The magiccave's intro from thexiyang

A more targetted platform for annotation of datasets using HMM sets.

quick install (if you have Conda installed)

bash setup.sh
source activate magiccave

Required Dependencies

Python (version 3.6 or higher)
BLAST (version 2.7.1+)
Prodigal (version 2.6.3)
HMMER (version 3.2.1)

Optional Dependencies

Diamond (version 0.9.22.123) -- if you performing cross-validation against a reference database
R (version 3.5.1) -- if generating plots
Rscript -- if generating plots

installation if you don't have Conda

Put MagicLamp.py script $PATH into your bash profile

export PATH=$PATH:$(pwd)

Usage

(for a list of available genies)

MagicLamp.py help

(for a detailed help menu for each genie)

  MagicLamp.py FeGenie -h
  MagicLamp.py LithoGenie -h
  MagicLamp.py WspGenie -h
  MagicLamp.py GasGenie -h
  MagicLamp.py MagnetoGenie -h
  MagicLamp.py RosGenie -h
  MagicLamp.py Lucifer -h
  MagicLamp.py HmmGenie -h

Quick-start

simplest form of the command

MagicLamp.py FeGenie -bin_dir genomes/ -bin_ext fna -out fegenie_output

if you are providing gene-calls

MagicLamp.py FeGenie -bin_dir genomes/ -bin_ext fna -out fegenie_output --orfs

you can also provide GenBank files

MagicLamp.py FeGenie -bin_dir genomes/ -bin_ext fna -out fegenie_output --gbk

if you want to normalize the number of identified genes to the total number of ORFs in the dataset

MagicLamp.py FeGenie -bin_dir genomes/ -bin_ext fna -out fegenie_output --norm

with LithoGenie, you can also specficy a specific category for heatmap analysis

MagicLamp.py LithoGenie -bin_dir genomes/ -bin_ext fna -out lithogenie_output --cat sulfur

if you already ran LithoGenie once, but want to re-do the heatmap file with a different category

MagicLamp.py LithoGenie -bin_dir genomes/ -bin_ext fna -out lithogenie_output --cat iron --skip

full list of LithoGenie categories (default action of the program is to create a broad-category heatmap)

iron
sulfur
nitrogen
oxygen
methane
hydrogen
arsenic
nitriles
manganese
carbon-monoxide
halogenetated-compounds
C1compounds
urea
selenium

(many of the HMMs used by LithoGenie were developed and compiled by Karthik Anantharaman: https://github.com/kanantharaman/metabolic-hmms)

thexiyang / magiccave Goto Github PK

magiccave's Introduction

A more targetted platform for annotation of datasets using HMM sets.

quick install (if you have Conda installed)

Required Dependencies

Optional Dependencies

installation if you don't have Conda

Usage

Quick-start

simplest form of the command

if you are providing gene-calls

you can also provide GenBank files

if you want to normalize the number of identified genes to the total number of ORFs in the dataset

with LithoGenie, you can also specficy a specific category for heatmap analysis

if you already ran LithoGenie once, but want to re-do the heatmap file with a different category

full list of LithoGenie categories (default action of the program is to create a broad-category heatmap)

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