Description Usage Arguments Value Author(s) Examples
View source: R/remap_fasta_entry_names.R
Remaps entries in the FASTA file from one protein identifier to another according to provided conersion table. Input is a path to FASTA file. Output is also a path to a new FASTA file with updated entry names.
1 2 3 4 5 | remap_fasta_entry_names(path_to_FASTA,
conversion_table,
extraction_pttrn=c("\\|([^|-]+)(-\\d+)?\\|",
"([A-Z]P_\\d+)",
"(ENS[A-Z0-9]+)"))
|
path_to_FASTA |
(string) path to FASTA file |
conversion_table |
(data.frame) first column in the data frame corresponds to identifiers in the FASTA file. Second column is the new identifier. |
extraction_pttrn |
(string) regex pattern that extract protein identifier from
FASTA entry name as first group (that is |
path to new FASTA file
Vladislav A Petyuk vladislav.petyuk@pnnl.gov
1 2 3 4 5 6 7 | library(Biostrings)
fst_path <- system.file("extdata","for_phospho.fasta.gz",package="MSnID")
readAAStringSet(fst_path)
conv_tab <- fetch_conversion_table("Homo sapiens", "UNIPROT", "SYMBOL")
fst_path_2 <- remap_fasta_entry_names(fst_path, conv_tab, "\\|([^|-]+)(-\\d+)?\\|")
readAAStringSet(fst_path_2)
file.remove(fst_path_2)
|
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