Retrieve the longest isoforms of several proteome files stored in a folder

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_all(
  proteome_folder,
  annotation_folder,
  output_folder,
  annotation_format = "gff"
)

Arguments

proteome_folder

file path to proteome in fasta file format.

annotation_folder

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

output_folder

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) {
orgs <- c("Arabidopsis lyrata", 
          "Capsella rubella", "Solanum lycopersicum")
# download proteome files for all species          
biomartr::getProteomeSet(db = "refseq", organisms = orgs, path = "of_proteomes")
# download annotation files for all species          
biomartr::getGFFSet(db = "refseq", organisms = orgs, path = "of_gff")
# select longest splice variant per gene locus
retrieve_longest_isoforms_all(proteome_folder = "of_proteomes", 
                              annotation_folder = "of_gff",
                              annotation_format = "gff", 
                              output_folder = "of_proteomes_longest_sv")
}