Format meta.retrieval output — clean.retrieval • biomartr
Description: Process the output of meta.retrieval by first un-zipping downloaded files and renaming them for more convenient downstream data analysis.

# 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.

    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()
    }