methylprep.read_geo exceptions

[marcmaxson]

• For files of the <GEO>_signals.txt.gz variety, it won't apply p-value detection to probes if the p-value column is there for each sample.
• IF meth and unmeth column names differ in case (e.g. SampleA Unmethylated Signal vs samplea Methylated Signal) it wont work. Instead you have to use pandas like this:

>>>import pandas as pd
>>> x = pd.read_csv('GSE67530_signals.txt', sep='\t')
>>> cols = {i:i.title() for i in list(x.columns)}
>>> x = x.rename(columns=cols)
>>> x.to_csv('GSE67530_signals_revised.txt', sep='\t')
>>> z = methylprep.read_geo('GSE67530_signals_revised.txt')
>>> z.to_csv('GSE67530_betas.csv.gz') 

(make samples case insensitive. It's possible to have the function try this trick before failing)