cli overlap command fails
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MeeshCompBio commented
When trying to run the cli command overlap, I keep getting an error saying that I have not supplied a GWAS argument when it is supplied.
(camoco) jmichno@helix15[~/MeeshCM/CamocoHelixInstall/test/PerGeneLocality]:camoco --debug overlap ZmRoot ZmAll locality --terms all --num-bootstraps 100 --snp2gene strongest --strongest-attr numIterations --strongest-higher --candidate-window-size 50000 --candidate-flank-limit 1 --out ZmRoot_Loc.csv
[LOG] Fri May 19 15:30:28 2017 - A baaaad thing happened.
__init__() missing 1 required positional argument: 'gwas'
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
/project/chadm/Meesh/CamocoHelixInstall/Camoco/camoco/cli/camoco in <module>()
4 __import__('pkg_resources').require('camoco==0.3.1.dev0')
5 __file__ = '/project/chadm/Meesh/CamocoHelixInstall/Camoco/camoco/cli/camoco'
----> 6 exec(compile(open(__file__).read(), __file__, 'exec'))
global os = <module 'os' from '/project/chadm/Meesh/CamocoHelixInstall/conda/envs/camoco/lib/python3.6/os.py'>
/project/chadm/Meesh/CamocoHelixInstall/Camoco/camoco/cli/camoco in <module>()
1102 log.warn("A baaaad thing happened.\n\n" + str(e))
1103 if args.debug:
-> 1104 raise e
global e = undefined
1105 else:
1106 sys.exit(1)
/project/chadm/Meesh/CamocoHelixInstall/Camoco/camoco/cli/camoco in <module>()
1094 # Execute the command
1095 try:
-> 1096 return_value = args.func(args)
global return_value = undefined
global args.func = <bound method Overlap.from_CLI of <class 'camoco.Overlap.Overlap'>>
global args = Namespace(candidate_flank_limit=1, candidate_window_size=50000, cob='ZmRoot', debug=True, dry_run=False, force=False, func=<bound method Overlap.from_CLI of <class 'camoco.Overlap.Overlap'>>, gwas='ZmAll', interactive=False, method='locality', num_bootstraps='100', out='ZmRoot_Loc.csv', skip_terms=[], snp2gene='strongest', strongest_attr='numIterations', strongest_higher=False, terms=['all'])
1097 except AttributeError as e:
1098 if args.debug:
/project/chadm/Meesh/CamocoHelixInstall/Camoco/camoco/Overlap.py in from_CLI(cls=<class 'camoco.Overlap.Overlap'>, args=Namespace(candidate_flank_limit=1, candidate_win...erations', strongest_higher=False, terms=['all']))
502 Analysis
503 '''
--> 504 self = cls()
global self = undefined
cls = <class 'camoco.Overlap.Overlap'>
505 # Build base camoco objects
506 self.args = args
TypeError: __init__() missing 1 required positional argument: 'gwas'
> /project/chadm/Meesh/CamocoHelixInstall/Camoco/camoco/Overlap.py(504)from_CLI()
502 Analysis
503 '''
--> 504 self = cls()
505 # Build base camoco objects
506 self.args = args
ipdb> Just showing that the GWAS object exists
In [1]: co.available_datasets()
Out[1]:
Name Description Date Added
Type
Camoco Camoco Camoco base 2017-05-16 20:10:26
Expr ZmRoot Rob Maize Root Network 2017-05-16 20:15:17
Expr ZmRootPA Rob Maize Root Network 2017-05-17 19:04:25
Expr ZmRNASeqTissueAtlas Maize RNASeq Tissue Atlas Network, Sekhon 2013... 2017-05-17 19:40:57
Expr ZmRootPA_Filter Rob Maize Root Network 2017-05-18 16:04:41
Expr ZmRootPA_Filter_No_Zero Rob Maize Root Network 2017-05-18 16:11:15
Expr ZmSubRoot Maize SubRoot Network Root Metrics 2017-05-18 18:34:29
Expr ZmSubPan Maize SubPan Network Root Metrics 2017-05-18 18:41:12
Expr ZmSubPanPlus Maize SubPanPlus Network Root Metrics 2017-05-18 18:47:00
Expr ZmSubPan46Bias Maize SubPan46Bias Network Root Metrics 2017-05-18 18:52:55
Expr ZmPAN ZmPAN Network Root Metrics 2017-05-18 18:59:20
GOnt TestGO Test GO 2017-05-17 19:41:37
GOnt ZmGO Maize Gene Ontology 2017-05-17 19:41:39
GWAS testGWAS Test GWAS Dataset 2017-05-17 19:42:46
GWAS ZmAll Baxter_Maize Data. 2017-05-17 20:28:06
Ontology ZmRootMCL ZmRoot MCL Clusters 2017-05-16 20:21:50
Ontology ZmRootPAMCL ZmRootPA MCL Clusters 2017-05-17 19:14:58
Ontology ZmRNASeqTissueAtlasMCL ZmRNASeqTissueAtlas MCL Clusters 2017-05-17 19:41:22
Ontology ZmRootPA_FilterMCL ZmRootPA_Filter MCL Clusters 2017-05-18 16:09:30
Ontology ZmRootPA_Filter_No_ZeroMCL ZmRootPA_Filter_No_Zero MCL Clusters 2017-05-18 16:15:59
Ontology ZmSubRootMCL ZmSubRoot MCL Clusters 2017-05-18 18:41:11
Ontology ZmSubPanMCL ZmSubPan MCL Clusters 2017-05-18 18:46:59
Ontology ZmSubPanPlusMCL ZmSubPanPlus MCL Clusters 2017-05-18 18:52:53
Ontology ZmSubPan46BiasMCL ZmSubPan46Bias MCL Clusters 2017-05-18 18:59:14
Ontology ZmPANMCL ZmPAN MCL Clusters 2017-05-18 19:14:38
RefGen Gmax_a2_V1 Gmax_275_Wm82.a2.v1 2017-05-16 20:10:30
RefGen Mt_4.0 Mt_4.0 2017-05-16 20:12:03
RefGen FilteredZmRoot Filtered Refgen 2017-05-16 20:15:39
RefGen FilteredZmRootPA Filtered Refgen 2017-05-17 19:04:49
RefGen FilteredZmRNASeqTissueAtlas Filtered Refgen 2017-05-17 19:41:17
RefGen Zm5bFGS Maize 5b Filtered Gene Set 2017-05-17 19:42:47
RefGen FilteredZmRootPA_Filter Filtered Refgen 2017-05-18 16:05:05
RefGen FilteredZmRootPA_Filter_No_Zero Filtered Refgen 2017-05-18 16:11:35
RefGen FilteredZmSubRoot Filtered Refgen 2017-05-18 18:34:52
RefGen FilteredZmSubPan Filtered Refgen 2017-05-18 18:41:33
RefGen FilteredZmSubPanPlus Filtered Refgen 2017-05-18 18:47:24
RefGen FilteredZmSubPan46Bias Filtered Refgen 2017-05-18 18:53:19
RefGen FilteredZmPAN Filtered Refgen 2017-05-18 19:00:46
RefGen Bd21 BdistachyonBd21-3v1.1 2017-05-19 19:39:05
RefGen Wheat Triticum_aestivum_CS42_TGACv1 2017-05-19 19:48:18Thanks!