set_diamond: Create a DIAMONDable database with 'diamond makedb'

In HajkD/orthologr: Comparative Genomics with R

Create a DIAMONDable database with diamond makedb

Description

This function reads a file storing a specific sequence type, such as "cds", "protein", or "dna" in a standard sequence file format such as "fasta", etc. and depending of the makedb parameter either creates a diamond-able database, or returns the corresponding protein sequences as data.table object for further DIAMOND2 searches.

Usage

set_diamond(
  file,
  seq_type = "cds",
  format = "fasta",
  makedb = FALSE,
  delete_corrupt_cds = TRUE,
  path = NULL,
  makedb_type = "protein",
  comp_cores = 1,
  quiet = TRUE,
  ...
)

Arguments

file	a character string specifying the path to the file storing the sequences of interest.
seq_type	a character string specifying the sequence type stored in the input file. Options are are: "cds", "protein", or "dna". In case of "cds", sequence are translated to protein sequences, in case of "dna", cds prediction is performed on the corresponding sequences which subsequently are translated to protein sequences. Default is seq_type = "cds".
format	a character string specifying the file format used to store the genome, e.g. "fasta", "gbk".
makedb	TRUE or FALSE whether a database should be created or not (diamond makedb).
delete_corrupt_cds	a logical value indicating whether sequences with corrupt base triplets should be removed from the input file. This is the case when the length of coding sequences cannot be divided by 3 and thus the coding sequence contains at least one corrupt base triplet.
path	a character string specifying the path to the DIAMOND2 program (in case you don't use the default path).
makedb_type	a character string specifying the sequence type stored in the DIAMOND2 database that is generated using 'diamond makedb'. Currently, the only option is "protein". Default is makedb_type = "protein".
comp_cores	a numeric value specifying the number of cores to be used for multicore 'diamond makedb' computations.
quiet	a logical value indicating whether diamond makedb should be run with the quiet mode. Default is quiet = TRUE (which adds --quiet to the diamond makedb run).
...	additional arguments that are used by the seqinr::read.fasta() function.

Value

A list storing two elements. The first element [[1]] corresponds to the data.table storing the gene ids in the first column and the corresponding dna (cds) sequence in the second column and the aminoacid sequence third column. The second list element [[2]] stores the name of the protein database that was created by 'diamond makedb'.

Author(s)

Jaruwatana Sodai Lotharukpong

References

Buchfink, B., Reuter, K., & Drost, H. G. (2021) "Sensitive protein alignments at tree-of-life scale using DIAMOND." Nature methods, 18(4), 366-368.

https://github.com/bbuchfink/diamond/wiki/3.-Command-line-options

See Also

diamond_best, diamond_rec, diamond, set_blast

Examples

## Not run: 
 # running the set function to see an example output
 head(set_diamond(file = system.file('seqs/ortho_thal_cds.fasta', package = 'orthologr'))[[1]] , 2)

## End(Not run)

HajkD/orthologr documentation built on Oct. 13, 2023, 12:11 a.m.