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IDR / idr0130-olszewski-herpes

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Corrupted ScreenC-annotation CSV #1

Open hamshkhawar opened 1 year ago

hamshkhawar commented 1 year ago

Hi idr0130-screenC-annotation.csv is corrupted. Could you please push it again???

sbesson commented 1 year ago

Morning @hamshkhawar 

>>> import csv
>>> from itertools import islice
>>> with open('idr0130-screenC-annotation.csv', 'r') as f:
...   r = csv.reader(f)
...   for row in islice(r, 10):
...     print(row)
... 
['\ufeffPlate', 'Well', 'Characteristics [Organism 1]', 'Term Source 1 REF', 'Term Source 1 Accession', 'Characteristics [Organism 2]', 'Term Source 2 REF', 'Term Source 2 Accession', 'Characteristics [Cell Line]', 'Term Source 3 REF', 'Term Source 3 Accession', 'Prestwick Chemical Library ID', 'Compound Name', 'Compound PubChem CID', 'Compound PubChem URL', 'Compound Concentration (microMolar)', 'CAS', 'Compound SMILES', 'Comment [Experimental Results]', 'Experimental Condition [DMSO solvent]', 'Control Type', 'Comment [Control Type Comments]', 'Quality Control', 'Comment [Quality Control Comments]', 'Channels']
['BSF020893-1A', 'A1', 'Homo sapiens', 'NCBITaxon', 'NCBITaxon_9606', 'Herpes simplex virus type 1', 'NCBITaxon', 'NCBITaxon_10298', 'A549', 'EFO', 'EFO_0001086', '', 'Dimethyl sulfoxide', '679', 'https://pubchem.ncbi.nlm.nih.gov/compound/679', '3519.3', '67-68-5', 'CS(=O)C', '', '0.03%', 'negative control', 'solvent control', 'pass', 'non-toxic in absence of infection', 'Hoechst:nuclei; GFP:infection']
['BSF020893-1A', 'A10', 'Homo sapiens', 'NCBITaxon', 'NCBITaxon_9606', 'Herpes simplex virus type 1', 'NCBITaxon', 'NCBITaxon_10298', 'A549', 'EFO', 'EFO_0001086', 'Prestw-1112', 'Procarbazine hydrochloride', '9703', 'https://pubchem.ncbi.nlm.nih.gov/compound/9703', '1.25', '366-70-1', 'C(NC(C)C)(c1ccc(cc1)CNNC)=O', '', '', '', '', 'pass', 'non-toxic in absence of infection', 'Hoechst:nuclei; GFP:infection']
['BSF020893-1A', 'A11', 'Homo sapiens', 'NCBITaxon', 'NCBITaxon_9606', 'Herpes simplex virus type 1', 'NCBITaxon', 'NCBITaxon_10298', 'A549', 'EFO', 'EFO_0001086', 'Prestw-1132', 'Celiprolol HCl', '42373', 'https://pubchem.ncbi.nlm.nih.gov/compound/42373', '1.25', '57470-78-7', 'C(Nc1cc(c(OCC(CNC(C)(C)C)O)cc1)C(=O)C)(N(CC)CC)=O', '', '', '', '', 'pass', 'non-toxic in absence of infection', 'Hoechst:nuclei; GFP:infection']
