panPrep: Preparing FASTA files for pan-genomics

Description

Preparing a FASTA file before starting comparisons of sequences.

Usage

panPrep(in.file, genome_id, out.file, protein = TRUE, min.length = 10, discard = "")

Arguments

in.file

The name of a FASTA formatted file with protein or nucleotide sequences for coding genes in a genome.

genome_id

The Genome Identifier, see below.

out.file

Name of file where the prepared sequences will be written.

protein

Logical, indicating if the in.file contains protein (TRUE) or nucleotide (FALSE) sequences.

min.length

Minimum sequence length

discard

A text, a regular expression, and sequences having a match against this in their headerline will be discarded.

Value

This function produces a FASTA formatted sequence file, and returns the name of this file.

Details

This function will read the in.file and produce another, slightly modified, FASTA file which is prepared for the comparisons using blastpAllAll, hmmerScan or any other method.

The main purpose of panPrep is to make certain every sequence is labeled with a tag called a genome_id identifying the genome from which it comes. This text contains the text “GID” followed by an integer. This integer can be any integer as long as it is unique to every genome in the study. If a genome has the text “GID12345” as identifier, then the sequences in the file produced by panPrep will have headerlines starting with “GID12345_seq1”, “GID12345_seq2”, “GID12345_seq3”...etc. This makes it possible to quickly identify which genome every sequence belongs to.

The genome_id is also added to the file name specified in out.file. For this reason the out.file must have a file extension containing letters only. By convention, we expect FASTA files to have one of the extensions .fsa, .faa, .fa or .fasta.

panPrep will also remove sequences shorter than min.length, removing stop codon symbols (*), replacing alien characters with X and converting all sequences to upper-case. If the input discard contains a regular expression, any sequences having a match to this in their headerline are also removed. Example: If we use the prodigal software (see findGenes) to find proteins in a genome, partially predicted genes will have the text partial=10 or partial=01 in their headerline. Using discard= "partial=01|partial=10" will remove these from the data set.

Examples

Run this code

# NOT RUN {
# Using a protein file in this package
# We need to uncompress it first...
pf <- file.path(path.package("micropan"),"extdata","xmpl.faa.xz")
prot.file <- tempfile(fileext = ".xz")
ok <- file.copy(from = pf, to = prot.file)
prot.file <- xzuncompress(prot.file)

# Prepping it, using the genome_id "GID123"
prepped.file <- panPrep(prot.file, genome_id = "GID123", out.file = tempfile(fileext = ".faa"))

# Reading the prepped file
prepped <- readFasta(prepped.file)
head(prepped)

# ...and cleaning...
ok <- file.remove(prot.file, prepped.file)

# }