Documentation

ParseGenbankManager extends ParseDbAbstractManager

in package

• Amelaye
• BioPHP
• Domain
• Parser
• Service

Class ParseGenbankManager

Tags

author

Amélie DUVERNET aka Amelaye amelieonline@gmail.com

Table of Contents

Constants

FEATURE_KEYS  : mixed = [ "assembly_gap", "C_region", "CDS", "centromer...

Every feature key of the INSDC Feature Table Definition (v11.4), followed by the keys it deprecated on 15-DEC-2014 in favour of "regulatory" + /regulatory_class, which plasmid files (SnapGene, Addgene...) still use widely. A key outside this list is skipped.

Properties

$accession  : array<string|int, mixed>

$authors  : array<string|int, mixed>

$features  : array<string|int, mixed>

$gbSequence  : GbSequence

$keywords  : array<string|int, mixed>

$references  : array<string|int, mixed>

$sequence  : Sequence

$spDatabank  : array<string|int, mixed>

$srcForm  : SrcForm

$aLines  : ArrayIterator|null

Methods

__construct()  : mixed

Constructor.

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

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

getEntryId()  : string

Extracts the identifier uniquely naming a GenBank entry, which is its primary accession (the key parseDataFile() gives to every row of the record, and ParseEntrezManager to its own). The LOCUS name is only a fallback for a record short of an ACCESSION line : the two differ in many records (LOCUS SCU49845, ACCESSION U49845).

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

getFormat()  : string

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

getGbSequence()  : GbSequence

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

getmin()  : int

Gets the minimum of three (usually numeric) values $x, $y, and $z.

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

getSequence()  : Sequence

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

getSrcForm()  : SrcForm

intrim()  : mixed

Removes "internal spaces" (as opposed to leading and trailing spaces) from a string.

isEntryEnd()  : bool

Tells whether a line closes a GenBank entry.

isEntryStart()  : bool

Tells whether a line opens a new GenBank entry.

left()  : bool|string

Returns the first $numchars characters of a string.

parseDataFile()  : Sequence

Parses a GenBank data file and returns a Seq object containing parsed data.

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

Reads the fields of a LOCUS line, word by word (see parseLocus()). Shared with ParseEntrezManager, whose records open on the same line.

rem_right()  : bool|string

Removes $charcount characters from the right (end) of a string.

right()  : bool|string

Returns the substring beginning at $numchars characters from the right end of a string.

setAccession()  : void

setAuthors()  : void

setFeatures()  : void

setGbSequence()  : void

setKeywords()  : void

setReferences()  : void

setSequence()  : void

setSpDatabank()  : void

setSrcForm()  : void

trim_element()  : mixed

trim_element() removes leading and trailing spaces from a string. In conjunction with the array_walk() function, it removes spaces from each element of an array.

parseInsdcFeature()  : mixed

Parses one feature of an INSDC feature table, shared by GenBank and EMBL, whose columns are the same : the key from column 6, the location (possibly wrapped over several lines) and the /qualifier lines from column 22. $aFlines is read ahead to find where the feature ends : a line holding something in its first 12 columns starts another feature or section, so EMBL hands its lines with their "FT" tag blanked out.

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

Parses an INSDC feature location (shared by GenBank and EMBL) into its outer bounds and strand, 1-based and inclusive. The location as written is kept apart (Feature::getFtLocation()) : these bounds only frame it.

parseAccession()  : mixed

Parses ACCESSION field : the primary accession, then the secondary ones, possibly continued on lines whose first 12 columns are blank. A record cut out of a larger one (a CON or contig sub-range) follows them with "REGION: from..to", which is not an accession.

parseDefinition()  : mixed

Parses DEFINITION field @ param array $flines

parseKeywords()  : mixed

Parses KEYWORDS field, possibly continued on lines whose first 12 columns are blank : the keywords are separated by ";" and the field closed by a period, alone when there is none.

parseLocus()  : mixed

Parses line LOCUS. NCBI writes its fields in fixed columns - name 13-28, length 30-40, strandedness 45-47, molecule type 48-53, topology 56-63, division 65-67, date 69-79 - but shifts them all right when the name is longer than its 16 columns (a WGS contig such as NZ_JAAXYZ010000001), so they are read as words : the name, the length before its unit (bp or aa), then the molecule type (absent from a protein record), topology, division and date, any of which may be missing.

parseOrganism()  : mixed

Parses information about organism

parseReferences()  : mixed

Parses a REFERENCE and its AUTHORS, CONSRTM, TITLE, JOURNAL, MEDLINE, PUBMED and REMARK lines, each possibly continued on lines whose first 12 columns are blank. Lines are read ahead : the iterator is left on the reference's last line, so that the section following it (FEATURES, COMMENT, the next REFERENCE) is read by the main loop and not skipped.

parseVersion()  : mixed

Parses VERSION field

readContinuedField()  : array<string|int, string>

Returns the data of the current line, past its 12 label columns, and of the lines continuing it (first 12 columns blank), leaving the iterator on the last of them.

setRecordKey()  : void

Gives the record its key, on the Sequence and on its GbSequence together : the one table joins the other on it, so they must never hold different values. LOCUS sets it first (the name), ACCESSION then replaces it with the primary accession, which is what getEntryId() indexes the record by.