This repository contains all the Bash, Python, and R scripts necessary to reproduce the figures published in Wheeler et al. 2020.

All Bash scripts use a convention for organizing data in local directories outside of GitHub version control. In our local .bash_profile, we add the following two lines to define local variables:

export GIT_PATH="$HOME/GitHub"
export GIT_DATA="$HOME/Box/GHdata"

In the header of each Bash script, we define proj as the repo name and reference to the GitHub repo as well as a local directory into which the GitHub repo will write out all resulting files, for example:

proj="BrugiaChemo-ms"

gh_dir="${GIT_PATH}"/"${proj}"
local_dir="${GIT_DATA}"/"${proj}"

For this repo to be cloned/forked and reproduced properly, the local variables GIT_DATA and GIT_PATH will need to be defined according to the user's organization.

NOTE: All bash scripts use GNU Coreutils. If using a Mac, you will need to install these via Homebrew. If a command isn't working try preceding the command with a 'g' (e.g. ggrep instead of grep).

CNG_analysis.sh: Bash script of all command line programs and parameters used for cyclic-nucleotide gated channel gene identification and annotation.

ChemoR_analysis.sh: Bash script of all command line programs and parameters used for chemoreceptor (GPCR) gene identification and annotation.

TRP_analysis.sh: Bash script of all command line programs and parameters used for transient receptor potential channel gene identification and annotation.

WBP_download.sh: Bash script used to populate a local directory with all genome files from the WormBase ParaSite FTP.

This directory contains a subdirectory for each gene family (chemoreceptors, CNGs, and TRPs), which contains R scripts for plotting trees and other figures where appropriate, and an experiments subdirectory. Everything in experiments relates to benchwork, while everything in the gene family subdirectories relates to computational work. Data used to create figures are held in data and output plots are written to plots.

CNG, ChemoR, and TRP: includes all seed sequences and alignments used for gene identification and annotation.

pfam_HMMs: includes hidden Markov models curated by Pfam.

species_info.csv: a spreadsheet of all the genomes analyzed in the comparative pipeline, their BioProject accessions, and their nematode clade designation.

species.txt: a list of species analyzed, used in all Bash scripts for iterating through species genome directories