REFERENCE_SUBKEYS
REFERENCE_SUBKEYS = ["AUTHORS", "TITLE", "JOURNAL", "MEDLINE", "PUBMED", "REMARK"]
Subkeys of a REFERENCE block, indented under it.
Class ParseEntrezManager An Entrez genome record describes a whole genome the way GenBank describes an entry : same LOCUS columns, same 12-character label column. It carries neither a FEATURES table nor an ORIGIN sequence though, so it holds annotation only and this class exposes plain scalars and EntrezReferenceInterface objects rather than the Sequence/Feature entities of ParseDbAbstractManager.
Two deliberate departures from Legacy/entrez.inc.php, which called three helpers (is_notmt(), monthno(), topo_code()) that exist nowhere in the original source and could therefore never run : the strand count reads SINGLE/DOUBLE/MIXED and the date is kept as the file writes it, both as ParseGenbankManager already does for the very same LOCUS columns, rather than being normalised to "SS"/"DS" and to an ISO date.
$references : \Amelaye\BioPHP\Domain\Parser\Interfaces\EntrezReferenceInterface[]
getEntryId(array $aFlines, string $sLine) : string
Extracts the identifier uniquely naming an Entrez genome record, which is its first accession number. A record short of an ACCESSION line falls back on its LOCUS name.
| array | $aFlines | The whole file, buffered |
| string | $sLine | The line opening the entry |
parseDataFile(array $aFlines) : \Amelaye\BioPHP\Domain\Sequence\Entity\Sequence
Parses an Entrez genome data file and populates this manager's fields.
| array | $aFlines | The lines the script has to parse |
$oSequence
accumulate(\ArrayIterator $aLines, array $aFlines, bool $bSkipFirstLine = false) : string
Accumulates a field written over several lines : the data of the current line, plus every continuation line below it, joined by a space. Advances $aLines past what it reads.
| \ArrayIterator | $aLines | |
| array | $aFlines | |
| bool | $bSkipFirstLine | Reads the continuation lines only |
startReference(string $sLine) : \Amelaye\BioPHP\Domain\Parser\Interfaces\EntrezReferenceInterface
Opens the reference a REFERENCE line announces.
Format : REFERENCE 1 (bases 1 to 48502)
| string | $sLine |
fillReference(string $sSubkey, \ArrayIterator $aLines, array $aFlines) : mixed
Fills one subkey of the reference being read. A subkey met before any REFERENCE line has no reference to belong to and is dropped.
| string | $sSubkey | |
| \ArrayIterator | $aLines | |
| array | $aFlines |
splitAuthors(string $sText) : array
Splits an AUTHORS field into individual names. Names are separated by a comma and a space, the last two by "and" - the comma inside a name itself ("Sanger,F.") carries no space and holds the name together.
Format : Sanger,F., Coulson,A.R., Hong,G.F. and Petersen,G.B.
| string | $sText |