Mercurial > repos > rliterman > csp2

diff CSP2/bin/screenSNPDiffs.py @ 39:93393808f415

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"planemo upload"
author rliterman
date Thu, 12 Dec 2024 13:53:15 -0500
parents 893a6993efe3
children
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line diff
--- a/CSP2/bin/screenSNPDiffs.py	Wed Dec 11 12:04:20 2024 -0500
+++ b/CSP2/bin/screenSNPDiffs.py	Thu Dec 12 13:53:15 2024 -0500
@@ -502,7 +502,8 @@
                     
                     # Write filtered SNP data to file
                     snp_file = log_file.replace(".log","_SNPs.tsv")
-                    filtered_snp_df.to_csv(snp_file, sep="\t", index=False)
+                    with open(snp_file,"w") as f:
+                        filtered_snp_df.to_csv(f, sep="\t", index=False)
                     
                     csp2_screen_snps = filtered_snp_df[filtered_snp_df.Cat == "SNP"].shape[0]
                     
@@ -630,7 +631,8 @@
                 'MUMmer_gSNPs','MUMmer_gIndels']
 
     results_df = pd.DataFrame([item.result() for item in results], columns = output_columns)
-    results_df.to_csv(output_file, sep="\t", index=False)
+    with open(output_file,"w") as f:
+        results_df.to_csv(f, sep="\t", index=False)
 except:
     run_failed = True
     print("Exception occurred:\n", traceback.format_exc())