For a given accession number, get the domain sequences using a interproscan output table & the original FASTA file

Usage

createIPRScanDomainTable(
  accnum,
  fasta,
  df_iprscan,
  analysis = c("Pfam", "Gene3D")
)

Arguments

accnum: chr a single accession number from the original fasta (fasta param) which will be used to search for its sequence's domains (df_iprscan param)
fasta: AAStringSet original fasta file which was fed into interproscan
df_iprscan: tbl_df the output TSV of interproscan, read as a tibble with readIPRScanTSV()
analysis: chr the domain databases to extract sequences from

Value

tbl_df table with each domain sequence and a new identifier column

Examples

if (FALSE) { # \dontrun{
path_molevol_scripts <- file.path(Sys.getenv("DEV", unset = "/data/molevolvr_transfer/molevolvr_dev"), "molevol_scripts")
setwd(path_molevol_scripts)
source("R/fa2domain.R")
fasta <- Biostrings::readAAStringSet("./tests/example_protein.fa")
df_iprscan <- readIPRScanTSV("./tests/example_iprscan_valid.tsv")
accnum <- df_iprscan$AccNum[1]
df_iprscan_domains <- createIPRScanDomainTable(accnum, fasta, df_iprscan)
} # }