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Format meta.retrieval output

Source: R/clean.retrieval.R
clean.retrieval.Rd

Process the output of meta.retrieval by first un-zipping downloaded files and renaming them for more convenient downstream data analysis.

Usage

clean.retrieval(x, gunzip = TRUE)

Arguments

x

a vector containing file paths to the output files generated by meta.retrieval.

gunzip

a logical value indicating whether or not files should only be renamed (gunzip = FALSE) or renamed AND unzipped (gunzip).

Details

The output of meta.retrieval usually contains compressed sequence files and a naming convention based on the database the respective file was retrieved from (e.g. Saccharomyces_cerevisiae_cds_from_genomic_refseq.fna.gz). This function helps to format the meta.retrieval output files by

  • 1) Automatically uncompress all sequence files in the meta.retrieval output folder

  • 2) Automatically rename files from e.g. Saccharomyces_cerevisiae_cds_from_genomic_refseq.fna.gz to Scerevisiae.fa. This allows more convenient downstream analyses and visualizations.

See also

meta.retrieval

Author

Hajk-Georg Drost

Examples

if (FALSE) {
# The easiest way to use 'clean.retrieval()' in combination with
# 'meta.retrieval()' is to use the pipe operator from the 'magrittr' package
library(magrittr)
meta.retrieval(kingdom = "vertebrate_mammalian", 
               db = "refseq", 
               type = "genome") %>% clean.retrieval()
}