cebel/pyhgnc

A Python package to access and query data provided by HGNC-approved gene nomenclature, gene families and associated resources including links to genomic, proteomic and phenotypic information.

pyhgnc's Issues

Name mapping function

Create a function that can generically map between different sources.

Improve testing

Need proper testing!

Fix ER Model for PyPI

ER Model is too big and sizing by rst does not apply somehow.

Error in update method (get_mgds)

There appears to be an issue with the update method, specifically in the get_mgds method. At least one of the mgd ids appears to be simply "M" which causes the code to fall over.

Line 187 in database.py. I solved this by:

def get_mgds(self, hgnc):
    mgds = []

    if 'mgd_id' in hgnc:

        for mgd in hgnc['mgd_id']:

            if mgd not in self.mgds:
                try:
                    mgdid = int(mgd.split(':')[-1])
                except ValueError:
                    mgdid = None
                if mgdid:
                    self.mgds[mgd] = models.MGD(mgdid=mgdid)
                    mgds.append(self.mgds[mgd])

    return mgds

However, I'm not sure if the real issue is in the download or not.

Update crashes

$ pyhgnc update
Traceback (most recent call last):
  File "/Users/cthoyt/.local/bin/pyhgnc", line 11, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.6/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/usr/local/lib/python3.6/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/usr/local/lib/python3.6/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/local/lib/python3.6/site-packages/click/core.py", line 895, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/local/lib/python3.6/site-packages/click/core.py", line 535, in invoke
    return callback(*args, **kwargs)
  File "/usr/local/lib/python3.6/site-packages/pyhgnc/cli.py", line 83, in update
    low_memory=low_memory)
  File "/usr/local/lib/python3.6/site-packages/pyhgnc/manager/database.py", line 419, in update
    database.db_import(silent=silent, hgnc_file_path=hgnc_file_path, hcop_file_path=hcop_file_path, low_memory=low_memory)
  File "/usr/local/lib/python3.6/site-packages/pyhgnc/manager/database.py", line 120, in db_import
    json_data = DbManager.load_hgnc_json(hgnc_file_path=hgnc_file_path)
  File "/usr/local/lib/python3.6/site-packages/pyhgnc/manager/database.py", line 402, in load_hgnc_json
    response = request.urlopen(HGNC_JSON)
NameError: name 'request' is not defined

It's hard to keep those request references straight, especially when writing code that's supposed to be 2/3 compatible. All that needs to be done is the namespace removed.

Can't run as module

There's no __main__.py module so this error happens:

$ python3 -m pyhgnc update
/usr/local/opt/python3/bin/python3.6: No module named pyhgnc.__main__; 'pyhgnc' is a package and cannot be directly executed

Fix Models documentation

The models documentation does not get insertet properly.