Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotations and intercellular communication roles.
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
I loaded pypath network:
from pypath.core import network
From the I get this message: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.