Merge pull request #62 from ramprasadn/master

update tmp file names

Author: J35P312

setup.py

@@ -19,7 +19,7 @@
     ext_modules = []
 
 setup(name='svdb',
-      version='2.7.0',
+      version='2.7.1',
       url="https://github.com/J35P312/SVDB",
       author="Jesper Eisfeldt",
       author_email="jesper.eisfeldt@scilifelab.se",

svdb/__main__.py

@@ -26,19 +26,21 @@ def make_query_calls (args, queries, keyword):
                     args.out_frq     = out_frqs[ind]
                     if ind < len(queries)-1:
                         args.prefix  = orig_prefix + "_" + str(ind)
+                        output_file  = args.prefix + "_query.vcf_tmp"    
                     else:
                         args.prefix = orig_prefix
-                    query_module.main(args)
+                        output_file  = args.prefix + "_query.vcf"    
+                    query_module.main(args, output_file)
                     if ind > 0:
                         os.remove(args.query_vcf)
-                    args.query_vcf = args.prefix + "_query.vcf"
+                    args.query_vcf = output_file
         else:
             print("please ensure that both count and frequency tags are specified for all samples")
     else:
         query_module.main(args)
 
 def main():
-    version = "2.7.0"
+    version = "2.7.1"
     parser = argparse.ArgumentParser(
         """SVDB-{}, use the build module to construct databases, use the query module to query the database usign vcf files, or use the hist module to generate histograms""".format(version), add_help=False)
     parser.add_argument('--build', help="create a db",

svdb/query_module.py

@@ -8,11 +8,11 @@
 from . import database, overlap_module, readVCF
 
 
-def main(args):
+def main(args, output_file):
     # start by loading the variations
     queries = []
     if args.prefix:
-        f = open(args.prefix + "_query.vcf", "w")
+        f = open(output_file, "w")
     noOCCTag = 1
     infoFound = 0