modifyAlns: modifyAlns.R

In judyheewonlee/ScoreVisualizer: Score Visualizer

Description

The modifyAlns function copies and modifies the alignments provided by the user in order to generate a valid texShade output. It adds a 'sample' alignment since texShade does not include gaps in the sequence length of the alignment. TexShare only counts the residues in the individual sequences. Lastly, the function returns the filepaths of the copied and modified alignments.

Details.

Usage

modifyAlns(reference, compare, filename)

Arguments

reference	A directory path to the reference alignment the user would like to use
compare	A directory path to the alignment being compared to the reference alignment
filename	The preferred name of the output file provided by the user in ScoreVisualizer

Value

The filepaths of the copied and modified alignments that will be used to generate the tex file

Examples

reference <- "data/BB11017ClustalW.fasta"
test <- "data/BB11017Muscle.fasta"

filepaths <- modifyAlns(reference, compare, "Test3")
filepaths

judyheewonlee/ScoreVisualizer documentation built on May 31, 2019, 5:20 p.m.