['BSF020893-1A', 'A12', 'Homo sapiens', 'NCBITaxon', 'NCBITaxon_9606', 'Herpes simplex virus type 1', 'NCBITaxon', 'NCBITaxon_10298', 'A549', 'EFO', 'EFO_0001086', 'Prestw-116', 'Naltrexone hydrochloride dihydrate', '5485201', 'https://pubchem.ncbi.nlm.nih.gov/compound/5485201', '1.25', '16676-29-2', '[C@]123[C@@]4([C@H](N(CC5CC5)CC1)Cc1c2c(O[C@H]3C(CC4)=O)c(cc1)O)O', '', '', '', '', 'pass', 'non-toxic in absence of infection', 'Hoechst:nuclei; GFP:infection']
['BSF020893-1A', 'A13', 'Homo sapiens', 'NCBITaxon', 'NCBITaxon_9606', 'Herpes simplex virus type 1', 'NCBITaxon', 'NCBITaxon_10298', 'A549', 'EFO', 'EFO_0001086', 'Prestw-1181', 'Tibolone', '444008', 'https://pubchem.ncbi.nlm.nih.gov/compound/444008', '1.25', '5630-53-5', 'C/1\\2=C(/C[C@H]([C@]3([C@]4([C@@]([C@](C#C)(CC4)O)(CC[C@]13[H])C)[H])[H])C)\\CC(=O)CC2', '', '', '', '', 'pass', 'non-toxic in absence of infection', 'Hoechst:nuclei; GFP:infection']
['BSF020893-1A', 'A14', 'Homo sapiens', 'NCBITaxon', 'NCBITaxon_9606', 'Herpes simplex virus type 1', 'NCBITaxon', 'NCBITaxon_10298', 'A549', 'EFO', 'EFO_0001086', 'Prestw-120', 'Triamcinolone', '31307', 'https://pubchem.ncbi.nlm.nih.gov/compound/31307', '1.25', '124-94-7', '[C@]12([C@]([C@@H](C[C@]1([C@]1([C@@]([C@@]\\3(\\C(=C/C(\\C=C3)=O)\\CC1)C)([C@H](C2)O)F)[H])[H])O)(C(=O)CO)O)C', '', '', '', '', 'pass', 'non-toxic in absence of infection', 'Hoechst:nuclei; GFP:infection']
['BSF020893-1A', 'A15', 'Homo sapiens', 'NCBITaxon', 'NCBITaxon_9606', 'Herpes simplex virus type 1', 'NCBITaxon', 'NCBITaxon_10298', 'A549', 'EFO', 'EFO_0001086', 'Prestw-123', 'Dehydrocholic acid', '6674', 'https://pubchem.ncbi.nlm.nih.gov/compound/6674', '1.25', '81-23-2', '[C@]12([C@]([C@]3([C@@]([C@@]4([C@](CC3=O)(CC(=O)CC4)[H])C)(CC1=O)[H])[H])(CC[C@@H]2[C@@H](CCC(=O)O)C)[H])C', '', '', '', '', 'pass', 'non-toxic in absence of infection', 'Hoechst:nuclei; GFP:infection']
['BSF020893-1A', 'A16', 'Homo sapiens', 'NCBITaxon', 'NCBITaxon_9606', 'Herpes simplex virus type 1', 'NCBITaxon', 'NCBITaxon_10298', 'A549', 'EFO', 'EFO_0001086', 'Prestw-1254', 'Fentiazac', '28871', 'https://pubchem.ncbi.nlm.nih.gov/compound/28871', '1.25', '18046-21-4', 'n1c(c(sc1c1ccccc1)CC(=O)O)c1ccc(cc1)Cl', '', '', '', '', 'pass', 'non-toxic in absence of infection', 'Hoechst:nuclei; GFP:infection']
['BSF020893-1A', 'A17', 'Homo sapiens', 'NCBITaxon', 'NCBITaxon_9606', 'Herpes simplex virus type 1', 'NCBITaxon', 'NCBITaxon_10298', 'A549', 'EFO', 'EFO_0001086', 'Prestw-1271', 'Escitalopram', '146570', 'https://pubchem.ncbi.nlm.nih.gov/compound/146570', '1.25', '128196-01-0', '[C@]1(c2c(CO1)cc(C#N)cc2)(c1ccc(cc1)F)CCCN(C)C', '', '', '', '', 'pass', 'non-toxic in absence of infection', 'Hoechst:nuclei; GFP:infection']

Can you expand on what you mean by "corrupted"?