replaceWithOriginalInFigTree: Uses GNU sed to replace the sanitized gene identifiers with...

In asishallab/GeneFamilies: Analyses different properties of gene families

Uses GNU sed to replace the sanitized gene identifiers with the original ones in the Fig-Tree file - consensus tree generated by Mr. Bayes.

Description

Uses GNU sed to replace the sanitized gene identifiers with the original ones in the Fig-Tree file - consensus tree generated by Mr. Bayes.

Usage

replaceWithOriginalInFigTree(name.mappings, path.2.fig.tree,
  path.2.fig.tree.orig = sub(".con.tre", "_original_identifiers.con.tre",
  path.2.fig.tree, fixed = TRUE))

Arguments

name.mappings	data.frame with two columns 'original', and 'sanitized', holding the pairs of original gene ID to sanitized gene ID.
path.2.fig.tree	the valid file path to the tree file to process
path.2.fig.tree.orig	the valid file path to the output file in which the original gene identifiers are used. Must not be identical to 'path.2.fig.tree'. Default is 'path.2.fig.tree' with its suffix '.con.tre' modified to '_original_identifiers.con.tre'.

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