HMMScanParse: Utility for parsing HMMScan and retrieving domain sequences

In carolinafishes/toast: Transcriptome Ortholog Alignment Sequence Tools

Utility for parsing HMMScan and retrieving domain sequences

Description

Utility for parsing hmmScan output

Usage

HMMScanParse("~/Downloads/hmmscanSRR26417824.out", fasta_file="~/Downloads/SRR26417824_extracted_sequences.fasta")
)

Arguments

input_file	your hmmscan output
outputfile	whether you want to write out a CSV of results, default is TRUE
user_threshold	the minimum eValue to retain, defaults to 1e-5
fasta_file	the fasta file you ran hmmScan on that this function will extract sequence from
clean	whether you want only unique domains returned. Default is TRUE and avoids needing to wade through a domaine starting at position 151 or 150

Value

This function use the hmmScan output and a fasta file to return a CSV of all the domains for each query as well as a dataframe of the output including the sequence, start and stop position, query, evalue, and domain identification. This can be subsampled just like any dataframe.

Author(s)

Alex Dornburg, [e-mail]

Examples

HMMScanParse("~/Downloads/hmmscanSRR26417824.out", fasta_file="~/Downloads/SRR26417824_extracted_sequences.fasta")

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