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Cannot retrieve progeny weights for mouse: url for homologene needs to be updated #278

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ruhisayana opened this issue Feb 5, 2024 · 4 comments
Open

Cannot retrieve progeny weights for mouse: url for homologene needs to be updated #278

ruhisayana opened this issue Feb 5, 2024 · 4 comments
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@deeenes
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bug Problem in the code

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@ruhisayana
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ruhisayana commented Feb 5, 2024 •
edited

Describe the bug
UPDATE:
The main issue seems to be that the url for homologene is inactive - would it be possible for this to be updated?
Original:
I'm trying to run progeny = dc.get_progeny(organism = 'Mus musculus', top=500) in Python 3.9 with decoupler-py 1.5 and pypath-omnipath version 0.16.4. I'm getting a modulenotfound error for pypath-omnipath even though I've installed via pip install git+https://github.com/saezlab/pypath.git and it shows up when I run pip show pypath-omnipath. The command works fine when I don't use organism='Mus musculus' or organism='mouse' and seems to be related to both not being able to import homology and the translate_net function.

To Reproduce
Steps to reproduce the behavior:

  1. Run progeny = dc.get_progeny(organism = 'Mus musculus', top=500) or progeny = dc.get_progeny(organism = 'mouse', top=500)

Expected behavior
Expected to get progeny annotation. Command works when I run progeny = dc.get_progeny(top=500), so for human.

Traceback (UPDATED)
TypeError Traceback (most recent call last)
Cell In[2], line 5
3 sys.path.insert(0, "~/opt/miniconda3/envs/py39/lib/python3.9/site-packages/pypath")
4 print(sys.path)
----> 5 progeny = dc.get_progeny(organism='mouse',top=500)

File ~/opt/miniconda3/envs/py39/lib/python3.9/site-packages/decoupler/omnip.py:160, in get_progeny(organism, top, **kwargs)
156 p.columns = ['source', 'target', 'weight', 'p_value']
158 if not _is_human(organism):
--> 160 p = translate_net(
161 p,
162 columns='target',
163 source_organism=9606,
164 target_organism=organism,
165 )
167 return p.reset_index(drop=True)

File ~/opt/miniconda3/envs/py39/lib/python3.9/site-packages/decoupler/omnip.py:587, in translate_net(net, columns, source_organism, target_organism, id_type, unique_by, **kwargs)
584 hom_net = net.copy()
586 # Translate
--> 587 hom_net = homology.translate_df(
588 df=hom_net,
589 target=_target_organism,
590 cols=columns,
591 source=_source_organism,
592 )
594 unique_by = common.to_list(unique_by)
596 if unique_by and all(c in hom_net.columns for c in unique_by):
597
598 # Remove duplicated based on source and target

File ~/opt/miniconda3/envs/py39/lib/python3.9/site-packages/pypath/utils/homology.py:1904, in translate_df(df, target, cols, source, homologene, ensembl, ensembl_hc, ensembl_types, **kwargs)
1901 args.pop('manager')
1902 kwargs = args.pop('kwargs')
-> 1904 return manager.translate_df(**args, **kwargs)

File ~/opt/miniconda3/envs/py39/lib/python3.9/site-packages/pypath/utils/homology.py:483, in HomologyManager.translate_df(self, df, target, cols, source, homologene, ensembl, ensembl_hc, ensembl_types, **kwargs)
480 source = taxonomy.ensure_ncbi_tax_id(source)
481 target = taxonomy.ensure_ncbi_tax_id(target)
--> 483 table = self.which_table(
484 target = target,
485 source = source,
486 )
488 param = self._translation_param(locals())
490 return table.translate_df(
491 df = df,
492 cols = cols,
(...)
495 **kwargs
496 )

File ~/opt/miniconda3/envs/py39/lib/python3.9/site-packages/pypath/utils/homology.py:184, in HomologyManager.which_table(self, target, source, only_swissprot)
180 self.expiry[key] = time.time()
182 if key not in self.tables:
--> 184 self.load(key)
186 if key in self.tables:
188 return self.tables[key]

