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fusor test failures
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[ issue-132-tests ⚙ venv] ~/code/fusor % ipython | |
Python 3.11.0 (main, Sep 6 2023, 12:48:52) [Clang 14.0.3 (clang-1403.0.22.14.1)] | |
Type 'copyright', 'credits' or 'license' for more information | |
IPython 8.16.1 -- An enhanced Interactive Python. Type '?' for help. | |
In [1]: from gene.database import create_db | |
In [2]: db = create_db() | |
In [3]: db.get_source_metadata("NCBI") | |
Out[3]: | |
{'data_license': 'custom', | |
'data_license_url': 'https://www.ncbi.nlm.nih.gov/home/about/policies/', | |
'version': '20231031', | |
'data_url': {'info_file': 'ftp.ncbi.nlm.nih.govgene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz', | |
'history_file': 'ftp.ncbi.nlm.nih.govgene/DATA/gene_history.gz', | |
'assembly_file': 'ftp.ncbi.nlm.nih.govgenomes/refseq/vertebrate_mammalian/Homo_sapiens/latest_assembly_versions/'}, | |
'rdp_url': 'https://reusabledata.org/ncbi-gene.html', | |
'data_license_attributes': {'non_commercial': False, | |
'attribution': False, | |
'share_alike': False}, | |
'genome_assemblies': ['GRCh38.p14']} | |
In [4]: db.get_source_metadata("HGNC") | |
Out[4]: | |
{'data_license': 'CC0', | |
'data_license_url': 'https://www.genenames.org/about/license/', | |
'version': '20231031', | |
'data_url': {'complete_set_archive': 'ftp://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/json/hgnc_complete_set.json'}, | |
'rdp_url': None, | |
'data_license_attributes': {'non_commercial': False, | |
'attribution': False, | |
'share_alike': False}, | |
'genome_assemblies': []} | |
In [5]: db.get_source_metadata("Ensembl") | |
Out[5]: | |
{'data_license': 'custom', | |
'data_license_url': 'https://useast.ensembl.org/info/about/legal/disclaimer.html', | |
'version': '110', | |
'data_url': {'genome_annotations': 'ftp://ftp.ensembl.org/pub/current_gff3/homo_sapiens/Homo_sapiens.GRCh38.110.gff3.gz'}, | |
'rdp_url': None, | |
'data_license_attributes': {'non_commercial': False, | |
'attribution': False, | |
'share_alike': False}, | |
'genome_assemblies': ['GRCh38']} | |
In [6]: !pip show gene-normalizer | |
/Users/jss009/code/fusor/venv/lib/python3.11/site-packages/IPython/core/interactiveshell.py:2622: UserWarning: You executed the system command !pip which may not work as expected. Try the IPython magic %pip instead. | |
warnings.warn( | |
Name: gene-normalizer | |
Version: 0.1.40.dev1 | |
Summary: VICC normalization routines for genes | |
Home-page: | |
Author: Alex Wagner, Kori Kuzma, James Stevenson | |
Author-email: | |
License: MIT License |
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