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Pandas 0.17 has deprecated DataFrame.sort() #9

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Pandas 0.17 has deprecated DataFrame.sort() #9

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4 changes: 2 additions & 2 deletions src/python/depict_library.py
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Original file line number Diff line number Diff line change
Expand Up @@ -261,7 +261,7 @@ def write_background_loci(loci_requested):
continue
depictloci_background_df, log_back_dict = write_depict_loci_helper(clumped_file,\
collection, df_gene_boundaries, mhc_start,mhc_end)
depictloci_background_df.sort('gwas_pvalue',inplace=True)
depictloci_background_df.sort_values('gwas_pvalue',inplace=True)
background_plink_clumping_pvalue_relaxed = background_plink_clumping_pvalue
while len(depictloci_background_df) < loci_requested:
print('Not enough background loci in iteration {} (need: n={}, found: {}).\
Expand All @@ -279,7 +279,7 @@ def write_background_loci(loci_requested):
plink_clumping_pvalue_column_header)
depictloci_background_df, log_back_dict = write_depict_loci_helper("{}/{}.clumped".format(background_loci_dir,i+1),\
collection, df_gene_boundaries, mhc_start,mhc_end)
depictloci_background_df.sort('gwas_pvalue',inplace=True)
depictloci_background_df.sort_values('gwas_pvalue',inplace=True)
output_file = "{}/permutation{}.txt".format(background_loci_dir,i+1)
depictloci_background_df.iloc[0:loci_requested,:].to_csv(\
output_file,\
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