Package: uropa
Universal RObust Peak AnnotatorTheUniversal 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.FeaturesDetect the most appropriate annotation with flexible parameter keys that allow
robustness and simple customization, such asfeature typefeature anchorfeature direction relative to peak locationfilter for attribute values, e.g. “protein_coding”strand specificityUtilization of all available GTF files as annotation databaseOne run with variable sets of parameters by multiple queriesGraduated annotation due to priorizationDifferent easily-readable output tables (allhits, finalfits, besthits).Visual summary for annotation evaluationPreparation of custom annotation filesDocumentationA detailed description of how to apply UROPA to your data can be foundhere.InstallationFrom PyPIYou can install UROPA by simply running:pipinstalluropaConda package managerYou can also install UROPA using the conda package manager. Make sure to havecondainstalled, e.g. viaMinicondadownload the Miniconda installer forPython 3runbash Miniconda3-latest-Linux-x86_64.shto install MinicondaAnswer the question "Do you wish the installer to prepend the Miniconda install location to PATH in your /home/.../.bashrc ?" with yes
OR doPATH=dir/to/miniconda3:$PATHafter installation processThe UROPA installation is now as easy asconda create --name uropaconda activate uropaconda install python uropa -c biocondaBiocontainers / DockerIf you have a runningDockerenvironment, you can pull a biocontainer with UROPA and all dependencies viadocker pull quay.io/biocontainers/uropa:latest_tagusing the latest tag from thetaglist, e.g.1.2.1--py27r3.3.2_0UsageTest commandIt is possible to run UROPA using either a config file (supports multiple queries):uropa-isample_config.json-t4Or directly using a .bed-file (supports only one query):uropa--bedtest_data/genomic_regions.bed--gtftest_data/gencode.v29.annotation.chr19.gtfCommand-line usageTo effectively use UROPA, make yourself familiar with the command-line options:$uropaUsage:uropa[options]optionalarguments:-h,--helpshowthishelpmessageandexitArgumentsforonequery:-b,--bedFilenameof.bed-filetoannotate-g,--gtfFilenameof.gtf-filewithfeatures--feature[[...]]Featureforannotation--feature_anchor[[...]]Featureanchortoannotateto--distance[[...]]Maximumpermitteddistancefromfeature(1or2arguments)--strand[[...]]Desiredstrandofannotatedfeaturerelativetopeak--relative_location[[...]]Peaklocaionrelativetofeaturelocation--internalsSetminimumoverlapfractionforinternalfeatureannotations.0equatestointernals=Falseand1equatestointernals=True.DefaultisFalse.--filter_attributeFilteron9thcolumnofGTF--attribute_values[[...]]Value(s)ofattributecorrespondingto--filter_attribute--show_attributes[[...]]Alistofattributestoshowinoutput

Multi-queryconfigurationfile:-iconfig.json,--inputconfig.jsonFilenameofconfigurationfile(keysinthisfileoverwritecommand-lineargumentsaboutquery)Additionalarguments:-p,--prefixPrefixforresultfilenames(defaultstobasenameof.bed-file)-o,--outdirOutputdirectoryforoutputfiles(default:currentdir)-s,--summaryFilenameofadditionalvisualisationofresultsingraphicalformat-tn,--threadsnMultiprocessedrun:n=numberofthreadstorunannotationprocess-luropa.log,--loguropa.logLogfilenameformessagesandwarnings(default:logiswrittentostdout)-d,--debugPrintverbosemessages(fordebugging)-v,--versionPrintstheversionandexitsBiocontainer usageRunning UROPA from a docker container can be done using the following command:sudodockerrun--rm-v<path-to-input-files-on-HOST>:<path-to-container-mnt>UROPA:LATESTuropa<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 runMake sure to use the uropa -p option specifying the output directory and prefix, otherwise results are lost in the container environment.How to citeKondili M, Fust A, Preussner J, Kuenne C, Braun T, and Looso M. UROPA: a tool for Universal RObust Peak Annotation.Scientific Reports7(2017), doi:10.1038/s41598-017-02464-yContributeSource CodehereIssue TrackerhereSupportIf you have any questions please feel free to contact Mario Looso (mario.looso@mpi-bn.mpg.de).LicenseThe project is licensed under the MIT License.