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Remove unnecessary set_index to fix stat module for function-taxonomy analysis #50

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Remove unnecessary set_index to fix stat module for function-taxonomy analysis #50

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4 changes: 1 addition & 3 deletions metaquantome/modules/stat.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ def stat(infile, sinfo, paired, parametric, ontology, mode, outfile, control_gro
:param paired: Whether or not the sample should be analyzed as paired samples
:param parametric: whether or not parameteric tests should be used
:param ontology: for function, is either 'go', 'ec', or 'cog'
:param mode: 't', 'f', or 'taxf'
:param mode: 't', 'f', or 'ft'
:param outfile: path to write to
:return: original dataframe with p value and fold change columns appended
"""
Expand Down Expand Up @@ -119,8 +119,6 @@ def test_norm_intensity(df, samp_grps, paired, parametric):
#df_means[P_CORR_COLNAME] = mc.fdrcorrection0(test_results, method='indep')[1]
df_means[P_CORR_COLNAME+"_"+samp_grps.fc_name.replace("log2fc_","")] = mc.fdrcorrection0(test_results, method='indep')[1]

# reset the index to be 'id' - this is mostly for testing, and doesn't affect the output file
df_means.set_index('id', drop=False, inplace=True)
return df_means


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2 changes: 1 addition & 1 deletion setup.py
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@@ -1,7 +1,7 @@
from setuptools import setup, find_packages


VERSION = '2.0.4'
VERSION = '2.0.5'
URL = 'https://github.com/galaxyproteomics/metaquantome'
AUTHOR = 'Caleb Easterly'
AUTHOR_EMAIL = 'caleb.easterly@gmail.com'
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