Documentation

ParseKeggGenomeManager extends ParseKeggAbstractManager

in package

• Amelaye
• BioPHP
• Domain
• Parser
• Service

Class ParseKeggGenomeManager A genome record names one sequenced organism KEGG holds pathways for, and ties it to the NCBI taxonomy. Not to be confused with ParseGenomeManager, which reads the sequencing statistics of the Legacy "DOGS" records.

Tags

author

Amélie DUVERNET aka Amelaye amelieonline@gmail.com

Table of Contents

Properties

$entry  : string

$names  : array<string|int, mixed>

$rawFields  : array<string|int, mixed>

The lines of each field as readFields() gathered them, but with the indentation past the thirteenth column kept : it tells a wrapped line from a new item.

$definition  : string

$lineage  : array<string|int, mixed>

$taxonomy  : string

NCBI taxonomy identifier, read out of the "TAX:" prefix the field writes it with.

Methods

__construct()  : mixed

Constructor.

getDefinition()  : string

getEntry()  : string

getEntryId()  : string

Extracts the identifier uniquely naming a KEGG record.

getFormat()  : string

The name this format is known by in the collection records and in DatabaseParserFactory.

getLineage()  : array<string|int, mixed>

getNames()  : array<string|int, mixed>

getTaxonomy()  : string

isEntryEnd()  : bool

Tells whether a line closes a KEGG record. KEGG closes on three slashes where most flat files use two.

isEntryStart()  : bool

Tells whether a line opens a new KEGG record.

parseDataFile()  : Sequence

Parses a KEGG genome data file and populates this manager's fields.

joinLines()  : string

Joins the lines of a field into one string. A line opening with "$" continues the word the line above broke off, so it joins without a space.

parseDbLinks()  : array<string|int, mixed>

Reads a DBLINKS field into pairs of database name and identifier, one per line.

parsePathways()  : array<string|int, mixed>

Reads a PATHWAY field into pairs of map identifier and pathway name, one per line : the identifier is the first word (map00010, ec00010, ko00010...), behind a "PATH:" tag in the files before 2008. A line not opening on an identifier continues the name above it.

readData()  : string

Reads the data a line carries, which starts at its thirteenth column.

readEntryId()  : string

Reads the identifier out of an ENTRY line. The words after it name the kind of record rather than the record itself - "C00031 Compound", "T01001 Complete Genome" - so the identifier is the first word, or for an enzyme the two words "EC" and its number ("EC 2.7.1.1 Enzyme").

readFields()  : array<string|int, mixed>

Gathers a record into its fields : one entry per label, holding the data of its own line and of every continuation line below it.

readItems()  : array<string|int, mixed>

Reads a field listing one item per line, a trailing ";" dropped. A long item wraps onto a line indented past the column the items start at, which continues it.

readLabel()  : string

Reads the label a line carries in its first twelve columns.

splitTokens()  : array<string|int, mixed>

Splits the lines of a field into the whitespace-separated identifiers they list.

readTaxonomy()  : string

Reads the TAXONOMY line, which carries the identifier behind a "TAX:" prefix.