added virsorter2 nan fix

replikation · Aug 16, 2022 · 59e6021 · 59e6021
1 parent 1fa19d4
commit 59e6021
Showing 1 changed file with 15 additions and 0 deletions.
diff --git a/workflows/process/virsorter2/filter_virsorter2.nf b/workflows/process/virsorter2/filter_virsorter2.nf
@@ -7,6 +7,7 @@ process filter_virsorter2 {
     script:
         """
         tail -n+2 *.tsv |  awk '{ print \$1, \$2 }' OFS='\\t' | awk '{ print \$1, \$2 }' OFS='||' | cut -d "|" -f1,5 | awk -F"|" '{ print \$1, \$2 }' OFS='\t' > virsorter2_\${PWD##*/}.tsv
+        sed -i 's/nan/0/g' virsorter2_\${PWD##*/}.tsv
         """
 }
 
@@ -19,3 +20,17 @@ ctg6_len=5303||full     0.967   0.733   0.967   dsDNAphage      3585    1
 
 //awk '{ gsub(/||full/,"", $3); print }' OFS='\t' tmp_result.tsv > tmp_results2.tsv
 //awk '{ print \$1, \$2 }' OFS='||' virsorter2_\${PWD##*/}.tsv
+
+// nan  if row contains nan make to 0
+// GT1_27252	0.840	virsorter2
+// GT1_27276	0.640	virsorter2
+// GT1_27283	0.560	virsorter2
+// GT1_27330	0.633	virsorter2
+// GT1_27380	0.180	virsorter2
+// GT1_1	0.840	virsorter2
+// GT1_396	0.567	virsorter2
+// GT1_2577	nan	virsorter2
+// GT1_5431	nan	virsorter2
+// GT1_5765	nan	virsorter2
+// GT1_7346	nan	virsorter2
+//sed -i 's/nan/0/g' virsorter2_test_nan.txt