Skip to content
Companion scripts for Wheeler et al. 2019
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
R
auxillary
bash
circos
.gitignore
LICENSE
README.md

README.md

BrugiaChemo-ms

This repository contains all the Bash, Python, and R scripts necessary to reproduce the data published in Wheeler et al. 2019.

Description of scripts in bash/:

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.

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.

Description of scripts in R/:

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.

Description of files in auxillary/:

CNG, ChemoR, and TRP: includes all seed sequences and alignment 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

You can’t perform that action at this time.