transdecoder_predict: Predict coding regions.

In joelnitta/baitfindR: Find Baits for Sequence Capture

Description

This is a wrapper for transdecoder.predict. It must be run in the same directory containing the .transdecoder_dir output folders from transdecoder_long_orfs. Optionally include the results of a blastp search to make sure that peptides with a blastp hit against the reference database are retained in the TransDecoder output.

Usage

transdecoder_predict(
  transcriptome_file,
  blast_result = NULL,
  wd = here::here(),
  other_args = NULL,
  echo = pkgconfig::get_config("baitfindR::echo", fallback = FALSE),
  ...
)

Arguments

transcriptome_file	Character vector of length one; the path to the fasta file containing transcript sequences (i.e., the transcriptome).
blast_result	Character vector of length one; the path to the tab-separated text file containing the results from a blastp search of the transcriptome against a reference blast protein database. For the blast search, the output format should specified as: -outfmt 6.
wd	Character vector of length one; the directory where the command will be run. Must contain .transdecoder_dir folder with results from transdecoder_long_orfs.
other_args	Character vector; other arguments to pass to TransDecoder. Each should be an element of the vector.
echo	Logical; should the standard output and error be printed to the screen?
...	Additional other arguments. Not used by this function, but meant to be used by drake_plan for tracking during workflows.

Details

For a more detailed example, see vignettes.

Value

Within the R environment, a list with components specified in run.

Externally, four output files (.cds, .pep, .bed, and .gff3) for each input transcriptome file will be written to the working directory.

Author(s)

Joel H Nitta, [e-mail]

References

http://transdecoder.github.io

Examples

## Not run: 
transdecoder_predict("some/transcriptome_file.fa", "some/blast_result.txt")

## End(Not run)

joelnitta/baitfindR documentation built on May 7, 2020, 6:21 p.m.