diff vcf2neo_wrapper.py @ 0:3e14eda348d3 draft default tip

planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 0245b4efed8ced6d06d76f1249a47d2178285385

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcf2neo_wrapper.py	Mon Jun 19 00:08:18 2017 -0400
@@ -0,0 +1,51 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+import argparse
+import os
+import shlex
+import subprocess
+import uuid
+import sys
+
+parser = argparse.ArgumentParser(
+    description="Call vcf2neo on VCF inputs from Galaxy")
+
+parser.add_argument('--vcf_dataset_names', nargs='+',
+                    help='Names of VCF datasets')
+parser.add_argument('--neo4j_db_path', help='Neo4j database directory')
+parser.add_argument('--user', help='Email of Galaxy user running this tool')
+parser.add_argument('--variantset_name',
+                    help='Name for the VariantSet containing all the variants')
+parser.add_argument('--vcf_files',
+                    help='VCF format variant file', nargs='+')
+
+args = parser.parse_args()
+
+os.mkdir(args.variantset_name)
+
+print("VCF names:", len(args.vcf_dataset_names), args.vcf_dataset_names, file=sys.stderr)
+print("VCF files:", len(args.vcf_files), args.vcf_files, file=sys.stderr)
+for i, vcf_file in enumerate(args.vcf_files):
+    print("XXXX I:", i, vcf_file, file=sys.stderr)
+    callset_name = args.vcf_dataset_names[i]
+    os.symlink(vcf_file, os.path.join(args.variantset_name,
+                                      callset_name) + '.vcf')
+# Usage: vcf2neo init [OPTIONS] VCF_DIR OWNER [HISTORY_ID] [OUTPUT_DIR]
+#
+#   Copy reference database and load VCF to Neo4j Graph database. :param
+#   vcf_dir: :param refdb_dir: :param d: :return:
+#
+# Options:
+#   -d / -D  Run Neo4j docker container.
+#   --help   Show this message and exit.
+
+history_id = str(uuid.uuid4())
+cmd_str = ('vcf2neo init -d ' +
+           '{input_vcf_dir} {email} {history_id} {neo4j_db_path}'.format(
+               input_vcf_dir=args.variantset_name,
+               email=args.user,
+               history_id=history_id,
+               neo4j_db_path=args.neo4j_db_path))
+cmd = shlex.split(cmd_str)
+subprocess.check_call(cmd)