ThresholdExtract: Utility for retrieving species sequences givin a dataframe of...

In carolinafishes/toast: Transcriptome Ortholog Alignment Sequence Tools

Utility for retrieving species sequences givin a dataframe of missing data

Description

User defines a threshold and is returned a dataframe containing only the samples/species with at least that many sequences. This dataframe can be fed into ExtractBuscoSeqs() as the busco_table parameter

Usage

ThresholdExtract(aligned_dir, missing_df, threshold_fasta_folder)

Arguments

aligned_dir	Directory where fasta alignments can be found
missing_df	Dataframe created by ParseBuscoResults() or MissingDataTable()
threshold_fasta_folder	Folder to store extracted fasta files

Value

Reads through a dataframe of missing and extracts sequences from the aligned_dir and writes to threshold_fasta_folder. Fasta files must be realigned and this can be accomplished with MafftOrientAlign()

Author(s)

Dustin J Wcisel, [e-mail]

James Thomas Howard, [e-mail]

Jeffrey A Yoder, [e-mail]

Alex Dornburg, [e-mail]

Examples

ThresholdExtract(aligned_dir = ad, missing_df = threshold_df, threshold_fasta_folder = "/path/to/store/fastas/threshold100")

carolinafishes/toast documentation built on June 28, 2023, 8:10 p.m.