PhenotypesToGenes (2022_04-62-gc5232248)
Converts a phenotype list to a list of matching genes.
For each given HPO term, the genes associated with the term itself and the genes associated with any sub-term are returned.
Optional parameters:
-in <string> Input file, containing one HPO term identifier per line, e.g. HP:0002066. Text after the identifier is ignored. If unset, reads from STDIN.
Default value: ''
-out <file> Output TSV file with genes (column 1) and matched phenotypes (column 2). If unset, writes to STDOUT.
Default value: ''
-test Uses the test database instead of on the production database.
Default value: 'false'
-ignore_invalid Ignores invalid HPO identifiers instead of throwing an error.
Default value: 'false'
-ignore_non_phenotype Ignores HPO identifiers that are sub-terms of 'Mode of inheritance' or 'Frequency'
Default value: 'false'
-source <string> Comma-separated list of phenotype-gene source databases.
Default value: 'HPO,OMIM,ClinVar,Decipher,HGMD,GenCC'
-evidence <string> Comma-separated list of phenotype-gene evidence levels.
Default value: 'n/a,low,medium,high'
Special parameters:
--help Shows this help and exits.
--version Prints version and exits.
--changelog Prints changeloge and exits.
--tdx Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
PhenotypesToGenes 2022_04-62-gc5232248
2020-11-23 Added parameter 'ignore_invalid'.
2020-05-24 First version.