update minION/BCFtools code

scripts/tbprofiler_generate_haplotypes.py

@@ -6,9 +6,27 @@
 from tqdm import tqdm
 import sys
 import pathogenprofiler as pp
+
+
+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):
 	change_field = "change" if args.variant_format=="hgvs" else "_internal_change"
-	conf = json.load(open(sys.prefix+"/share/tbprofiler/%s.config.json" % args.db))
+	conf = conf = get_conf_dict(sys.base_prefix + "/share/tbprofiler/%s" % args.db)
 	drug2genes = defaultdict(set)
 	gene2drugs = defaultdict(set)
 	for l in open(conf["bed"]):

setup.py

@@ -4,7 +4,7 @@
 setuptools.setup(
 
 	name="tbprofiler",
-	version="2.6.2",
+	version="2.7.1",
 	packages=["tbprofiler",],
 	license="MIT",
 	long_description="TBProfiler command line tool",

tb-profiler

@@ -119,6 +119,8 @@ def main_profile(args):
     pp.run_cmd("rm -f  %(dir)s/%(prefix)s.targets*.vcf.gz %(dir)s/%(prefix)s*.del_pos.bed %(dir)s/%(prefix)s.*.csi" % vars(args))
     if args.platform=="Illumina":
         pp.run_cmd("rm %(dir)s/%(prefix)s.targets.delly.bcf" % vars(args))
+    if args.platform=="minION" or args.caller=="BCFtools":
+        pp.run_cmd("rm %(dir)s/%(prefix)s.targets.gbcf" % vars(args))
     if args.webserver:
         html_output = args.webserver_root+"/output/"+args.prefix+".html"
         tbp.write_html(results,conf,html_output,extra_columns,["isoniazid","rifampicin","ethambutol","pyrazinamide","streptomycin","ethionamide","fluoroquinolones","amikacin","capreomycin","kanamycin"])

tbprofiler/__init__.py

@@ -7,4 +7,4 @@
 from .vcfprofile import *
 import os
 _ROOT = os.path.abspath(os.path.dirname(__file__))
-_VERSION = "2.6.1"
+_VERSION = "2.7.1"