biofiles (version 1.0.0)

An Interface for GenBank/GenPept Flat Files

Description

Parse GenBank/GenPept records into native R objects to easily access and manipulate the sequence and annotation information.

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Install

install.packages('biofiles')

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Version

1.0.0

License

MIT + file LICENSE

Issues

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Repository

https://github.com/gschofl/biofiles

Maintainer

Gerhard Schöfl

Last Published

November 21st, 2017

Functions in biofiles (1.0.0)

.filter

Filter gbFeatures from a FeatureTable

.select

Select annotations from a FeatureTable

[[,gbFeature,character,missing-method

Method extensions to extraction operator for gbRecord objects.

featureTable

Tabulate Genbank features

biofiles

biofiles is an R package for interfacing with GenBank or Embl flat file records.

getLocus

Access the various fields of a GenBank record.

dbxref

Access the db_xrefs of GenBank features

as.gbLocation

Create a gbLocation.

fuzzy

Has a feature fuzzy locations?

embl_record

Parser for Embl Records.

end

Get or set the end position of genomic features

Return the gene qualifiers from GenBank features.

gbLocus-class

Generator object for the "gbLocus" reference class

genomeRecordFromNCBI

Fetch genomes from NCBI

gbRecordList-class

Class "gbRecordList"

qualifTable

Tabulate Genbank qualifiers

ranges

Extract features as "'>GRanges" objects.

gbReference-class

Generator object for the "gbReference" reference class

strand

Get or set the strand information of genomic features

getHeader

Extract the header from a "'>gbRecord" object.

summary

Summarise a GenBank record.

getSequence

Get the sequence from a GenBank record.

note

Return the note qualifiers from GenBank features.

pad

Pad a string

has_command

Test if an external executable is available

index

Access the indices of GenBank features

hasKey

Has a feature a specific key?

revcomp

Reverse-complement features in a GenBank record

hasQualif

Has a feature a specific qualifier?

saveRecord

Save and load gbRecord objects.

linebreak

Format paragraphs

write.FeatureTable

Write GenBank records or features to file in Feature Table format

gbRecord-class

Class "gbRecord"

write.GenBank

Write GenBank records or features to file in GenBank format

gbRecord

Read a GenBank/GenPept or Embl format file.

key

Get/set keys of GenBank features

length,gbRecord-method

Get the number of gbFeatures.

getContigSeq

Retrieve the sequence of a contig

product

Return the product qualifiers from GenBank features.

getFeatures

Get the feature table from a GenBank record.

proteinID

Return the protein_id qualifiers from GenBank features.

gbFeatureTable-class

Class "gbFeatureTable"

upstream

Find flanking features.

gbHeader-class

Generator object for the "gbHeader" reference class

location

Access genomic locations of GenBank features

shift

Shift the location of features in a GenBank record

gbReferenceList-class

Generator object for the "gbReferenceList" reference class

view

View all features in a gbFeatureTable

gbk_record

Parser for GenBank/GenPept records.

start

Get or set the start position of genomic features

locusTag

Return the locus_tag qualifiers from GenBank features.

seqinfo-class

Generator object for the "seqinfo" reference class

filter

Return a subset of features or annotations from a GenBank Record

translation

Return the translations from GenBank features.

uniqueQualifs

Quickly list all qualifier names.

qualif

Get/set qualifiers of GenBank features

qualifList

List the names of Genbank qualifiers.

span

Get the span of genomic features.