Package 'genbankr'

Annotation extraction api

Description

Accessor functions shared with the larger Bioconductor ecosystem.

Usage

## S4 method for signature 'GenBankRecord'
cds(x)

## S4 method for signature 'GenBankRecord'
exons(x)

## S4 method for signature 'GenBankRecord'
genes(x)

## S4 method for signature 'GenBankRecord'
transcripts(x)

## S4 method for signature 'GenBankRecord'
getSeq(x, ...)

## S4 method for signature 'GenBankFile'
getSeq(x, ...)

## S4 method for signature 'GBAccession'
getSeq(x, ...)

## S4 method for signature 'GenBankRecord'
cdsBy(x, by = c("tx", "gene"))

## S4 method for signature 'GenBankRecord'
exonsBy(x, by = c("tx", "gene"))

## S4 method for signature 'GenBankRecord'
isCircular(x)

## S4 method for signature 'GenBankRecord'
seqinfo(x)

Arguments

x	The object containing the annotations
...	unused.
by	character. Factor to group the resulting GRanges by.

Value

The expected types, GenomicRanges for most functions, a DNAStrimgSet for getSeq

Examples

gb = readGenBank(system.file("sample.gbk", package="genbankr"))
cds(gb)
exons(gb)
genes(gb)

---

GBAccession ID class

Description

A class representing the (versioned) GenBank accession

Usage

GBAccession(id)

Arguments

id	A versioned GenBank Accession id

Value

a GBAccession object.

Examples

id = GBAccession("U49845.1")
## Not run: gb = readGenBank(id)

---

genbankr specific api

Description

Accessor functions specific to genbankr objects.

Usage

accession(x, ...)

## S4 method for signature 'GenBankRecord'
accession(x)

definition(x, ...)

## S4 method for signature 'GenBankRecord'
definition(x)

locus(x, ...)

## S4 method for signature 'GenBankRecord'
locus(x)

vers(x, ...)

## S4 method for signature 'GenBankRecord'
vers(x)

sources(x, ...)

## S4 method for signature 'GenBankRecord'
sources(x)

Arguments

x	A genbank annotation object
...	unused.

Value

Character vectors for accession and vers

Examples

gb = readGenBank(system.file("sample.gbk", package="genbankr"))
accession(gb)
vers(gb)

---

GenBank File

Description

A resource class for use within the rtracklayer framework

Create a GenBankFile object.

Usage

GenBankFile(fil)

Arguments

fil	character. Path to the genbank file

Value

A GenBankFile object

Examples

fil = GenBankFile(system.file("sample.gbk", package="genbankr"))
gb = import(fil)

---

GenBank data objects

Description

These objects represent GenBank annotations

Examples

gb = readGenBank(system.file("sample.gbk", package="genbankr"))
gb

---

Import genbank file

Description

Import a genbank file using the rtracklayer API.

Usage

## S4 method for signature 'GenBankFile,ANY,ANY'
import(con, format, text, ...)

Arguments

con	See import docs.
format	See import docs.
text	See import docs.
...	Arguments passed to readGenBank

Value

A GenBankRecord object.

---

Extract intergenic regions from processed GenBank annotations

Description

Extract the intergenic regions from a set of GenBank annotations.

Usage

## S4 method for signature 'GenBankRecord'
intergenic(x)

Arguments

x	A GenBankRecord object

Value

A GRanges for the intergenic regions, defined as regions not overlapping any genes defined in the annotations on either strand.

Examples

gb = readGenBank(system.file("sample.gbk", package="genbankr"))
intergenic(gb)

---

GenBank object constructors

Description

Constructors for GenBankRecord objects.

Usage

make_gbrecord(rawgbk, verbose = FALSE)

Arguments

rawgbk	list. The output of parseGenBank
verbose	logical. Should informative messages be shown

Value

A GenBankRecord object

Examples

prsed = parseGenBank(system.file("sample.gbk", package="genbankr"))
gb = make_gbrecord(prsed)

---

Create a TxDb from a GenBank record

Description

Create a TxDb object from a GenBankRecord.

Usage

makeTxDbFromGenBank(gbr, reassign.ids = FALSE)

## S4 method for signature 'GenBankRecord'
makeTxDbFromGenBank(gbr, reassign.ids = FALSE)

## S4 method for signature 'GBAccession'
makeTxDbFromGenBank(gbr, reassign.ids = FALSE)

Arguments

gbr	A GenBankRecord or GBAccession object
reassign.ids	logical. Passed down to makeTxDb

Value

A TxDb object

Examples

thing = readGenBank(system.file("unitTests/compjoin.gbk", package="genbankr"))
tx = makeTxDbFromGenBank(thing)

---

Retrieve 'other' features

Description

Retrieve the other features (not covered by a different accessor) from the set of annotations

Usage

otherFeatures(x)

## S4 method for signature 'GenBankRecord'
otherFeatures(x)

Arguments

x	a GenBankRecord object

Value

A GRanges containing the features which don't fall into another category (ie not gene, exon, transcript, cds, or variant) annotated in the source file

Examples

gb = readGenBank(system.file("sample.gbk", package="genbankr"))
otherFeatures(gb)

---

Parse raw genbank file content

Description

Parse genbank content and return a low-level list object containing each component of the file.

