Feature-aware orthology prediction tool
Project description
HaMStR-OneSeq
Table of Contents
How to install
0. Basic system tools requirement
You need to have wget, grep and sed (or gsed for MacOS) to install HaMStR. So please install them if they are missing. For MacOS users, we recommend using Homebrew to install those command line tools.
To use FAS tool (a dependency of HaMStR), you also need Python 3.
1. Dependencies
HaMStR-oneSeq has some dependencies, that either will be automatically installed via the setup script, or must be installed by your system admin if you don't have the root privileges. In our wiki you will find the full list of HaMStR-oneSeq's dependencies for Ubuntu system as well as the alternatives for MacOS.
In Ubuntu, you can install those system and bioinformatics tools/libraries using apt-get tool
sudo apt-get update -y
sudo apt-get install tool_name -y
In MacOS, we suggest using Homebrew as a replacement for apt-get. After having Homebrew, you can install tools/libraries by using the command
brew install tool_name
In both operation systems, you can install Perl modules using cpanm.
# first, install cpanm
curl -L http://cpanmin.us | perl - --sudo App::cpanminus
# then, install perl module using cpanm
sudo cpanm perl_module_name
If you do not have root privileges, ask your admin to install these dependencies using the install_lib.sh script.
cd HaMStR
sudo ./install_lib.sh
2a. Install using Anaconda
Follow this link to install conda (anaconda or miniconda) to your system.
Add additional channels bioconda and conda-forge:
conda config --add channels bioconda
conda config --add channels conda-forge
Create and activate a conda environment for HaMStR
conda create --name hamstr -y
conda activate hamstr
Install HaMStR
conda install -c BIONF hamstr
setup_hamstr
HaMStR will be installed under the subfolder HaMStR in side your current working directory. After the setup run successfully, you can start using HaMStR (in some cases you should restart the terminal).
2b. Install in Ubuntu/MacOS
Get HaMStR source code from GitHub
git clone --depth=1 https://github.com/BIONF/HaMStR
Run setup.sh script in the HaMStR folder to install HaMStR and its dependencies
cd HaMStR
./setup.sh
You should have the sudo password ready, otherwise some missing dependencies cannot be installed. See dependency list for more info. If you do not have root privileges, ask your admin to install those dependencies using install_lib.sh script.
After the setup run successfully, you can start using HaMStR (in some cases you should restart the terminal).
For debugging the installation, please create a log file by running the setup as e.g. bin/setup.sh | tee log.txt for Linux/MacOS or setup_hamstr | tee log.txt for Anaconda and send us that log file, so that we can trouble shoot the issues. Most of the problems can be solved by just re-running the setup.
Usage
HaMStR will run smoothly with the provided sample input file in 'HaMStR/data/infile.fa' if everything is set correctly.
oneSeq -seqFile=infile.fa -seqName=test -refspec=HUMAN@9606@3 -minDist=genus -maxDist=kingdom -coreOrth=5 -cleanup -cpu=8
The output files with the prefix test will be saved at your current working directory.
You can have an overview about the available options with the command
oneSeq -h
If you get the error message that oneSeq command not found, you should restart the terminal, or replace oneSeq by perl bin/oneSeq
Please find more information in our wiki to learn about the input and outputs files of HaMStR-oneSeq.
HaMStR data set
Within the data package (https://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml) we provide a set of 78 reference taxa. They can be automatically downloaded during the setup. This data comes "ready to use" with the HaMStR-OneSeq framework. Species data must be present in the three directories listed below:
- genome_dir (Contains sub-directories for proteome fasta files for each species)
- blast_dir (Contains sub-directories for BLAST databases made with
makeblastdbout of your proteomes) - weight_dir (Contains feature annotation files for each proteome)
For each species/taxon there is a sub-directory named in accordance to the naming schema ([Species acronym]@[NCBI ID]@[Proteome version])
HaMStR-oneSeq is not limited to those 78 taxa. If needed the user can manually add further gene sets (multifasta format) using provided python scripts.
Adding a new gene set into HaMStR
For adding one gene set, please use the bin/addTaxonHamstr.py script:
python3 bin/addTaxonHamstr.py -f newTaxon.fa -i tax_id -o /path/to/HaMStR [-n abbr_tax_name] [-c] [-v protein_version] [-a]
in which, the first 3 arguments are required including newTaxon.fa is the gene set that need to be added, tax_id is its NCBI taxonomy ID, /path/to/HaMStR is where the sub-directories can be found (genome_dir, blast_dir and weight_dir). Other arguments are optional, which are -n for specify your own taxon name (if not given, an abbriviate name will be suggested based on the NCBI taxon name of the input tax_id), -c for calculating the BLAST DB (only needed if you need to include your new taxon into the list of taxa for compilating the core set), -v for identifying the genome/proteome version (default will be 1), and -a for turning off the annotation step (not recommended).
Adding a list of gene sets into HaMStR
For adding more than one gene set, please use the bin/addTaxaHamstr.py script:
python3 bin/addTaxaHamstr.py -i /path/to/newtaxa/fasta -m mapping_file -o /path/to/HaMStR [-c]
in which, /path/to/taxa/fasta is a folder where the FASTA files of all new taxa can be found. mapping_file is a tab-delimited text file, where you provide the taxonomy IDs that stick with the FASTA files:
#filename tax_id abbr_tax_name version
filename1 12345678
filename2 9606
filename3 4932 my_fungi
...
The header line (started with #) is a Must. The values of the last 2 columns (abbr. taxon name and genome version) are, however, optional. If you want to specify a new version for a genome, you need to define also the abbr. taxon name, so that the genome version is always at the 4th column in the mapping file.
NOTE: After adding new taxa into HaMStR-oneSeq, you should check for the validity of the new data before running HaMStR.
Bugs
Any bug reports or comments, suggestions are highly appreciated. Please open an issue on GitHub or be in touch via email.
How to cite
Ebersberger, I., Strauss, S. & von Haeseler, A. HaMStR: Profile hidden markov model based search for orthologs in ESTs. BMC Evol Biol 9, 157 (2009), doi:10.1186/1471-2148-9-157
Contributors
Contact
For further support or bug reports please contact: ebersberger@bio.uni-frankfurt.de
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