Retrieving annotated sequences
Retrieving from a genome the sequences specified in a gff.table.
gff2fasta(gff.table, genome)
gff.table |
A |
genome |
A fasta object ( |
Each row in gff.table (see readGFF) describes a genomic feature
in the genome, which is a tibble with columns Header and
Sequence. The information in the columns Seqid, Start, End and Strand are used to
retrieve the sequences from the Sequence column of genome. Every Seqid in
the gff.table must match the first token in one of the Header texts, in
order to retrieve from the correct Sequence.
A fasta object with one row for each row in gff.table.
The Header for each sequence is a summary of the information in the
corresponding row of gff.table.
Lars Snipen and Kristian Hovde Liland.
# Using two files in this package
gff.file <- file.path(path.package("microseq"),"extdata","small.gff")
genome.file <- file.path(path.package("microseq"),"extdata","small.fna")
# Reading the genome first
genome <- readFasta(genome.file)
# Retrieving sequences
gff.table <- readGFF(gff.file)
fa.tbl <- gff2fasta(gff.table, genome)
# Alternative, using piping
readGFF(gff.file) %>% gff2fasta(genome) -> fa.tblPlease choose more modern alternatives, such as Google Chrome or Mozilla Firefox.