renderCodemlInputs: Generates the tree and control file to run PAML's codeml in...

In asishallab/GeneFamilies: Analyses different properties of gene families

Generates the tree and control file to run PAML's codeml in order to compute the Ks of 'gene.pair'

Description

Generates the tree and control file to run PAML's codeml in order to compute the Ks of 'gene.pair'

Usage

renderCodemlInputs(gene.pair, cds.msa.path,
  ks.out.path = sub("_CDS_MSA.fasta", "_codeml_out.txt", cds.msa.path,
  fixed = TRUE), cds.codeml.path = sub("_CDS_MSA.fasta",
  "_codeml_in.cnt", cds.msa.path, fixed = TRUE),
  tree.path = sub("_CDS_MSA.fasta", "_tree.newick", cds.msa.path, fixed =
  TRUE))

Arguments

gene.pair	a character of length 2 holding the identifiers of the pair's genes.
cds.msa.path	the file path to the gene pair's codon sequences alignment
ks.out.path	the file path to the gene pair's codeml output file, defaut is generated from 'cds.msa.path' substituting '_CDS_MSA.fasta' with '_codeml_out.txt'
cds.codeml.path	the file path to the gene pair's codeml input file, defaut is generated from 'cds.msa.path' substituting '_CDS_MSA.fasta' with '_codeml_in.cnt'
tree.path	the file path to the gene pair's tree file, defaut is generated from 'cds.msa.path' substituting '_CDS_MSA.fasta' with '_tree.newick'. The tree will be the trivial one: '(A,B);'.

Value

A list with two string entries: 'in' the path to the control file used as input to PAML's codeml, and 'out' path to the output file generated by PAML's codeml.

asishallab/GeneFamilies documentation built on May 22, 2023, 11:30 a.m.