Simply put, the genbankr package parses files in the NCBI’s GenBank (gb/gbk)
format into R.
The primary workhorse is provided by the readGenBank function, which accepts
either a GenBank file (via the file argument) or raw text in the GenBank
format (via the text argument).
suppressPackageStartupMessages(library(genbankr))
smpfile = system.file("sample.gbk", package="genbankr")
gb = readGenBank(smpfile)## Annotations don't have 'locus_tag' label, using 'gene' as gene_id column
## Annotations don't have 'locus_tag' label, using 'gene' as gene_id column## No exons read from genbank file. Assuming sections of CDS are full exons## No transcript features (mRNA) found, using spans of CDSs## Warning in fill_stack_df(feats[!typs %in% c("gene", "exon", "CDS",
## "variation", : Got unexpected multi-value field(s) [ rpt_type ]. The resulting
## column(s) will be of class CharacterList, rather than vector(s). Please contact
## the maintainer if multi-valuedness is expected/meaningful for the listed
## field(s).gb## GenBank Annotations
## Human herpesvirus 5 strain VR1814, complete genome.
## Accession: GU179289
## 1 Sequence(s) with total length length: 235233
## 174 genes
## 170 transcripts
## 191 exons/cds elements
## 61 variations
## 24 other featuresreadGenBank generates a GenBankFull object, which contains the annotations and
the origin sequence. genbankr provides methods for the AnnotationDbi API
functions for retrieving information from the object.
We can retreive the genes via the function of the same name:
genes(gb)## GRanges object with 174 ranges and 5 metadata columns:
## seqnames ranges strand | type gene loctype
## <Rle> <IRanges> <Rle> | <character> <character> <character>
## [1] VR1814 1232-2164 + | gene RL1 normal
## [2] VR1814 2353-4863 - | gene RNA2.7 normal
## [3] VR1814 5252-5539 - | gene RL5A normal
## [4] VR1814 5888-6223 - | gene RL6 normal
## [5] VR1814 6622-7677 - | gene RNA1.2 normal
## ... ... ... ... . ... ... ...
## [170] VR1814 229242-229793 + | gene US32 normal
## [171] VR1814 229995-230168 + | gene US33A normal
## [172] VR1814 230337-230828 + | gene US34 normal
## [173] VR1814 230822-231016 + | gene US34A normal
## [174] VR1814 231986-234349 - | gene TRS1 normal
## note gene_id
## <character> <character>
## [1] <NA> RL1
## [2] <NA> RNA2.7
## [3] <NA> RL5A
## [4] <NA> RL6
## [5] <NA> RNA1.2
## ... ... ...
## [170] <NA> US32
## [171] <NA> US33A
## [172] <NA> US34
## [173] <NA> US34A
## [174] putative beta gene; .. TRS1
## -------
## seqinfo: 1 sequence from GU179289.1 genomeWe can also do the same for exons, cds elements, and transcripts (code run but output ommitted for brevity):
cds(gb)
exons(gb)
transcripts(gb)We can also access elements not in the standard TxDb API, such as variants and features which don’t fit into any of the other categories:
variants(gb)
otherFeatures(gb)Furthermore, we can access header-level information via accessors as well:
accession(gb)## [1] "GU179289"vers(gb)## accession.version GenInfoID
## "GU179289.1" "270355759"We can get the seqinfo for a GenBankAnnot/GenBankFull object:
seqinfo(gb)## Seqinfo object with 1 sequence from GU179289.1 genome:
## seqnames seqlengths isCircular genome
## VR1814 235233 FALSE GU179289.1Finally, we can ge the sequence itself from a GenBankFull object:
getSeq(gb)## DNAStringSet object of length 1:
## width seq names
## [1] 235233 CCATTCCGGGCCGCGTGCTGGGT...GCCGCCAGTGCGGGACAGGGCT VR1814While use and integration of the Bioconductor machinery is recommended, we also provide low-level parsing capabilities via the workhorse parseGenBank function. This function returns a list structure roughly corresponding to the top-level headings within the genbank format itself:
pg = parseGenBank(smpfile)
str(pg, max.level = 1)## List of 10
## $ LOCUS : chr "LOCUS GU179289 235233 bp DNA linear VRL 09-MAY-2013"
## $ FEATURES :List of 429
## ..- attr(*, "dim")= int 429
## ..- attr(*, "dimnames")=List of 1
## $ ORIGIN :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots
## $ ACCESSION : chr "GU179289"
## $ COMMENT : NULL
## $ DEFINITION: chr "Human herpesvirus 5 strain VR1814, complete genome."
## $ KEYWORDS : chr NA
## $ REFERENCE : NULL
## $ SOURCE :List of 3
## $ VERSION : Named chr [1:2] "GU179289.1" "270355759"
## ..- attr(*, "names")= chr [1:2] "accession.version" "GenInfoID"If desired, readGenBank and parseGenBank can omit full sequence of the organism by specifying ret.seq=FALSE. In this case, readGenBank returns a GenBankAnnot object, rather than a GenBankFull
gbf = readGenBank(smpfile, ret.seq = FALSE)## Annotations don't have 'locus_tag' label, using 'gene' as gene_id column
## Annotations don't have 'locus_tag' label, using 'gene' as gene_id column## No exons read from genbank file. Assuming sections of CDS are full exons## No transcript features (mRNA) found, using spans of CDSs## Warning in fill_stack_df(feats[!typs %in% c("gene", "exon", "CDS",
## "variation", : Got unexpected multi-value field(s) [ rpt_type ]. The resulting
## column(s) will be of class CharacterList, rather than vector(s). Please contact
## the maintainer if multi-valuedness is expected/meaningful for the listed
## field(s).gbf## GenBank Annotations
## Human herpesvirus 5 strain VR1814, complete genome.
## Accession: GU179289
## 1 Sequence(s) with total length length: 235233
## 174 genes
## 170 transcripts
## 191 exons/cds elements
## 61 variations
## 24 other featuresAll of the accessor methods discussed above work for GenBankFull objects as they do for GenBankAnnot objects.
