process.orf.fasta.file: Import contig data from a fasta file

In rbhwilliams/orf.lcam: Processing taxonomic and functional data from lcamapper

Description

Extracts basic information about ORFs obtained by MetaGeneMark

Usage

process.orf.fasta.file(orf.fa,mainSplitString)

Arguments

orf.fa	'orf.fa' is a .fasta file generated by MetaGeneMark, containing the DNA sequence from each predicted ORF
mainSplitString	'mainSplitString' (character string) gives you flexibility about how to split up the ORF header...seems to be some variability in how MetaGeneMark encodes this?

Value

A data.frame containing three columns (contig /cov/erage, contig /len/ength and cognate ORF-id (simplified)). Row names are ORF identifiers.

Examples

## Not run: a<-extract.contig.data()
## Not run: b<-process.orf.fasta.file("UM-32-0_nucl_mod.fasta")

rbhwilliams/orf.lcam documentation built on May 27, 2019, 3 a.m.