pypath
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saezlab
Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular communication roles.
Hi, I have used pypath to download the proteome uniprot accession IDs associated to yeast reference strain (tax id = 559292), done as follows: ``` from pypath.inputs import uniprot from...
In the GO.py file in the inputs directory, running line 503 for the url https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms?page=670 gives the error: `json.decoder.JSONDecodeError: Expecting ',' delimiter: line 1 column 7961 (char 7960)` **To Reproduce**...
**Describe the bug** Hello! As always, great job with pypath! As discussed previously with @deeenes , I am getting an error when I load an existing interaction from two different...
When I try to map from genesymbol to entrez id, I get the following error: ``` ValueError Traceback (most recent call last) ~\AppData\Local\Temp\ipykernel_4272\2864091030.py in ----> 1 mapping.map_name("ABCC1", "genesymbol", "entrez") C:\anaconda3\lib\site-packages\pypath\utils\mapping.py...
Steps used: from pypath import resources rc = resources.get_controller() rc Error: UnicodeDecodeError: 'charmap' codec can't decode byte 0x9d in position 40814: character maps to Complete snapshot:  Additional query: I...
**Describe the bug** [This function](https://github.com/saezlab/pypath/blob/3820c3a28c13ce701f1d2b5f9ac6e00834c757da/pypath/inputs/kegg_api.py#L51) in the kegg_api module has a faulty behavior. It iterates through the types of relations but the last relation it takes to generate function overwrites...
**Describe the bug** Tried downloading the progeny mouse model but I get a TypeError: Nonetype is not iterable. Human works fine. **To Reproduce** ``` model = dc.get_progeny(organism='mouse', top=100) ``` ```...
When calling `omnipath.requests.Complexes.complex_genes()`, the `references` column always reports stripped references which, in turn, results in the `references_stripped` column containing rubbish data. This seems to be a problem with the web...
Dealing with and building named tuples are harder than dealing with dictionaries. So here I propose using dictionaries instead of them. What do you think? Were there some reasons to...
**Describe the bug** In the file `pypath/core/evidence.py` at line 324 it checks if value is instance of _const.LIST_LIKE, however _const is not in namespace. I fixed it by adding `import...
