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Error from Importing MSigDB and progeny of mouse organism (and translate_net) #155
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Hi, @deeenes. I opened a new issue for my problem. And this is my traceback. error Traceback (most recent call last) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/site-packages/decoupler/omnip.py:360, in get_resource(name, organism, genesymbol_resource, **kwargs) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/site-packages/decoupler/omnip.py:919, in _annotation_identifiers(net, organism, genesymbol_resource) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/site-packages/decoupler/omnip.py:758, in translate_net(net, columns, source_organism, target_organism, id_type, unique_by, **kwargs) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/site-packages/pypath/utils/orthology.py:2262, in translate_df(df, target, source, cols, id_type, only_swissprot, oma, homologene, ensembl, oma_rel_type, oma_score, ensembl_hc, ensembl_types, **kwargs) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/site-packages/pypath/utils/orthology.py:620, in OrthologyManager.translate_df(self, df, target, source, cols, id_type, only_swissprot, oma, homologene, ensembl, oma_rel_type, oma_score, ensembl_hc, ensembl_types, **kwargs) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/site-packages/pypath/utils/orthology.py:515, in OrthologyManager.get_df(self, target, source, id_type, only_swissprot, oma, homologene, ensembl, oma_rel_type, oma_score, ensembl_hc, ensembl_types, full_records, **kwargs) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/site-packages/pypath/utils/orthology.py:233, in OrthologyManager.which_table(self, target, source, only_swissprot, resource, id_type) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/site-packages/pypath/utils/orthology.py:242, in OrthologyManager.load(self, key) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/site-packages/pypath/utils/orthology.py:1492, in OmaOrthology.init(self, target, source, id_type, only_swissprot, rel_type, score) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/site-packages/pypath/utils/orthology.py:869, in ProteinOrthology.init(self, target, source, id_type, only_swissprot, **kwargs) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/site-packages/pypath/utils/orthology.py:1506, in OmaOrthology.load(self) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/site-packages/pypath/inputs/oma.py:125, in oma_orthologs(organism_a, organism_b, id_type, rel_type, score, return_df) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/site-packages/pypath/inputs/oma.py:139, in (.0) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/site-packages/pypath/inputs/oma.py:244, in id_translate(id, taxon, id_type) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/site-packages/pypath/utils/mapping.py:3551, in map_name(name, id_type, target_id_type, ncbi_tax_id, strict, expand_complexes, uniprot_cleanup) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/site-packages/pypath_common/_misc.py:2936, in ignore_unhashable..wrapper(*args, **kwargs) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/site-packages/pypath/utils/mapping.py:1978, in Mapper.map_name(self, name, id_type, target_id_type, ncbi_tax_id, strict, expand_complexes, uniprot_cleanup) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/site-packages/pypath/utils/mapping.py:2510, in Mapper._map_name(self, name, id_type, target_id_type, ncbi_tax_id) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/site-packages/pypath/utils/mapping.py:1562, in Mapper.which_table(self, id_type, target_id_type, load, ncbi_tax_id) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/site-packages/pypath/utils/mapping.py:3208, in Mapper.load_mapping(self, resource, **kwargs) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/site-packages/pypath/utils/mapping.py:258, in MapReader.init(self, param, ncbi_tax_id, entity_type, load_a_to_b, load_b_to_a, uniprots, lifetime, resource_id_types) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/site-packages/pypath/utils/mapping.py:288, in MapReader.load(self) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/site-packages/pypath/utils/mapping.py:450, in MapReader.read(self) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/site-packages/pypath/utils/mapping.py:893, in MapReader.read_mapping_uniprot(self) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/site-packages/pypath/inputs/uniprot.py:681, in UniprotQuery.perform(self) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/site-packages/pypath/inputs/uniprot.py:660, in UniprotQuery.iter(self) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/site-packages/pypath/share/curl.py:766, in FileOpener.iterfile(fileobj) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/gzip.py:313, in GzipFile.read1(self, size) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/_compression.py:68, in DecompressReader.readinto(self, b) File /opt/homebrew/Caskroom/miniconda/base/envs/decoupler_env/lib/python3.9/gzip.py:495, in _GzipReader.read(self, size) error: Error -3 while decompressing data: too many length or distance symbols Thank you!! |
Hi @deeenes, I found out how to solve my issue. I needed to clear the omnipathdb cache and pypath cache which I could find its path by "from pypath.share import cache; cache.get_cachedir()". Sorry to bother you and thank you! |
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Hi, When I used "dc.get_resource('MSigDB', organism='mouse')" or "dc.translate_net(target_organism = 'mouse')", I got this error "error: Error -3 while decompressing data: too many length or distance symbols". I also tried to remove my cache by "rm ~/.cache/omnipathdb/*", but it didn't solve the issue.
Also, when I used "dc.get_progeny(organism = 'mouse', top = 500)", it returned same error.
"dc.get_collectri(organism = 'mouse', split_complexes = False)" was fine.
Please give me any advice, thanks!
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