phenopackets / pxftools Goto Github PK
View Code? Open in Web Editor NEWA command line utility for operating over Phenotype eXchange Format (PXF) files.
License: BSD 3-Clause "New" or "Revised" License
A command line utility for operating over Phenotype eXchange Format (PXF) files.
License: BSD 3-Clause "New" or "Revised" License
-h
is common, but pxftools expects --help
, which is confusing for the newbie
Many groups use GAFs for phenotypes as well as GO - e.g. planteome (cc @jhpoelen)
Conversely, pxf is generic enough for GO annotations (which are essentially normal, evolved phenotypes for genes)
It would be useful to read/write from GAFs into the phenopacket datamodel.
There are also a family of similar formats which could follow the same pattern. E.g. PAFs:
phenopackets/phenopacket-format#67
And of course the HPOA (non-phenote) TSVs
The project currently depends on a phenopackets-api SNAPSHOT version. Not being available in Maven central, this is causing the Travis build to fail.
Different input files may have different embedded contexts. Identifiers need to be expanded before trying to merge.
An idea from Chris, see https://github.com/owlcollab/owltools/wiki/Annotation-Extension-Folding
What are the requirements for compare
?
What are the requirements for summarize
?
Occasionally multiple publications are entered, separated by '; '. Example in OMIM-194190.tab.
Should the ontologies be provided on the command line? Obtained automatically somehow?
The merge command needs implementation.
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