add ranking script

scripts/tbprofiler_rank_mutations.py

@@ -0,0 +1,53 @@
+#! /usr/bin/env python
+import json
+from collections import defaultdict
+import argparse
+import os
+from tqdm import tqdm
+import sys
+import pathogenprofiler as pp
+from collections import Counter
+try:
+    sys.base_prefix
+except:
+    sys.base_prefix = getattr(sys, 'base_prefix', getattr(sys, 'real_prefix', sys.prefix))
+
+
+def get_conf_dict(library_prefix):
+    files = {"gff":".gff","ref":".fasta","ann":".ann.txt","barcode":".barcode.bed","bed":".bed","json_db":".dr.json","version":".version.json"}
+    conf = {}
+    for key in files:
+        sys.stderr.write("Using %s file: %s\n" % (key,library_prefix+files[key]))
+        conf[key] = pp.filecheck(library_prefix+files[key])
+    return conf
+
+
+def main(args):
+   # conf = get_conf_dict(sys.base_prefix + "/share/tbprofiler/%s" % args.db)
+    if args.samples:
+        samples = [x.rstrip() for x in open(args.samples).readlines()]
+    else:
+        samples = [x.replace(".results.json", "") for x in os.listdir(args.dir) if x[-13:] == ".results.json"]
+    variants = []
+    for s in samples:
+        data_to_add = set()
+        tmp = json.load(open(f"{args.dir}/{s}.results.json"))
+        for var in tmp["dr_variants"]:
+            nt = var["nucleotide_change"] if "nucleotide_change" in var else var["change"]
+            data_to_add.add((nt,var["change"],var["gene"]))
+        variants += list(data_to_add)
+    count = Counter(variants)
+    for c in count.most_common(len(count)):
+        nt,aa,gene = c[0]
+        print("%s\t%s\t%s\t%s" % (gene,nt,aa,c[1]))
+
+parser = argparse.ArgumentParser(description='TBProfiler pipeline',formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+parser.add_argument('--samples',type=str,help='NGS Platform')
+parser.add_argument('--dir',default="results/",type=str,help='NGS Platform')
+parser.add_argument('--db',default="tbdb",type=str,help='NGS Platform')
+parser.add_argument('--variant-format',default="hgvs",choices=["hgvs","bcftools"],type=str,help='NGS Platform')
+parser.add_argument('--non-dr',action="store_true",help='NGS Platform')
+parser.set_defaults(func=main)
+
+args = parser.parse_args()
+args.func(args)