extractBuscoSeqsFrag: Utility for extracting fragmented BUSCO sequences into...

In carolinafishes/toast: Transcriptome Ortholog Alignment Sequence Tools

Utility for extracting fragmented BUSCO sequences into individual fasta files

Description

Utility for extracting fragmented BUSCO sequences into individual fasta files

Usage

extractBuscoSeqsFrag(
  tsvtable,
  fasta,
  ed,
  seqID = "Genus_species",
  threshold = 300
)

Arguments

tsvtable	the resulting tsv table from a busco analysis
fasta	original fasta sequence file
ed	extracted directory where extracted sequences will be written
seqID	name of sequence, defaults to Genus_species
threshold	minimum number of base pairs required for a fragmented sequence to be extracted. Defaults to 300

Value

This function uses the output of a busco analysis and specified fasta file to extract fragmented busco sequences and write these into fasta files. Fasta files are written into the directory specified by the parameter ed. Each sequence will be named based on the seqID specified

Author(s)

Alex Dornburg, [e-mail]

Phillip Souza, [e-mail]

Examples

extractBuscoSeqsFrag(tsvtable=tsvtable, fasta=fasta,ed="path/to/extracted/", seqID="Genus_species",threshold=300)

carolinafishes/toast documentation built on Dec. 19, 2024, 12:47 a.m.