is reused here so a read-then-write round trip is lossless. A feature built some other way (hand-constructed, imported from GenBank, produced by neighbor-joining-adjacent tooling...) has no such metadata, and FeatureType's own richer vocabulary (INSERT, MARKER, REPORTER, TAG, RESTRICTION_SITE...) has no exact Sequence Ontology counterpart for most of its members ; those fall back to the genuine generic SO term "sequence_feature" rather than a plausible-looking but wrong guess. Class GffFeatureWriter

Tags
author

Amélie DUVERNET aka Amelaye amelieonline@gmail.com

Table of Contents

Interfaces

GffFeatureWriterInterface
Interface GffFeatureWriterInterface - the inverse of GffFeatureReaderInterface : serializes PlasmidFeature instances into GFF3 text.

Constants

GENERIC_SO_TERM  : mixed = "sequence_feature"
SO_TERM_BY_FEATURE_TYPE  : array<string, string> = [\Amelaye\BioPHP\Domain\Cloning\ValueObject\Fea...

Methods

write()  : string
escapeAttributeValue()  : string
Percent-encodes the GFF3 column-9 reserved characters (and control characters that would otherwise break the one-line-per-feature format).
formatPhase()  : string
isCircularLandmark()  : bool
True for a feature read in from GFF3 as the "region" landmark spanning the whole molecule.
writeFeatureLine()  : string

Constants

SO_TERM_BY_FEATURE_TYPE

private array<string, string> SO_TERM_BY_FEATURE_TYPE = [\Amelaye\BioPHP\Domain\Cloning\ValueObject\FeatureType::CDS => "CDS", \Amelaye\BioPHP\Domain\Cloning\ValueObject\FeatureType::PROMOTER => "promoter", \Amelaye\BioPHP\Domain\Cloning\ValueObject\FeatureType::TERMINATOR => "terminator", \Amelaye\BioPHP\Domain\Cloning\ValueObject\FeatureType::ORIGIN_OF_REPLICATION => "origin_of_replication"]

Methods

write()

public write(string $sSeqId, array<string|int, PlasmidFeature> $aFeatures[, int|null $iSequenceLength = null ]) : string
Parameters
$sSeqId : string
$aFeatures : array<string|int, PlasmidFeature>
$iSequenceLength : int|null = null

Length of the circular molecule the features lie on ; required to write an origin-crossing feature, which GFF3 encodes as end + this length on a landmark flagged Is_circular=true

Return values
string

escapeAttributeValue()

Percent-encodes the GFF3 column-9 reserved characters (and control characters that would otherwise break the one-line-per-feature format).

private escapeAttributeValue(string $sValue) : string
Parameters
$sValue : string
Return values
string

isCircularLandmark()

True for a feature read in from GFF3 as the "region" landmark spanning the whole molecule.

private isCircularLandmark(PlasmidFeature $oFeature, int $iSequenceLength) : bool
Parameters
$oFeature : PlasmidFeature
$iSequenceLength : int
Return values
bool

writeFeatureLine()

private writeFeatureLine(string $sSeqId, PlasmidFeature $oFeature, int|null $iSequenceLength, bool $bIsLandmark) : string
Parameters
$sSeqId : string
$oFeature : PlasmidFeature
$iSequenceLength : int|null
$bIsLandmark : bool

Flags the line as the circular landmark

Return values
string
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