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Trimming down a protein FASTA file to certain proteins

Source: R/trimFASTA.R
trimFASTA.Rd

Trim down a FASTA file to only contain proteins present in an associated Spectronaut report file.

Usage

trimFASTA(
  FASTAFileName,
  reportFileName,
  outputFileName = "trimFASTA_output.txt",
  by = "PG.ProteinNames",
  selectString = "*BOVIN"
)

Arguments

FASTAFileName

A character string specifying the name of the input FASTA .txt file.

reportFileName

A character string specifying the name of the Spectronaut report .csv file.

outputFileName

A character string (default = "trimFASTA_output.txt") specifying the name of the output file.

by

A character string (default = "PG.ProteinNames") specifying the identifier (column name) used for selection in the report file.

selectString

A character string specifying the regular expression to search for.

Value

A FASTA file with only the specified proteins present.

Details

Depending on the size of the FASTA file, this function may run slowly and take several minutes. The FASTA file must be in .txt format; other formats will not work.