ibn-salem / position_effect Goto Github PK

Hi Jonas,

The phenomatch.jar script is not working with the newest releases of hpo.obo. I get the following error:

Oct 11, 2021 6:02:36 PM ontologizer.go.OBOParser doParse
INFO: Got 11785 terms and 15459 relations in 61 ms
Details of parsed obo file:
date: null
format: 1.2
term definitions: 11785
Oct 11, 2021 6:02:36 PM ontologizer.go.Ontology assignLevel1TermsAndFixRoot
INFO: Ontology contains a single level-one term (All (HP:0000001)
WARN: Frequency of 4576 terms was zero!! Calculated by -1 * (Math.log(1/(double)maxFreq)) = -1 * (Math.log(1/(double)3525)))
Set IC of these to : 8.16763571524637
[INFO] Ontology and annotation table were parsed.
WARNING term is null:
HP:0410030
Exception in thread "main" java.io.IOException: [ERROR] this term 'HP:0410030'. is null. Probably it was not found in the provied phenotype ontology.
at phenotypeontology.PhenotypeData.getTermIncludingAlternatives(PhenotypeData.java:535)
at io.TabFileParser.parseCNVwithHpoTerms(TabFileParser.java:384)
at de.charite.compbio.phenomatch.core.Phenomatch.(Phenomatch.java:100)
at de.charite.compbio.phenomatch.commandline.PhenomatchCMD.main(PhenomatchCMD.java:27)

Can this be fixed?
Thanks!
Cinthya

some used java libraries might be outdated and newer versions in different sources exist.

• ontologizer seems to be available now from here: https://github.com/ontologizer/ontologizerlib
• However, this might not yet work together with the similarity implementation in the similarity.concepts.ResnikSimilarity implementation from the de.sonumina.javautil package. See: ontologizer/ontologizerlib#1
• There seems to be a new library implementing similar functionality (but was not updated since 2017): https://github.com/Phenomics/ontolib
• jannovar has a newer version: https://doc-openbio.readthedocs.io/projects/jannovar/en/master/jannovar_lib.html