GetHOG v3. (Under development)

prerequisites

GETHOG3 needs following software packages: omamer, Nextflow, Biopython,dendropy , ete3, fasttree and mafft (multiple sequence aligner).

You can start with conda.

conda create --name gethog3 python=3.9
conda activate gethog3

For installing omamer, please check its page github page. (You may need to install omamer with scipy==1.4.1 numpy==1.20.0 pytables==3.6.1)

You can install the rest using conda.

conda install -c conda-forge biopython ete3  
conda install -c bioconda mafft iqtree fasttree nextflow

And for wrappers, we need

conda install -c biopython dendropy
conda install -c conda-forge pyparsing

Input and Output:

Input:

1- Sets of protein sequences in FASTA format (with .fa extension) in the folder proteome. The name of each fasta file is the name of species.

2- The omamer database which you can download from here which is this link. This file is 13 Gb containing all the gene families of the Tree of Life or a subset of them, e.g. Primates (352MB).

3- Sepecies tree in nwk or phyloxml format. Note that the internal node should not contain any special character (e.g. \ / or space). The reason is that gethog3 write some files whose names contains the internal node's name.

Output:

Orthology information as HOG strcutre in OrthoXML format.

How to run GETHOG3 the test data

First, download the GETHOG3 package:

wget https://github.com/sinamajidian/gethog3/archive/refs/heads/master.zip
unzip master.zip
mv gethog3-master gethog3

or clone it

git clone [email protected]:sinamajidian/gethog3.git

Then, cd to the testdata folder and download the omamer database.

cd gethog3/testdata
wget https://omabrowser.org/All/Primates.h5    # 352MB
mv Primates.h5  working_folder 

If you are using omamer database of different name (e.g. LUCA.h5), please change params.omamer_db in gethog3/gethog3/nextflow.config.

Next, set the path to working_folder (as a global path) in two places gethog3/gethog3/_config.py and gethog3/gethog3/nextflow.config :

1- The variable working_folder in the file _config.py

working_folder = "/work/FAC/FBM/DBC/cdessim2/default/smajidi1/test/gethog3/testdata/working_folder"+ "/"

2- The variable params.working_folder in the file nextflow.config (the same as item 1).

params.working_folder= "/work/folder/gethog3/testdata/working_folder"+"/"
params.gethog3= "/work/folder/gethog3/gethog3"+"/"

Make sure that it ends with "/".

Finally, run the package using nextflow as below:

cd gethog3/testdata
nextflow ../gethog3/gethog3_script.nf

After few minutes, the run for test data finishes. Then, following files and folders should appear in the folder gethog3/testdata.

gene_id_dic_xml.pickle  hogmap  output_hog_.orthoxml  pickle_rhogs 
 Primates.h5  proteome  rhogs_all  rhogs_big  rhogs_rest  species_tree.nwk

among which output_hog_.orthoxml is the final output. Its content looks like this

<?xml version="1.0" ?>
<orthoXML xmlns="http://orthoXML.org/2011/" origin="OMA" originVersion="Nov 2021" version="0.3">
   <species name="MYCGE" NCBITaxId="1">
      <database name="QFO database " version="2020">
         <genes>
            <gene id="1000000000" protId="sp|P47500|RF1_MYCGE"/>
            <gene id="1000000001" protId="sp|P13927|EFTU_MYCGE"/>
            <gene id="1000000002" protId="sp|P47639|ATPB_MYCGE"/>
            
 ...
      <orthologGroup id="HOG:B0885011_sub10003">
         <property name="TaxRange" value="inter1"/>
         <geneRef id="1002000004"/>
         <geneRef id="1001000004"/>
      </orthologGroup>
   </groups>
</orthoXML>

How to config and run GETHOG3

Please first try the test data. Now you should have the GETHOG3 package.

GETHOG3 is based on nextflow. We consider a working folder which contains the omamer database Primates.h5, the proteome folder of the species of interst proteome (of fa files inside), and the speceis tree species_tree.phyloxml (or nwk).

$ ls working_folder
Primates.h5  proteome  species_tree.phyloxml

After running the package, the outputs will appear in this working folder.

Please set the working_folder in two places gethog3/gethog3/_config.py and gethog3/gethog3/nextflow.config : 1- The variable working_folder in the file _config.py 2- The variable params.working_folder in the file nextflow.config (the same as item 1).

Then, provide the address of the gethog3 code as params.gethog3 in the file nextflow.config.

Finally you can run:

nextflow gethog3/gethog3/gethog3_script.nf

log changes

prelease v.0.0.4 (Feb 15 2022)