FileNames.to.Table: collect the names of sequence files in a folder

In biodiversity-aq/OmicsMetaData: OmicsMetaData: an R-package for interoperable and re-usable biodiversity 'omics (meta)data

Description

makes a table with the all the names of sequence files in a folder. see details.

Usage

FileNames.to.Table(file.dir, paired=TRUE, seq.file.extension=".fastq.gz", 
  pairedEnd.extension=c("_1", "_2"))

Arguments

file.dir	a character string. The path to the directory where the sequence files are stored
paired	boolean. wether or not the sequence files are paired-end (forward _1, reverse_2) or single-end
seq.file.extension	a character string. The file-extension of the sequence files
pairedEnd.extension	a character vector of length 2. If the data is paired-end data, specify the forward (first element of the vector) and reverse (second) extension tags here. Default is c("_1", "_2")

Details

fastq files from sequencing facilities often come with long and complex file names that were automatically generated by the sequencer machine and no longer resemble the original name of the sample. This function is part of tools that help to get file names and easily convert them back into the original file names. It makes a table with the all the names of sequence files in a folder that can be saved as a CSV file. Using a text editor or excell, the user can then fill in the column with new name (that is, the desired name), and then use the renameSequenceFiles() function to rename the files.

Value

a data frame with a column "OldName" that list the sequence file names, an empty column "NewName" to be filled in by the user and a column "FileName" with the full file name.

Author(s)

Maxime Sweetlove

See Also

Other data archiving functions: get.ENAName(), prep.metadata.ENA(), renameSequenceFiles(), sync.metadata.sequenceFiles()

Examples

FileNames.to.Table(file.dir="path/to/the/sequenceFilesFolder", paired=TRUE, 
                   seq.file.extension=".fastq.gz",
                   pairedEnd.extension=c("_1", "_2"))

biodiversity-aq/OmicsMetaData documentation built on Dec. 19, 2021, 9:44 a.m.