Shorten names in fasta headers.

Source: R/yang_and_smith.R

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

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

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")
# }