Package: dna-analyser-ibp
DNA analyser IBPTool for creating R-loop tracker, P53predictor, G4Killer and G4Hunter analysis. Work as API wrapper for IBP DNA analyzer APIbioinformatics.ibp.
Currently working with an instance of DNA analyser server running onhttp://bioinformatics.ibp.czcomputational core but can be switched
to the local instance of the server.Getting StartedPrerequisitespython >= 3.10InstallingTo install test version fromPypi.pipenv install dna-analyser-ibppip install dna-analyser-ibpQuick startDNA analyser usespandas.Dataframeorpandas.Series. Firstly the user  has to createApiobject and login to API.fromDNA_analyser_IBP.apiimportApiAPI=Api()Enteryouremailexample@example.czEnteryourpassword········2020-09-1618:51:17.943398[INFO]:Userhostistryingtologin...2020-09-1618:51:17.990580[INFO]:Userhostissuccessfullylogedin...If DNA analyser API server is not running onhttp://bioinformatics.ibp.czthen you have to set server paramether to createApiobject.fromDNA_analyser_IBP.apiimportApiAPI=Api(server='http://hostname:port/api')Sequence uploadingSequences can be uploaded from NCBI, plain text or text file. Example bellow illustrates NCBI sequence uploadingHomo sapiens chromosome 12.API.sequence.ncbi_creator(circular=True,tags=['Homo','sapiens','chromosome'],name='Homo sapiens chromosome 12',ncbi_id='NC_000012.12')API.sequence.load_all(tags=['Homo'])G4HunterG4Hunter is a tool for prediction of G-quadruplex propensity in nucleic acids, this algorithm considers G-richness and G-skewness of a tested sequence and shows a quadruplex propensity score.sapiens=API.g4hunter.load_all(tags=['Homo'])API.g4hunter.analyse_creator(sequence=sapiens,tags=['analyse','Homo','sapiens'],threshold=1.4,window_size=30)To load results of G4Hunter analysis.API.g4hunter.load_all(tags=['analyse','Homo','sapiens'])R-loop trackerR-loop tracker is a toll for prediction of R-loops in nucleic acids. The algorithms search for R-loop initiation zone based on presence of G-clusters and R-loop elongation zone containing at least 40% of Guanine density.sapiens=API.g4hunter.load_all(tags=['Homo'])API.rloopr.analyse_creator(sequence=sapiens,tags=['analyse','Homo','sapiens'],riz_2g_cluster=True,riz_3g_cluster=False)To load results of R-loop tracker analysis.API.rloopr.load_all(tags=['analyse','Homo','sapiens'])G4KillerG4Killer algorithm allows to mutate DNA sequences with desired G4Hunter score with minimal mutation steps.API.g4killer.run(sequence='AATTATTTGGAAAGGGGGGGTTTTCCGA',threshold=0.5)API.g4killer.run_multiple(sequences=['AATTATTTGGAAAGGGGGGGTTTTCCGA','AATTATTTGGAAAGGGGGGGTTTTCCGA'],threshold=0.5)P53 predictorP53 binding predictor for 20 base pairs sequences.API.p53.run(sequence='GGACATGCCCGGGCATGTCC')API.p53.run_multiple(sequences=['GGACATGCCCGGGCATGTCC','GGACATGCCCGGGCATGTCC'])DevelopmentDependenciesrequests = "2.31.0"pandas = "2.0.0"tqdm = "4.66.0"pyjwt = "2.8.0"matplotlib = "3.7.2"requests-toolbelt = "1.0.0"tenacity = "8.2.3"DEV dependenciespytest = "7.4.2"TestsTo run tests only when downloaded directly from this repository.pytest -v tests/AuthorsPatrik Kaura-Main developer-patrikkauraLicenseThis project is licensed under the GPL-3.0 License - see theLICENSE.mdfile for details.