UROPA is a command line based tool, intended for genomic region annotation
Universal RObust Peak Annotator
The Universal RObust Peak Annotator (UROPA) is a command line based tool, intended for genomic region annotation. Based on a configuration file, different target features can be prioritized with multiple integrated queries. These can be sensitive for feature type, distance, strand specificity, feature attributes (eg. protein_coding) or the anchor position relative to the feature. UROPA can incorporate reference annotation files (GTF) from different sources, like Gencode, Ensembl, or RefSeq, as well as custom reference files produced by the user.
Detect the most appropriate annotation with flexible parameter keys that allow robustness and simple customization, such as
- feature type
- feature anchor
- feature direction relative to peak location
- filter for attribute values, e.g. “protein_coding”
- strand specificity
Utilization of all available GTF files as annotation database
One run with variable sets of parameters by multiple queries
Graduated annotation due to priorization
Different easily-readable output tables (allhits, finalfits, besthits).
Visual summary for annotation evaluation
Preparation of custom annotation files
A detailed description of how to apply UROPA to your data can be found here.
Installation and Command-line usage
Conda package manager
We recommend to install UROPA using the conda package manager. Make sure to have
conda installed, e.g. via
- download the Miniconda installer for Python 3
bash Miniconda3-latest-Linux-x86_64.shto install Miniconda
- Answer the question "Do you wish the installer to prepend the Miniconda install location to PATH in your /home/.../.bashrc ?" with yes
PATH=dir/to/miniconda3:$PATHafter installation process
The UROPA installation is now as easy as
conda create --name uropa
conda activate uropa
conda install python uropa -c bioconda
Biocontainers / Docker
If you have a running Docker environment, you can pull a biocontainer with UROPA and all dependencies via
docker pull quay.io/biocontainers/uropa:latest_tagusing the latest tag from the taglist, e.g.
Installation from source
You can also install UROPA from the source PyPI package. Note that this comes without the R dependencies for auxillary scripts:
pip install uropa
To fulfill all other dependencies, follow the instructions below:
- R/Rscript (v3.3.0 or higher; follow instructions on url)
- install required packages step by step:
install.packages(c("ggplot2", "devtools", "gplots", "gridExtra", "jsonlite", "VennDiagram", "getopt", "tidyr", "UpSetR")) source("https://bioconductor.org/biocLite.R") biocLite(c("RBGL", "graph"))
In order to plot the Chow-Ruskey plot with uropa_summary.R, install the modified Vennerable package from our fork:
To effectively use UROPA, make yourself familiar with the command-line options:
$ uropa Usage: uropa [options] optional arguments: -h, --help show this help message and exit Arguments for one query: -b , --bed Filename of .bed-file to annotate -g , --gtf Filename of .gtf-file with features --feature [ [ ...]] Feature for annotation --feature_anchor [ [ ...]] Feature anchor to annotate to --distance [ [ ...]] Maximum permitted distance from feature (1 or 2 arguments) --strand [ [ ...]] Desired strand of annotated feature relative to peak --relative_location [ [ ...]] Peak locaion relative to feature location --internals Set minimum overlap fraction for internal feature annotations. 0 equates to internals=False and 1 equates to internals=True. Default is False. --filter_attribute Filter on 9th column of GTF --attribute_values [ [ ...]] Value(s) of attribute corresponding to --filter_attribute --show_attributes [ [ ...]] A list of attributes to show in output Multi-query configuration file: -i config.json, --input config.json Filename of configuration file (keys in this file overwrite command-line arguments about query) Additional arguments: -p , --prefix Prefix for result file names (defaults to basename of .bed-file) -o , --outdir Output directory for output files (default: current dir) -s, --summary Filename of additional visualisation of results in graphical format -t n, --threads n Multiprocessed run: n = number of threads to run annotation process -l uropa.log, --log uropa.log Log file name for messages and warnings (default: log is written to stdout) -d, --debug Print verbose messages (for debugging) -v, --version Prints the version and exits
It is also possible to run UROPA using queries as given in sample_config.json:
uropa -i sample_config.json -t 4
Running UROPA from a docker container can be done using the following command:
sudo docker run --rm -v <path-to-input-files-on-HOST>:<path-to-container-mnt> UROPA:LATEST uropa <UROPA-Paramters> -p <path-to-container-mnt>/'your-file-prefix'
-v parameter mounts a HOST folder into your docker CONTAINER. This folder should contain the input files for UROPA and also the result files will be stored here. No files will be stored in the container!
--rm removes/closes the container after the run
Make sure to use the uropa -p option specifying the output directory and prefix, otherwise results are lost in the container environment.
How to cite
Kondili M, Fust A, Preussner J, Kuenne C, Braun T, and Looso M. UROPA: a tool for Universal RObust Peak Annotation. Scientific Reports 7 (2017), doi: 10.1038/s41598-017-02464-y
If you have any questions please feel free to contact Mario Looso (firstname.lastname@example.org).
The project is licensed under the MIT License.
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