File ~/opt/miniconda3/envs/py39/lib/python3.9/site-packages/pypath/utils/homology.py:215, in HomologyManager.load(self, key)
208 self._log(
209 'Homology table from taxon %u to %u (only SwissProt: %s) '
210 'has been loaded from %s.' % (key + (cachefile,))
211 )
213 else:
--> 215 self.tables[key] = self._load(key)
216 pickle.dump(self.tables[key], open(cachefile, 'wb'))
217 self._log(
218 'Homology table from taxon %u to %u (only SwissProt: %s) '
219 'has been saved to %s.' % (key + (cachefile,))
220 )

File ~/opt/miniconda3/envs/py39/lib/python3.9/site-packages/pypath/utils/homology.py:225, in HomologyManager._load(self, key)
223 def _load(self, key):
--> 225 return ProteinHomology(
226 target = key[1],
227 source = key[0],
228 only_swissprot = key[2],
229 homologene = self.homologene,
230 ensembl = self.ensembl,
231 ensembl_hc = self.ensembl_hc,
232 ensembl_types = self.ensembl_types,
233 )

File ~/opt/miniconda3/envs/py39/lib/python3.9/site-packages/pypath/utils/homology.py:718, in ProteinHomology.init(self, target, source, only_swissprot, homologene, ensembl, ensembl_hc, ensembl_types)
714 self.load_proteome(self.target, self.only_swissprot)
716 if source is not None:
--> 718 self.load(source)

File ~/opt/miniconda3/envs/py39/lib/python3.9/site-packages/pypath/utils/homology.py:734, in ProteinHomology.load(self, source)
730 def load(self, source = None):
732 if self.homologene:
--> 734 self.load_homologene(source)
736 if self.ensembl:
738 self.load_ensembl(source)

File ~/opt/miniconda3/envs/py39/lib/python3.9/site-packages/pypath/utils/homology.py:1175, in ProteinHomology.load_homologene(self, source)
1171 if source not in self.orthologs:
1173 self.orthologs[source] = collections.defaultdict(set)
-> 1175 hge = homologene_input.homologene_dict(source, self.target, 'entrez')
1176 hgr = homologene_input.homologene_dict(source, self.target, 'refseq')
1178 self.load_proteome(source, self.only_swissprot)

File ~/opt/miniconda3/envs/py39/lib/python3.9/site-packages/pypath/inputs/homologene.py:95, in homologene_dict(source, target, id_type)
92 hgroup = None
93 result = collections.defaultdict(set)
---> 95 for l in hg:
97 l = l.strip().split('\t')
98 this_hgroup = l[0].strip()

TypeError: 'NoneType' object is not iterable
Log file
n/a

Desktop (please complete the following information):

  • OS: Mac0S
  • Python version: 3.9
  • Version or commit hash: 0.15.4 (changed from pypath-omnipath v0.16.4 since simple homology import did not work)
@ruhisayana ruhisayana added the bug Problem in the code label Feb 5, 2024
@ruhisayana ruhisayana changed the title Cannot retrieve progeny weights for mouse with dc.get_progeny Cannot retrieve progeny weights for mouse: url for homologene needs to be updated Feb 5, 2024
@deeenes deeenes self-assigned this Feb 5, 2024
@deeenes
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deeenes commented Feb 5, 2024

Hello @ruhisayana ,

Thanks for reporting this! I'll check the HomoloGene URL soon, however, we've recently transitioned to OMA (orthologous Matrix) as the default resource for orthology data. And I think since then, using the release that I've just published today, it should work fine. I've just tested PROGENy access (by decoupler.get_progeny(organism = 'mouse')) right now, and it worked. Let me know if you still experience issues.

