Mercurial > repos > rliterman > csp2
diff CSP2/bin/saveSNPDiffs.py @ 39:93393808f415
"planemo upload"
| author | rliterman |
|---|---|
| date | Thu, 12 Dec 2024 13:53:15 -0500 |
| parents | 893a6993efe3 |
| children |
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--- a/CSP2/bin/saveSNPDiffs.py Wed Dec 11 12:04:20 2024 -0500 +++ b/CSP2/bin/saveSNPDiffs.py Thu Dec 12 13:53:15 2024 -0500 @@ -58,7 +58,8 @@ header_rows.append(processHeader(top_line,snpdiffs_file,trim_name)) output_data = pd.concat(header_rows, ignore_index=True) -output_data.to_csv(summary_file, sep='\t', index=False) +with open(summary_file,"w") as f: + output_data.to_csv(f, sep='\t', index=False) # If ref_ids is empty, save isolate data ref_header = ['Reference_ID','Reference_Assembly','Reference_Contig_Count','Reference_Assembly_Bases','Reference_N50','Reference_N90','Reference_L50','Reference_L90','Reference_SHA256'] @@ -79,5 +80,6 @@ cols = combined_df.columns.tolist() cols = cols[:1] + cols[-1:] + cols[1:-1] combined_df = combined_df[cols] -combined_df.to_csv(isolate_data_file, sep='\t', index=False) +with open(isolate_data_file,"w") as f: + combined_df.to_csv(f, sep='\t', index=False)