@@ -4,7 +4,7 @@

 \alias{tmhmm_fix_path}

 \title{Retrieve Data from TMHMM and Fix Functionality of TMHMM R Package}

 \usage{

-tmhmm_fix_path(fasta_filename, folder_name = tmhmm::get_default_tmhmm_folder())

+tmhmm_fix_path(fasta_filename, folder_name)

 }

 \arguments{

 \item{fasta_filename}{Parameter containing input fasta file to be run on

new file mode 100644

@@ -0,0 +1,29 @@

+% 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 = tmhmm::get_default_tmhmm_folder())

+}

+\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.

+}