Best,

Denes

@haleymac
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haleymac commented Feb 26, 2024 •
edited by deeenes

Hi,

I'm having a similar issue when trying to run progeny = dc.get_progeny(organism = 'mouse', top=500) with pypath-omnipath version 0.16.9 and decoupler version 1.6.0. I have also installed via pip install git+https://github.com/saezlab/pypath.git and it shows up when I run pip show pypath-omnipath, but am getting an import error when I try to run dc.get_progeny with mouse (it works fine with human). Any help you can provide would be much appreciated.

Traceback: ---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
File [~/miniconda3/envs/countanal/lib/python3.10/site-packages/decoupler/omnip.py:648](https://file+.vscode-resource.vscode-cdn.net/Users/haleymacdonald/Desktop/msc/scanpy/RamDA/~/miniconda3/envs/countanal/lib/python3.10/site-packages/decoupler/omnip.py:648), in translate_net(net, columns, source_organism, target_organism, id_type, unique_by, **kwargs)
    [647](https://file+.vscode-resource.vscode-cdn.net/Users/haleymacdonald/Desktop/msc/scanpy/RamDA/~/miniconda3/envs/countanal/lib/python3.10/site-packages/decoupler/omnip.py:647) import pypath
--> [648](https://file+.vscode-resource.vscode-cdn.net/Users/haleymacdonald/Desktop/msc/scanpy/RamDA/~/miniconda3/envs/countanal/lib/python3.10/site-packages/decoupler/omnip.py:648) from pypath.utils import orthology
    [649](https://file+.vscode-resource.vscode-cdn.net/Users/haleymacdonald/Desktop/msc/scanpy/RamDA/~/miniconda3/envs/countanal/lib/python3.10/site-packages/decoupler/omnip.py:649) from pypath.share import common

File [~/miniconda3/envs/countanal/lib/python3.10/site-packages/pypath/utils/orthology.py:45](https://file+.vscode-resource.vscode-cdn.net/Users/haleymacdonald/Desktop/msc/scanpy/RamDA/~/miniconda3/envs/countanal/lib/python3.10/site-packages/pypath/utils/orthology.py:45)
     [43](https://file+.vscode-resource.vscode-cdn.net/Users/haleymacdonald/Desktop/msc/scanpy/RamDA/~/miniconda3/envs/countanal/lib/python3.10/site-packages/pypath/utils/orthology.py:43) import pandas as pd
---> [45](https://file+.vscode-resource.vscode-cdn.net/Users/haleymacdonald/Desktop/msc/scanpy/RamDA/~/miniconda3/envs/countanal/lib/python3.10/site-packages/pypath/utils/orthology.py:45) import pypath.utils.mapping as mapping
     [46](https://file+.vscode-resource.vscode-cdn.net/Users/haleymacdonald/Desktop/msc/scanpy/RamDA/~/miniconda3/envs/countanal/lib/python3.10/site-packages/pypath/utils/orthology.py:46) import pypath.share.common as common

File [~/miniconda3/envs/countanal/lib/python3.10/site-packages/pypath/utils/mapping.py:65](https://file+.vscode-resource.vscode-cdn.net/Users/haleymacdonald/Desktop/msc/scanpy/RamDA/~/miniconda3/envs/countanal/lib/python3.10/site-packages/pypath/utils/mapping.py:65)
     [64](https://file+.vscode-resource.vscode-cdn.net/Users/haleymacdonald/Desktop/msc/scanpy/RamDA/~/miniconda3/envs/countanal/lib/python3.10/site-packages/pypath/utils/mapping.py:64) import pypath.share.cache as cache_mod
---> [65](https://file+.vscode-resource.vscode-cdn.net/Users/haleymacdonald/Desktop/msc/scanpy/RamDA/~/miniconda3/envs/countanal/lib/python3.10/site-packages/pypath/utils/mapping.py:65) import pypath.internals.maps as maps
     [66](https://file+.vscode-resource.vscode-cdn.net/Users/haleymacdonald/Desktop/msc/scanpy/RamDA/~/miniconda3/envs/countanal/lib/python3.10/site-packages/pypath/utils/mapping.py:66) import pypath.resources.urls as urls

