Support MetaPhlAn2

bin/metafx-scripts/metaphlan_to_csv.py

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+#!/usr/bin/env python
+# Utility transform Kraken class report to csv file for Bandage visualization
+# -*- coding: UTF-8 -*-
+
+import sys
+import getopt
+from ete3 import NCBITaxa
+
+if __name__ == "__main__":
+    inputFile = ''
+    resFile = ''
+
+    helpString = 'Please add all mandatory parameters: --class-file and --res-file'
+
+    argv = sys.argv[1:]
+    try:
+        opts, args = getopt.getopt(argv, "h", ["class-file=", "res-file="])
+    except getopt.GetoptError:
+        print(helpString)
+        sys.exit(2)
+    for opt, arg in opts:
+        if opt == "-h":
+            print(helpString)
+            sys.exit()
+        elif opt == "--class-file":
+            inputFile = arg
+            if inputFile[0] == "'" or inputFile[0] == '"':
+                inputFile = inputFile[1:]
+            if inputFile[-1] == "'" or inputFile[-1] == '"':
+                inputFile = inputFile[:-1]
+        elif opt == "--res-file":
+            resFile = arg
+            if resFile[0] == "'" or resFile[0] == '"':
+                resFile = resFile[1:]
+            if resFile[-1] == "'" or resFile[-1] == '"':
+                resFile = resFile[:-1]
+
+    tax_ids = []
+    fileR = open(inputFile, 'r')
+    fileW = open(resFile, 'w')
+    count = 0
+    while True:
+        line = fileR.readline()
+        if not line:
+            break
+        count += 1
+        listLine = line.split('\t')
+        if listLine[0][0] != "#":
+            tax_id = listLine[1].split('__')[0]
+            tax_ids.append((listLine[0], tax_id))
+    fileR.close()
+
+    ncbi = NCBITaxa()
+    fileW.write("Node name,Superkingdom,Phylum,Class,Order,Family,Genus,Species,Serotype,Strains\n")
+    ranks = {'superkingdom': 1, 'phylum': 2, 'class': 3, 'order': 4, 'family': 5, 'genus': 6, 'species': 7, 'serotype': 8, 'strain': 9}
+    for (node, tax) in tax_ids:
+        lineage = ncbi.get_lineage(tax)
+        names = ncbi.get_taxid_translator(lineage)
+        fileW.write(node + ",")
+        prevCount = 0
+        for taxid in lineage:
+            rank = ncbi.get_rank([taxid])[taxid]
+            if (rank in ranks):
+                curCount = ranks[ncbi.get_rank([taxid])[taxid]]
+                for i in range(curCount - prevCount - 1):
+                    fileW.write(",")
+                fileW.write(names[taxid]+",")
+                prevCount = curCount
+        fileW.write("\n")
+    fileW.close()