fix_names_from_transdecoder: Shorten names in fasta headers.

In joelnitta/baitfindR: Find Baits for Sequence Capture

Description

Does the same thing as Yang and Smith (2014) fix_names_from_transdecoder.py, but works on one fasta file at at time.

Usage

fix_names_from_transdecoder(transdecoder_output, mol_type = "dna")

Arguments

transdecoder_output	Character vector of length one; the path to the .transdecoder.cds file produced by transdecoder_predict. It is assumed that the first part of the filename (immediately preceding .transdecoder.cds) is the sample code.
mol_type	Character vector of length one; "dna" for DNA or "aa" for proteins.

Value

Object of class DNAbin or AAbin with names shortened to sample_code`"@"`gene

Author(s)

Joel H Nitta, [e-mail]

References

Yang, Y. and S.A. Smith. 2014. Orthology inference in non-model organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics. Molecular Biology and Evolution 31:3081-3092. https://bitbucket.org/yangya/phylogenomic_dataset_construction/overview

Examples

## Not run: fix_names_from_transdecoder(transdecoder_output = "some/folder/CODE.transdecoder.cds")

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