altcdfenvs (version 2.34.0)

read.FASTA.entry: Functions to work with FASTA files / connections

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, ...)
"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

Value

The value returned depends on the function. See above.

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.

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)