extractBuscos: Utility for extracting BUSCO sequences into individual fasta...

In carolinafishes/toast: Transcriptome Ortholog Alignment Sequence Tools

Utility for extracting BUSCO sequences into individual fasta files from multiple directories.

Description

Utility for extracting BUSCO sequences into individual fasta files from multiple directories.

Usage

extractBuscos(
  tsvLocations,
  fastaLocations,
  ed,
  SampleIDs,
  complete = TRUE,
  fragmented = TRUE,
  threshold = 300,
  duplicated = TRUE
)

Arguments

tsvLocations	the paths that contain the tsv files from a busco analysis.
fastaLocations	the paths to the original fasta sequence files
ed	extracted directory where extracted sequences will be written
complete	whether or not to include complete sequences
fragmented	whether or not to include fragmented sequences
threshold	minimum number of base pairs required for a fragmented sequence to be extracted.Not used when fragmented = false
duplicated	whether or not to include duplicated sequences
sampleIDs	name of sequences

Value

This function uses the output of a busco analysis and specified fasta file to extract 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

extractBuscos(tsvLocations=c("path/to/first/tsvfile","path/to/second/tsvfile",...), fasta=c("path/to/first/fastafile","path/to/second/fastafile",...),ed="path/to/extracted/", sampleIDs=c("Genus_species","Othergenus_otherspecies",...),complete=TRUE, fragmented=TRUE, threshold=300, duplicated=TRUE)

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