Usage

parseGenBank(file, text = readLines(file), partial = NA, verbose = FALSE,
  ret.anno = TRUE, ret.seq = TRUE)

Arguments

file	character. The file to be parsed. Ignored if text is specified
text	character. The text to be parsed.
partial	logical. If TRUE, features with non-exact boundaries will be included. Otherwise, non-exact features are excluded, with a warning if partial is NA (the default).
verbose	logical. Should informative messages be printed to the console as the file is being processed.
ret.anno	logical. Should the annotations in the GenBank file be parsed and included in the returned object. (Defaults to TRUE)
ret.seq	logical. Should the origin sequence (if present) in the GenBank file be included in the returned object. (Defaults to TRUE)

Value

if ret.anno is TRUE, a list containing the parsed contents of the file, suitable for passing to make_gbrecord. If ret.anno is FALSE, a DNAStringSet object containing the origin sequence.

Note

This is a low level function not intended for common end-user use. In nearly all cases, end-users (and most developers) should call readGenBank or create a GenBankFile object and call import instead.

Examples

prsd = parseGenBank(system.file("sample.gbk", package="genbankr"))

---

Read a GenBank File

Description

Read a GenBank file from a local file, or retrieve and read one based on an accession number. See Details for exact behavior.

Usage

readGenBank(file, text = readLines(file), partial = NA, ret.seq = TRUE,
  verbose = FALSE)

Arguments

file	character or GBAccession. The path to the file, or a GBAccession object containing Nuccore versioned accession numbers. Ignored if text is specified.
text	character. The text of the file. Defaults to text within file
partial	logical. If TRUE, features with non-exact boundaries will be included. Otherwise, non-exact features are excluded, with a warning if partial is NA (the default).
ret.seq	logical. Should an object containing the raw ORIGIN sequence be created and returned. Defaults to TRUE. If FALSE, the sequence slot is set to NULL. See NOTE.
verbose	logical. Should informative messages be printed to the console as the file is processed. Defaults to FALSE.

Details

If a a GBAccession object is passed to file, the rentrez package is used to attempt to fetch full GenBank records for all ids in the

Often times, GenBank files don't contain exhaustive annotations. For example, files including CDS annotations often do not have separate transcript features. Furthermore, chromosomes are not always named, particularly in organisms that have only one. The details of how genbankr handles such cases are as follows:

In files where CDSs are annotated but individual exons are not, 'approximate exons' are defined as the individual contiguous elements within each CDS. Currently, no mixing of approximate and explicitly annotated exons is performed, even in cases where, e.g., exons are not annotated for some genes with CDS annotations.

In files where transcripts are not present, 'approximate transcripts' defined by the ranges spanned by groups of exons are used. Currently, we do not support generating approximate transcripts from CDSs in files that contain actual transcript annotations, even if those annotations do not cover all genes with CDS/exon annotations.

Features (gene, cds, variant, etc) are assumed to be contained within the most recent previous source feature (chromosome/physical piece of DNA). Chromosome name for source features (seqnames in the resulting GRanges/VRanges is determined as follows:

1. The 'chromosome' attribute, as is (e.g., "chr1");

2. the 'strain' attribute, combined with auto-generated count (e.g., "VR1814:1");

3. the 'organism' attribute, combined with auto-generated count (e.g. "Human herpesvirus 5:1".

In files where no origin sequence is present, importing varation features is not currently supported, as there is no easy/ self-contained way of determining the reference in those situations and the features themselves list only alt. If variation features are present in a file without origin sequence, those features are ignored with a warning.

Currently some information about from the header of a GenBank file, primarily reference and author based information, is not captured and returned. Please contact the maintainer if you have a direct use-case for this type of information.

Value

A GenBankRecord object containing (most, see detaisl) of the information within file/text Or a list of GenBankRecord objects in cases where a GBAccession vector with more than one ID in it is passed to file

Note

We have endeavored to make this parser as effcient as easily possible. On our local machines, a 19MB genbank file takes 2-3 minutes to be parsed. That said, this function is not tested and likely not suitable for processing extremely large genbank files.

The origin sequence is always parsed when calling readGenBank, because it is necessary to generate a VRanges from variant features. So currently ret.seq=FALSE will not reduce parsing time, or maximum memory usage, though it will reduce memory usage by the final GenBankRecord object. The lower-level parseGenBank does skil parsing the sequence at all via ret.seq=FALSE, but variant annotations will be excluded if make_gbrecord is called on the resulting parsed list.

Examples

gb = readGenBank(system.file("sample.gbk", package="genbankr"))

---

Retrieve variantion features

Description

Extract the annotated variants from a GenBankRecord object

Usage

variants(x)

## S4 method for signature 'GenBankRecord'
variants(x)

Arguments

x	a GenBankRecord object

Value

A VRanges containing the variations annotated in the source file

Examples

gb = readGenBank(system.file("sample.gbk", package="genbankr"))
variants(gb)

---