Just a simple tool to check if some HMM profiles are present in a bunch of fasta files. You can put input fasta files into subfolders to visualize groups in the heatmap.
usage: hmmvis [-h] [--hmm HMM] [--fasta_dir FASTA] [--output_dir OUT]
[--use_query] [--colorful] [--normalize] [--keep_order]
[--version]
optional arguments:
-h, --help show this help message and exit
--hmm HMM path to hmm file
--fasta_dir FASTA path to folder where .fasta files are located (fasta
files can be grouped within subfolder)
--output_dir OUT path to output folder
--use_query use query id insead of accession
--colorful use colors for heatmap
--normalize normalize cluster map
--keep_order do not cluster rows if groups are present
--version show program's version number and exit
hmmvis/hmmvis --hmm example/example.hmm --fasta_dir example/faa_grouped --use_query --colorful
hmmvis/hmmvis --hmm example/example.hmm --fasta_dir example/faa --use_query --colorful
install dependencies
sudo apt-get install python python-setuptools libblas-dev liblapack-dev gfortran libpython2.7-dev python-numpy
wget https://bootstrap.pypa.io/get-pip.py
python get-pip.py
pip install numpy # see bug https://github.com/scikit-learn/scikit-learn/issues/4164
install hmmvis
git clone https://github.com/philippmuench/hmmvis.git
cd hmmvis
python setup.py install
you also need dependencies:
prodigal
hmmer
GNU General Public License, version 3 (GPL-3.0)
this script is part of the PlasmidMiner toolkit. If you use this script please cite:
Muench et al., A method for the in silico detection of plasmid fragments in environmental samples