File [~/miniconda3/envs/countanal/lib/python3.10/site-packages/pypath/internals/maps.py:24](https://file+.vscode-resource.vscode-cdn.net/Users/haleymacdonald/Desktop/msc/scanpy/RamDA/~/miniconda3/envs/countanal/lib/python3.10/site-packages/pypath/internals/maps.py:24)
     [23](https://file+.vscode-resource.vscode-cdn.net/Users/haleymacdonald/Desktop/msc/scanpy/RamDA/~/miniconda3/envs/countanal/lib/python3.10/site-packages/pypath/internals/maps.py:23) import pypath_common._constants as _const
---> [24](https://file+.vscode-resource.vscode-cdn.net/Users/haleymacdonald/Desktop/msc/scanpy/RamDA/~/miniconda3/envs/countanal/lib/python3.10/site-packages/pypath/internals/maps.py:24) import pypath.internals.input_formats as input_formats
     [26](https://file+.vscode-resource.vscode-cdn.net/Users/haleymacdonald/Desktop/msc/scanpy/RamDA/~/miniconda3/envs/countanal/lib/python3.10/site-packages/pypath/internals/maps.py:26) __all__ = ['uniprot', 'mirbase', 'basic']

File [~/miniconda3/envs/countanal/lib/python3.10/site-packages/pypath/internals/input_formats.py:27](https://file+.vscode-resource.vscode-cdn.net/Users/haleymacdonald/Desktop/msc/scanpy/RamDA/~/miniconda3/envs/countanal/lib/python3.10/site-packages/pypath/internals/input_formats.py:27)
     [26](https://file+.vscode-resource.vscode-cdn.net/Users/haleymacdonald/Desktop/msc/scanpy/RamDA/~/miniconda3/envs/countanal/lib/python3.10/site-packages/pypath/internals/input_formats.py:26) import pypath_common._constants as _const
---> [27](https://file+.vscode-resource.vscode-cdn.net/Users/haleymacdonald/Desktop/msc/scanpy/RamDA/~/miniconda3/envs/countanal/lib/python3.10/site-packages/pypath/internals/input_formats.py:27) import pypath.inputs.uniprot as uniprot_input
...
--> [671](https://file+.vscode-resource.vscode-cdn.net/Users/haleymacdonald/Desktop/msc/scanpy/RamDA/~/miniconda3/envs/countanal/lib/python3.10/site-packages/decoupler/omnip.py:671)     raise ImportError(msg)
    [673](https://file+.vscode-resource.vscode-cdn.net/Users/haleymacdonald/Desktop/msc/scanpy/RamDA/~/miniconda3/envs/countanal/lib/python3.10/site-packages/decoupler/omnip.py:673) _source_organism = taxonomy.ensure_ncbi_tax_id(source_organism)
    [674](https://file+.vscode-resource.vscode-cdn.net/Users/haleymacdonald/Desktop/msc/scanpy/RamDA/~/miniconda3/envs/countanal/lib/python3.10/site-packages/decoupler/omnip.py:674) _target_organism = taxonomy.ensure_ncbi_tax_id(target_organism)

ImportError: pypath-omnipath is not installed. Please install it with: pip install git+https://github.com/saezlab/pypath.git

@deeenes
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deeenes commented Feb 26, 2024

Hi @haleymac,

Yours looks like a different issue. I was unable to reproduce it with the latest versions of decoupler-py and pypath-omnipath. Can you show us the pypath log after this error happens?

import decoupler as dc

pr_mouse = dc.get_progeny(organism = 'mouse')

The error happens here, then check the log:

import pypath
pypath.log()
# or to open the log elsewhere:
pypath.session._logger.fname

Also, you can check directly if any of these fail with error:

import pypath
from pypath.utils import orthology
from pypath.share import common
from pypath.utils import taxonomy

Best,

Denes

@deeenes
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deeenes commented Feb 26, 2024 •
edited

Btw, since c257159 HomoloGene access should be fine too (though it shouldn't affect decoupler any more)

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