Documentation

ParseSwissprotManager extends ParseDbAbstractManager

in package

• Amelaye
• BioPHP
• Domain
• Parser
• Service

Class ParseSwissprotManager

Tags

author

Amélie DUVERNET aka Amelaye amelieonline@gmail.com

Table of Contents

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

$geneNames  : array<string|int, mixed>

Gene names, as groups of synonyms: ( (GNAME1, GNAME2), (GNAME3) ).

$notupdDate  : string

Date of the last annotation update, read from the DT lines.

$sequpdDate  : string

Date of the last sequence update, read from the DT lines. The Sequence entity only carries the creation date, so the two other DT dates stay on the parser.

$taxonomyId  : string

NCBI taxonomy identifier of the source organism (OX line), "" when absent

Methods

__construct()  : mixed

Constructor.

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

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

getEntryId()  : string

Extracts the identifier uniquely naming a Swiss-Prot entry.

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

getFormat()  : string

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

getGbSequence()  : GbSequence

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

Gene names (GN line), as groups of synonyms.

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

getmin()  : int

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

getNotupdDate()  : string

Date of the last annotation update (DT line).

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

getSequence()  : Sequence

getSequpdDate()  : string

Date of the last sequence update (DT line).

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

getSrcForm()  : SrcForm

getTaxonomyId()  : string

NCBI taxonomy identifier of the source organism (OX line), "9606" for Homo sapiens ; "" when the entry has none.

intrim()  : mixed

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

isEntryEnd()  : bool

Tells whether a line closes a Swiss-Prot entry.

isEntryStart()  : bool

Tells whether a line opens a new Swiss-Prot entry.

left()  : bool|string

Returns the first $numchars characters of a string.

parseDataFile()  : Sequence

Parses a Swiss-Prot / UniProtKB data file. Both layouts are read : the original one ("ID TNFA_HUMAN STANDARD; PRT; 233 AA.", "DT ... (REL. 01, CREATED)", "RX MEDLINE; n.") and the current UniProt one ("ID POLS2_HUMAN Reviewed; 855 AA.", "DT ..., integrated into UniProtKB/Swiss-Prot.", "RX PubMed=n; DOI=...;", structured DE and GN lines), as described in the UniProtKB user manual. The feature table is read in its column layout (key, from, to, description, continued on lines whose key column is blank) and in the one used since release 2019_11 ("FT CHAIN 47..855" followed by /note="..." qualifiers).

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.

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

Parses AC lines, which may be several Format : AC P01375; Q9UIV3;

buildDEFields()  : mixed

Sets the description from the DE lines, joined, and whether the sequence is a fragment : "(FRAGMENT)." or "(FRAGMENTS)." ending the original layout, "Flags: Fragment;" or "Flags: Fragments;" in the UniProt one.

buildDRField()  : mixed

Parses DR lines Format : DR DATA_BANK; PRIMARY_IDENTIFIER; SECONDARY_IDENTIFIER[; ...]. [ISOFORM] The first two identifiers are kept ; a trailing isoform reference ("[Q5K4E3-1]") is not part of them.

buildDTFields()  : mixed

Parses DT Line, in the original layout ("21-JUL-1986 (REL. 01, CREATED)", "LAST SEQUENCE UPDATE", "LAST ANNOTATION UPDATE") or the UniProt one ("15-MAR-2005, integrated into UniProtKB/Swiss-Prot.", "sequence version 2.", "entry version 123.").

buildFTField()  : mixed

Parses one feature of the FT lines, with the lines continuing it.

buildGNField()  : mixed

Sets the gene names from the GN lines, as groups of synonyms.

buildIDFields()  : mixed

Parses ID line Format : ID PROTNAME_PROTSOURCE DATA_CLASS; [MOL_TYPE;] LENGTH AA.

buildKWFields()  : mixed

Parses KW Fields Format : KW WORD1; WORD2; WORD3; etc .

buildOCField()  : mixed

Parses OC lines Format : OC EUKARYOTA; METAZOA; CHORDATA; VERTEBRATA; TETRAPODA; MAMMALIA; OC EUTHERIA; PRIMATES.

buildOSFields()  : mixed

Parses OS line Format : OS HOMO SAPIENS (HUMAN).

buildRNField()  : mixed

Parses a reference : the RN line and the RP, RC, RX, RG, RA, RT and RL lines following it, each of which may span several lines.

buildSQField()  : mixed

Parses SQ lines and below SQ SEQUENCE XXXX AA; XXXXX MW; XXXXX CN;

featureDescription()  : string

Joins the description lines of a feature : free text continued over several lines, or the /note="..." qualifier of the 2019_11 layout. A line broken right after a hyphen continues the same word ("PROSITE-" + "ProRule"). The evidence tags ({ECO:0000255}), the /FTId, /id and /evidence qualifiers and the final period are provenance and punctuation, not description.

featurePosition()  : int|null

makeRefArray()  : mixed

Creates the Reference and Author entities, numbered as the RN lines number them.