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statgen / pheweb

A tool to build a website to browse hundreds or thousands of GWAS.
MIT License
154 stars 65 forks source link

failed on field 'sebeta' attempting to convert value 'Inf' to type <class 'float'> #176

Closed Shicheng-Guo closed 5 months ago

Shicheng-Guo commented 2 years ago

Regenie have 'inf' in sebeta column which will cause error for Pheweb parse. Maybe we can add one step to remove such records from regenie summary statistics output. 

pheweb.utils.PheWebError: failed on field 'sebeta' attempting to convert value 'Inf' to type <class 'float'> with constraints {'aliases': ['se'], 'type': <class 'float'>, 'nullable': True, 'sigfigs': 2, 'tooltip_underscoretemplate': False, 'tooltip_lztemplate': False, 'required': False, 'from_assoc_files': True} in '/expanse/projects/janssen4/dsci-csb/user/sguo2/pheweb2/input/UKB.phecode.v1.WGS.additive.SVA_X1013.regenie.gz' on line with values ['X', '155984365', 'C', 'T', 'NA', '0.5', 'NA', 'Inf', '120964']
pjvandehaar commented 2 years ago

Could you send the full error message? One of those NAs is the pvalue, right?