Merge pull request #26 from kdm9/check-index

Check for a vcf index before indexing
frankvogt · May 24, 2023 · 0a4028c · 0a4028c
2 parents 9b4ee5f + 53e0fc4
commit 0a4028c
Showing 1 changed file with 9 additions and 6 deletions.
diff --git a/vcf2gwas/starter.py b/vcf2gwas/starter.py
@@ -595,11 +595,14 @@
 
 #index VCF
 Log.print_log("\nIndexing VCF file..")
-timer = time.perf_counter()
-Converter.index_vcf(snp_file2)
-timer_end = time.perf_counter()
-timer_total = round(timer_end - timer, 2)
-Log.print_log(f'VCF file successfully indexed (Duration: {runtime_format(timer_total)})')
+if not os.path.exists(f"{snp_file2}.csi"):
+    timer = time.perf_counter()
+    Converter.index_vcf(snp_file2)
+    timer_end = time.perf_counter()
+    timer_total = round(timer_end - timer, 2)
+    Log.print_log(f'VCF file successfully indexed (Duration: {runtime_format(timer_total)})')
+else:
+    Log.print_log(f'VCF file already indexed')
 
 chr2, chr_num = Converter.check_chrom(snp_file2, chr)
 chr_list = chr2
@@ -889,4 +892,4 @@
 if model != None:
     shutil.move(os.path.join(path, f'vcf2gwas{pc_prefix}.log.txt'), os.path.join(path, f'vcf2gwas_{snp_prefix}{pc_prefix2}_{timestamp2}.log.txt'))
 
-shutil.rmtree(dir_temp, ignore_errors=True)
+shutil.rmtree(dir_temp, ignore_errors=True)