Retrieve the longest isoforms from a proteome file and save results as fasta file

Source: R/retrieve_longest_isoforms.R

Based on a fasta file storing the peptide isoforms of gene loci and an annotation file in gtf file format, this function extracts the longest isoform per gene locus and stores the results in a new fasta file. This procedure enables easier downstream analyses such as orthology inference etc when dealing with proteome fasta files which usually include isoform peptides.

retrieve_longest_isoforms(
  proteome_file,
  annotation_file,
  new_file,
  annotation_format = "gff"
)

Arguments

proteome_file

file path to proteome in fasta file format.

annotation_file

file path to the corresponding annotation file in gtf file format.

new_file

file path to new file storing only peptide sequences of the longest isoforms.

annotation_format

format of annotation_file. Options are:

  • annotation_file = "gff" (default)

  • annotation_file = "gtf"

Author

Hajk-Georg Drost

Examples

if (FALSE) {
# retrieve example data from ENSEMBLGENOMES
proteome <- biomartr::getProteome(db = "refseq", organism = "Arabidopsis thaliana")
annotation <- biomartr::getGFF(db = "refseq", organism = "Arabidopsis thaliana")
# retrieve longest isoforms and store in new file
retrieve_longest_isoforms(proteome_file = proteome, 
                          annotation_file = annotation, 
                          new_file = "Athaliana_pep_longest.fa")
# import new file into R session                          
Athaliana_pep_longest <- Biostrings::readAAStringSet("Athaliana_pep_longest.fa")
}