An lightweight R package parsing
FASTA (like those from
UniProt) files into an R usable list or
data.frame. The main function utilizes regular
expressions to
extract meta data along with the protein sequence. Some functions have been written
in Rust to optimize performance.
To install, open R and type:
install.packages("devtools")
devtools::install_github("jeffsocal/msfastar")Its simple to get started, just point the read_fasta() function at a
downloaded FASTA file and save as an object.
library(msfastar)
path_to_fasta <- system.file("extdata", "albu_human.fasta", package = "msfastar")
fasta_data <- read_fasta(path_to_fasta)
#> ℹ Parsing FASTA file albu_human.fasta
#> ✔ Parsing FASTA file albu_human.fasta ... done
#>
fasta_data[[1]]
#> $accession
#> [1] "P02768"
#>
#> $protein_name
#> [1] "ALBU_HUMAN"
#>
#> $gene_name
#> [1] "ALB"
#>
#> $organism
#> [1] "Homo sapiens"
#>
#> $description
#> [1] "Albumin"
#>
#> $sequence
#> [1] "MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEPERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLFFAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLKECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYARRHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVVLNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTLSEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLVAASQAALGL"In addition, the expected peptides can be generated with the digest()
function.
fasta_data <- lapply(fasta_data, digest)
fasta_data[[1]]
#> $accession
#> [1] "P02768"
#>
#> $protein_name
#> [1] "ALBU_HUMAN"
#>
#> $gene_name
#> [1] "ALB"
#>
#> $organism
#> [1] "Homo sapiens"
#>
#> $description
#> [1] "Albumin"
#>
#> $sequence
#> [1] "MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEPERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLFFAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLKECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYARRHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVVLNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTLSEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLVAASQAALGL"
#>
#> $peptides
#> [1] "AACLLPK" "AAFTECCQAADK"
#> [3] "AEFAEVSK" "ALVLIAFAQYLQQCPFEDHVK"
#> [5] "AVMDDFAAFVEK" "AWAVAR"
#> [7] "CASLQK" "CCAAADPHECYAK"
#> [9] "CCTESLVNR" "DDNPNLPR"
#> [11] "DLGEENFK" "DVFLGMFLYEYAR"
#> [13] "EFNAETFTFHADICTLSEK" "ETCFAEEGK"
#> [15] "ETYGEMADCCAK" "FQNALLVR"
#> [17] "HPDYSVVLLLR" "HPYFYAPELLFFAK"
#> [19] "LCTVATLR" "LVAASQAALGL"
#> [21] "LVNEVTEFAK" "LVTDLTK"
#> [23] "MPCAEDYLSVVLNQLCVLHEK" "NECFLQHK"
#> [25] "NYAEAK" "PCFSALEVDETYVPK"
#> [27] "PEVDVMCTAFHDNEETFLK" "PLVEEPQNLIK"
#> [29] "QNCELFEQLGEYK" "QTALVELVK"
#> [31] "SEVAHR" "SHCIAEVENDEMPADLPSLAADFVESK"
#> [33] "SLHTLFGDK" "TCVADESAENCDK"
#> [35] "TPVSDR" "TYETTLEK"
#> [37] "VFDEFK" "VHTECCHGDLLECADDR"
#> [39] "VPQVSTPTLVEVSR" "WVTFISLLFLFSSAYSR"
#> [41] "YICENQDSISSK" "YLYEIAR"Alternatively read_fasta the FASTA file into a data.frame.
library(tidyverse, warn.conflicts = FALSE)
fasta_data <- read_fasta(path_to_fasta) |> as.data.frame() |> as_tibble()
#> ℹ Parsing FASTA file albu_human.fasta
#> ✔ Parsing FASTA file albu_human.fasta ... done
fasta_data
#> # A tibble: 3 × 6
#> accession protein_name gene_name organism description sequence
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 P02768 ALBU_HUMAN ALB Homo sapiens Albumin MKWVTFISLL…
#> 2 P02768 ALBU_HUMAN <NA> Homo sapiens Isoform 2 of Albumin MKWVTFISLL…
#> 3 P02768 ALBU_HUMAN <NA> Homo sapiens Isoform 3 of Albumin MKWVTFISLL…