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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')

Monthly Downloads

10

Version

1.0.0

License

MIT + file LICENSE

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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
gbFeature-class

Class "gbFeature"
gbLocation-class

Class "gbLocation"
geneID

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.