parseDB: Parse a .fasta Database

In jmwozniak/PTMphinder: An R package for PTM localization and motif extraction from proteomic datasets

Description

parseDB() parses a .fasta proteome database into a data table containing each protein accession ID in one column and the protein sequence in another column. Can also filter out reverse and contaminant sequences.

Usage

parseDB(database, db_source, filt)

Arguments

database	a .fasta proteome database.
db_source	a string denoting the source of the input database. Key: "UP" - Uniprot; "RS" - RefSeq; "HM" - Homemade.
filt	a boolean variable (TRUE/FALSE) specifying whether or not to filter out reverse and contaminant sequences.

Details

File extension of database should be changed from ".fasta" to ".txt" prior to import into R. This function was built to organize .fasta databases for easier manipulation in R (such as prior to input into the phindPTMs() function) or other analysis software.

Value

a data table with two columns: protein accession ID and protein sequence

Author(s)

Jacob M. Wozniak ([e-mail])

Examples

# Locate example files
examples.path = system.file("/extdata", package = "PTMphinder")
uniprot_ref.path = paste(examples.path, "/Human_Uniprot_Example.txt", sep="")

# Read in proteome database example (or your own database)
uniprot_ref = readLines(uniprot_ref.path)

# Parse proteome database into 2 columns: protein accession and protein sequence (may take a while depending on database size)
parseDB_Example <- parseDB(uniprot_ref, "UP", FALSE)

# Create file name for parsed database
filename1 <- paste(examples.path, "/Human_Uniprot_Parsed_", Sys.Date(), ".txt", sep="")

# Write parsed  database to new file (will be found in the PTMphinder/extdata/ directory within R.framework)
write.table(parseDB_Example, filename1, row.names=FALSE, col.names=FALSE, sep="\t")

jmwozniak/PTMphinder documentation built on May 31, 2019, 10:34 a.m.