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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Not able to generate omnipath network #156

Closed ayadlin closed 3 years ago

ayadlin commented 3 years ago

I loaded pypath network:

from pypath.core import network From the I get this message:

[2020-09-30 11:06:10] [pypath] 
    - session ID: `5tiql`
    - working directory: `~/Datasets/Xena/TCGA/RNASeq/TPM`
    - logfile: `~/Datasets/Xena/TCGA/RNASeq/TPM/pypath_log/pypath-5tiql.log`
    - pypath version: 0.11.35
[2020-09-30 11:06:10] [curl] Module `fabric` not available.

I might be coming to it from the wrong side, but the command I think will help get the system started fails:

op=network.Network.omnipath() Error below -

Just as reference I have a list of 800 genes, what I want to do is get all upstream activators/inhibitors and downstream effectors/inhibtors for each gene at least for two levels for example MAPK one set of two levels effectors would be MAPKKK, MAPKK and doenstream will see RSK and P60S. I just added this casu meybe I am approcaching the problem the wrong way?

Anyway the bug seems to be real.

[2020-09-30 10:50:43] [network] `elm_interactions`: Could not find file or input function or failed preprocessing.
[2020-09-30 10:51:26] [network] `get_dip`: Could not find file or input function or failed preprocessing.
---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
<ipython-input-5-973d301f0c83> in <module>
----> 1 network.Network.omnipath()

~/anaconda3/envs/bioinfo/lib/python3.7/site-packages/pypath/core/network.py in omnipath(cls, omnipath, kinase_substrate_extra, ligand_receptor_extra, pathway_extra, extra_directions, remove_htp, htp_threshold, keep_directed, min_refs_undirected, old_omnipath_resources, exclude, ncbi_tax_id, **kwargs)
   3070             min_refs_undirected = min_refs_undirected,
   3071             old_omnipath_resources = old_omnipath_resources,
-> 3072             exclude = exclude,
   3073         )
   3074 

~/anaconda3/envs/bioinfo/lib/python3.7/site-packages/pypath/core/network.py in load_omnipath(self, omnipath, kinase_substrate_extra, ligand_receptor_extra, pathway_extra, extra_directions, remove_htp, htp_threshold, keep_directed, remove_undirected, min_refs_undirected, min_resources_undirected, old_omnipath_resources, exclude, pickle_file)
   2818         )
   2819 
-> 2820         self.load(omnipath, exclude = exclude)
   2821 
   2822         if kinase_substrate_extra:

~/anaconda3/envs/bioinfo/lib/python3.7/site-packages/pypath/core/network.py in load(self, resources, make_df, exclude, reread, redownload, keep_raw, top_call, cache_files, only_directions, pickle_file, allow_loops)
    601             ):
    602 
--> 603                 self.load_resource(resource, **kwargs)
    604 
    605             elif resource is not None:

~/anaconda3/envs/bioinfo/lib/python3.7/site-packages/pypath/core/network.py in load_resource(self, resource, clean, reread, redownload, keep_raw, only_directions, allow_loops, **kwargs)
    669             reread = reread,
    670             redownload = redownload,
--> 671             keep_raw = keep_raw,
    672         )
    673 

~/anaconda3/envs/bioinfo/lib/python3.7/site-packages/pypath/core/network.py in _read_resource(self, resource, reread, redownload, keep_raw, cache_files)
   1042             )
   1043 
-> 1044             for lnum, line in enumerate(prg):
   1045 
   1046                 if len(line) <= 1 or (lnum == 1 and networkinput.header):

~/anaconda3/envs/bioinfo/lib/python3.7/site-packages/pypath/share/progress.py in __iter__(self)
    118         )
    119 
--> 120         for it in iterable:
    121 
    122             self.set_status('busy')

~/anaconda3/envs/bioinfo/lib/python3.7/site-packages/pypath/inputs/huri.py in lit_bm_17_interactions()
    185 
    186         id_a = row[0][10:]
--> 187         id_b = row[1][10:]
    188 
    189         pubmed = row[8][7:]

IndexError: list index out of range
deeenes commented 3 years ago

Thanks for finding this, apparently the resource has been removed from the original URL. Fixed in ccf817b