adding quantification/magnitude in krona output

maxibor · Mar 21, 2018 · e52b8dd · e52b8dd
1 parent 15428ac
commit e52b8dd
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/bin/centrifuge2krona b/bin/centrifuge2krona
@@ -65,22 +65,22 @@ if __name__ == "__main__":
         print(cmd)
         os.system(cmd)
         if not taxo:
-            cmd = "ktImportTaxonomy -q 2 -t 5 -o "+basename+"_krona.html "+outpath+"/"+basename+"_centriKraken_LCA_minScore_"+minscore+"_minLength_"+minlen+".out"
+            cmd = "ktImportTaxonomy -q 2 -t 5 -m 3-o "+basename+"_krona.html "+outpath+"/"+basename+"_centriKraken_LCA_minScore_"+minscore+"_minLength_"+minlen+".out"
             print(cmd)
             os.system(cmd)
         else:
-            cmd = "ktImportTaxonomy -q 2 -t 5 -tax "+taxo+" -o "+basename+"_krona.html "+outpath+"/"+basename+"_centriKraken_LCA_minScore_"+minscore+"_minLength_"+minlen+".out"
+            cmd = "ktImportTaxonomy -q 2 -t 5 -m 3 -tax "+taxo+" -o "+basename+"_krona.html "+outpath+"/"+basename+"_centriKraken_LCA_minScore_"+minscore+"_minLength_"+minlen+".out"
             print(cmd)
             os.system(cmd)
     else:
         cmd = "centrifuge-kreport -x "+index+" --no-lca --min-score "+minscore+" --min-length "+minlen+" "+infile+" > "+basename+"_centriKraken_noLCA_minScore_"+minscore+"_minLength_"+minlen+".out"
         print(cmd)
         os.system(cmd)
         if not taxo:
-            cmd = "ktImportTaxonomy -q 2 -t 5 -o "+basename+"_krona.html "+outpath+"/"+basename+"_centriKraken_noLCA_minScore_"+minscore+"_minLength_"+minlen+".out"
+            cmd = "ktImportTaxonomy -q 2 -t 5 -m 3 -o "+basename+"_krona.html "+outpath+"/"+basename+"_centriKraken_noLCA_minScore_"+minscore+"_minLength_"+minlen+".out"
             print(cmd)
             os.system(cmd)
         else:
-            cmd = "ktImportTaxonomy -q 2 -t 5 -tax "+taxo+" -o "+basename+"_krona.html "+outpath+"/"+basename+"_centriKraken_noLCA_minScore_"+minscore+"_minLength_"+minlen+".out"
+            cmd = "ktImportTaxonomy -q 2 -t 5 -m 3 -tax "+taxo+" -o "+basename+"_krona.html "+outpath+"/"+basename+"_centriKraken_noLCA_minScore_"+minscore+"_minLength_"+minlen+".out"
             print(cmd)
             os.system(cmd)