daler / biomartpy Goto Github PK

mart_name = 'ensembl'
dataset = 'dmelanogaster_gene_ensembl'
attributes = ['flybase_gene_id', 'flybasename_gene', 'description']
filters = ['flybase_gene_id']
values = [['FBgn0031208', 'FBgn0002121', 'FBgn0031209', 'FBgn0051973']]

res = bmp.make_lookup(mart_name = mart_name,
                      dataset = dataset,
                      attributes = attributes,
                      filters = filters,
                      values = values)

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-8-1bd03cbc42bb> in <module>()
      3                                           attributes = attributes,
      4                                           filters = filters,
----> 5                       values = values)

/Users/nwieder/miniconda3/lib/python3.5/site-packages/biomartpy/__init__.py in make_lookup(mart_name, dataset, attributes, filters, values, unique_rows)
    234 
    235         filter_value_dict = dict(zip(filters, values))
--> 236         _filters, _values = _filter_and_values_to_RList(filter_value_dict)
    237         kwargs['filters'] = _filters
    238         kwargs['values'] = _values

/Users/nwieder/miniconda3/lib/python3.5/site-packages/biomartpy/__init__.py in _filter_and_values_to_RList(d)
    199         # Could use ListVector directly with the dict, but want to guarantee
    200         # positional order of filters and values
--> 201         f = robjects.StrVector(d.keys())
    202         v = robjects.ListVector(
    203             rpy2.rlike.container.TaggedList(

/Users/nwieder/miniconda3/lib/python3.5/site-packages/rpy2-2.7.8-py3.5-macosx-10.5-x86_64.egg/rpy2/robjects/vectors.py in __init__(self, obj)
    363     def __init__(self, obj):
    364         obj = StrSexpVector(obj)
--> 365         super(StrVector, self).__init__(obj)
    366 
    367     def factor(self):

/Users/nwieder/miniconda3/lib/python3.5/site-packages/rpy2-2.7.8-py3.5-macosx-10.5-x86_64.egg/rpy2/robjects/vectors.py in __init__(self, o)
    240         if not isinstance(o, SexpVector):
    241             o = conversion.py2ri(o)
--> 242         super(Vector, self).__init__(o)
    243         self.ro = VectorOperationsDelegator(self)
    244         self.rx = ExtractDelegator(self)

ValueError: Invalid SEXP type '0' (should be 16).

Downloading/unpacking biomartpy
  Downloading biomartpy-0.1.tar.gz
  Running setup.py (path:/Users/u0089478/.virtualenvs/test/build/biomartpy/setup.py) egg_info for package biomartpy
    Traceback (most recent call last):
      File "<string>", line 17, in <module>
      File "/Users/u0089478/.virtualenvs/test/build/biomartpy/setup.py", line 1, in <module>
        import ez_setup
    ImportError: No module named ez_setup
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):

  File "<string>", line 17, in <module>

  File "/Users/u0089478/.virtualenvs/test/build/biomartpy/setup.py", line 1, in <module>

    import ez_setup

ImportError: No module named ez_setup

get_bm_lookup ('ensembl', 'hsapiens_gene_ensembl', 
    attributes=['ensembl_gene_id', 'external_gene_id'])

Error: attempt to use zero-length variable name
Segmentation fault: 11

{'biotype': ['protein_coding']}