View source: R/ThresholdExtract.R
ThresholdExtract | R Documentation |
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
ThresholdExtract(aligned_dir, missing_df, threshold_fasta_folder)
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 |
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()
Dustin J Wcisel, djwcisel@ncsu.edu
James Thomas Howard, jthowar3@ncsu.edu
Jeffrey A Yoder, jayoder@ncsu.edu
Alex Dornburg, dornburgalex@gmail.com
ThresholdExtract(aligned_dir = ad, missing_df = threshold_df, threshold_fasta_folder = "/path/to/store/fastas/threshold100")
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