% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/tmhmm_fix_path.R
 \name{tmhmm_fix_path}
 \alias{tmhmm_fix_path}
 \title{Retrieve Data from TMHMM and Fix Functionality of TMHMM R Package}
 \usage{

 tmhmm_fix_path(fasta_filename, folder_name)

 }
 \arguments{
 \item{fasta_filename}{Parameter containing input fasta file to be run on
 tmhmm}
 
 \item{folder_name}{Path to folder containing installed tmhmm software}
 }
 \value{
 Raw results from tmhmm containing membrane locations for
 each transcript
 }
 \description{
 This function retrieves the raw data from tmhmm containing information
 about the membrane location of each amino acid in a transcript.
 In order to set a standard path that allows tmhmm to run, the path
 is set to match that of the fasta file contining the amino acids.
 }
 \note{
 In order for this function to work, there needs to be a .fasta file
 containing the amino acid sequences for each transcript called "AA.fasta"
 saved to a folder called output within the working directory.
 }