utils.FASTA: Functions to work with FASTA files / connections

In altcdfenvs: alternative CDF environments (aka probeset mappings)

Description

Set of function to work with biological sequences stored in FASTA format.

Usage

countskip.FASTA.entries(con, linebreaks = 3000)
grep.FASTA.entry(pattern, con, ...)
## S3 method for class 'FASTA'
print(x, ...)
read.FASTA.entry(con, linebreaks = 3000)
read.n.FASTA.entries(con, n, linebreaks = 3000)
read.n.FASTA.entries.split(con, n, linebreaks = 3000)
read.n.FASTA.headers(con, n, linebreaks = 3000)
read.n.FASTA.sequences(con, n, linebreaks = 3000)
skip.FASTA.entry(con, skip, linebreaks = 3000)
write.FASTA(x, file="data.fasta", append = FALSE)

Arguments

append	append to the file (or not)
con	a connection
file	a file name
linebreaks	(to optimize the parsing, probably safe to leave it as it is)
n	number of entries to read
pattern	a pattern (to be passed to the function grep)
skip	number of entries to skip
x	a FASTA sequence object
...	optional arguments to be forwarded to the function print or to the function grep

Details

countskip.FASTA.entries skips the remaining FASTA entries currently remaining in the connection and return the count. grep.FASTA.entry returns the next FASTA entry in the connection that matches a given regular expression. print.FASTA prints a FASTA object. read.FASTA.entry reads the next FASTA entry in the connection. read.n.FASTA.entries reads the n next FASTA entries and returns a list of FASTA objects. read.n.FASTA.entries.split reads the n next FASTA entries and returns a list of two elements: headers and sequences. read.n.FASTA.headers reads the n next FASTA headers. read.n.FASTA.sequences reads the n next FASTA sequences. skip.FASTA.entry skips a given number of FASTA entries. write.FASTA write a FASTA object into a connection.

Value

The value returned depends on the function. See above.

Author(s)

Laurent Gautier

Examples

filename <- system.file("exampleData", "sample.fasta",
                        package="altcdfenvs")
con <- file(filename, open="r")

fasta.seq <- grep.FASTA.entry("NM_001544\\.2", con)
close(con)


print(fasta.seq)

Example output

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: affy
Loading required package: makecdfenv
Loading required package: affyio
Loading required package: Biostrings
Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: hypergraph
Loading required package: graph

Attaching package: 'graph'

The following object is masked from 'package:Biostrings':

    complement

Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'
FASTA sequence:
  NULL

altcdfenvs documentation built on Nov. 8, 2020, 7:12 p.m.