We also provide a convenience method for using rtracklayer import style mechanics for reading GenBank files:
gbkfile = GenBankFile(smpfile)## Warning: This class is extending the deprecated RTLFile class from rtracklayer.
## Use BiocFile from BiocIO in place of RTLFile.gb2 = import(gbkfile)## Annotations don't have 'locus_tag' label, using 'gene' as gene_id column
## Annotations don't have 'locus_tag' label, using 'gene' as gene_id column## No exons read from genbank file. Assuming sections of CDS are full exons## No transcript features (mRNA) found, using spans of CDSs## Warning in fill_stack_df(feats[!typs %in% c("gene", "exon", "CDS",
## "variation", : Got unexpected multi-value field(s) [ rpt_type ]. The resulting
## column(s) will be of class CharacterList, rather than vector(s). Please contact
## the maintainer if multi-valuedness is expected/meaningful for the listed
## field(s).genbankr provides the GBAccession class and constructor for representing versioned Nuccore accession numbers.
gba = GBAccession("U49845.1")
gba## GenBank Accession Number(s): U49845.1These accession objects can be passed directly to readGenBank:
readGenBank(gba, partial=TRUE)## Loading required namespace: rentrez## Annotations don't have 'locus_tag' label, using 'gene' as gene_id column
## Annotations don't have 'locus_tag' label, using 'gene' as gene_id column## genes not available for all CDS ranges, using internal grouping ids## No exons read from genbank file. Assuming sections of CDS are full exons## Annotations don't have 'locus_tag' label, using 'gene' as gene_id column
## Annotations don't have 'locus_tag' label, using 'gene' as gene_id column## GenBank Annotations
## Saccharomyces cerevisiae TCP1-beta gene, partial cds; and Axl2p (AXL2) and Rev7p (REV7) genes, complete cds.
## Accession: U49845
## 1 Sequence(s) with total length length: 5028
## 2 genes
## 3 transcripts
## 3 exons/cds elements
## 0 variations
## 0 other featuresgenbankr also provides a fastpath for extracting only the sequence of an
organism. We can call getSeq on a GenBankFile or GBAccession object
getSeq(gbkfile)## DNAStringSet object of length 1:
## width seq names
## [1] 235233 CCATTCCGGGCCGCGTGCTGGGT...GCCGCCAGTGCGGGACAGGGCT VR1814Additionally, we can specify ret.anno = FALSE in parseGenBank
parseGenBank(smpfile, ret.anno=FALSE)## DNAStringSet object of length 1:
## width seq names
## [1] 235233 CCATTCCGGGCCGCGTGCTGGGT...GCCGCCAGTGCGGGACAGGGCT VR1814genbankr provides the makeTxDbFromGenBank function, which accepts a
GenBankRecord or GBAccession object and returns a TxDb of the
annotations.
gbr = readGenBank(smpfile)## Annotations don't have 'locus_tag' label, using 'gene' as gene_id column
## Annotations don't have 'locus_tag' label, using 'gene' as gene_id column## No exons read from genbank file. Assuming sections of CDS are full exons## No transcript features (mRNA) found, using spans of CDSs## Warning in fill_stack_df(feats[!typs %in% c("gene", "exon", "CDS",
## "variation", : Got unexpected multi-value field(s) [ rpt_type ]. The resulting
## column(s) will be of class CharacterList, rather than vector(s). Please contact
## the maintainer if multi-valuedness is expected/meaningful for the listed
## field(s).tx = makeTxDbFromGenBank(gbr)
tx## TxDb object:
## # Db type: TxDb
## # Supporting package: GenomicFeatures
## # accession.version: GU179289.1
## # GenInfoID: 270355759
## # genome: GU179289.1
## # source: NCBI (GenBank)
## # definition: Human herpesvirus 5 strain VR1814, complete genome.
## # Db content generated by: genbankr package from Bioconductor
## # genbankr version at creation time: 1.20.0
## # Nb of transcripts: 170
## # Db created by: GenomicFeatures package from Bioconductor
## # Creation time: 2021-05-19 20:14:09 -0400 (Wed, 19 May 2021)
## # GenomicFeatures version at creation time: 1.44.0
## # RSQLite version at creation time: 2.2.7
## # DBSCHEMAVERSION: 1.2Often 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:
Some GenBank files do not include origin sequence. In these cases, variation features are not supported, as there is no self-contained way to determine reference sequence and the features themselves typically contain only alt information (if that). In the case of files containing variation features but no 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.
We have taken pains to make the genbankr parser as effcient as easily possible. On our local machines, a 19MB genbank file takes 2-3 minutes to be parsed. That said, this package is not tested and likely is not suitable for processing extremely large genbank files. We suggest obtaining the annotations in a different format in such cases.