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saezlab / pypath

Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular communication roles.
http://omnipathdb.org/
GNU General Public License v3.0
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extra Omnipath loading error #96

Closed luli7 closed 5 years ago

luli7 commented 5 years ago

Dear Denes and Nick,

I am trying to construct Omnipath with all the extras. I have first did: pall.load_omnipath(kinase_substrate_extra=True,ligand_receptor_extra=True,pathway_extra=True,remove_htp=False,keep_directed=False).

Then I wanted to add netpath and alz back: pall.load_resources({'netpath':data_formats.interaction['netpath'],'alz':data_formats.interaction['alz']})

I get following error for netpath: File "/home/luli7/.local/lib/python3.6/site-packages/pypath/main.py", line 2312, in read_data_file infile = input_func(**param.input_args) File "/home/luli7/.local/lib/python3.6/site-packages/pypath/dataio.py", line 5008, in netpath_interactions data = dict([(k, v) for k, v in iteritems(data) if k.endswith('xml')]) File "/home/luli7/.local/lib/python3.6/site-packages/future/utils/init.py", line 308, in iteritems func = obj.items [2019-06-21 10:57:52] [network] netpath_interactions: Could not find file or dataio function or failed preprocessing.

I have also tried to load interaction_misc, and obtained the following error messages: File "/home/luli7/.local/lib/python3.6/site-packages/pypath/main.py", line 2312, in read_data_file infile = input_func(**param.input_args) File "/home/luli7/.local/lib/python3.6/site-packages/pypath/dataio.py", line 6642, in get_hsn c = curl.Curl(url, silent = False).split('\n')[1:] [2019-06-21 11:01:48] [network] get_hsn: Could not find file or dataio function or failed preprocessing.

File "/home/luli7/.local/lib/python3.6/site-packages/pypath/main.py", line 2312, in read_data_file infile = input_func(**param.input_args) File "/home/luli7/.local/lib/python3.6/site-packages/pypath/dataio.py", line 3828, in get_acsn url = urls.urls['acsn']['url'] [2019-06-21 11:01:49] [network] get_acsn: Could not find file or dataio function or failed preprocessing.

File "/home/luli7/.local/lib/python3.6/site-packages/pypath/main.py", line 2312, in read_data_file infile = input_func(**param.input_args) File "/home/luli7/.local/lib/python3.6/site-packages/pypath/dataio.py", line 7633, in rolland_hi_ii_14 xlsname = xls.name [2019-06-21 11:02:09] [network] rolland_hi_ii_14: Could not find file or dataio function or failed preprocessing.

[2019-06-21 11:02:10] [network] /home/denes/Documents/pw/data/hi3-2.3.tsv: Could not find file or dataio function or failed preprocessing.

Thank you very much for your help. Best regards Lu

deeenes commented 5 years ago

Hi Lu,

Sorry somehow I missed this bug until now. Everything fixed in 0.8.33.

Best,

Denes