builder: update ensembl version to 110

cellbase-app/app/cloud/docker/cellbase-builder/Dockerfile

@@ -28,4 +28,4 @@ RUN cd /opt/ensembl && \
     git clone https://github.com/Ensembl/ensembl-compara.git && \
     git clone https://github.com/Ensembl/ensembl-io.git
 
-ENV PERL5LIB=$PERL5LIB:/opt/ensembl/bioperl-live:/opt/ensembl/ensembl/modules:/opt/ensembl/ensembl-variation/modules:/opt/ensembl/ensembl-funcgen/modules:/opt/ensembl/ensembl-compara/modules:/opt/ensembl/lib/perl/5.18.2:/opt/cellbase
+ENV PERL5LIB=$PERL5LIB:/opt/ensembl/bioperl-live:/opt/ensembl/ensembl/modules:/opt/ensembl/ensembl-variation/modules:/opt/ensembl/ensembl-funcgen/modules:/opt/ensembl/ensembl-compara/modules:/opt/ensembl/lib/perl/5.18.2:/opt/cellbase/scripts/ensembl-scripts

cellbase-app/app/scripts/ensembl-scripts/DB_CONFIG.pm

@@ -134,10 +134,10 @@ our $ENSEMBL_GENOMES_PORT = "4157";
 our $ENSEMBL_GENOMES_USER = "anonymous";
 
 ## Vertebrates
-our $HOMO_SAPIENS_CORE = "homo_sapiens_core_104_38";
-our $HOMO_SAPIENS_VARIATION = "homo_sapiens_variation_104_38";
-our $HOMO_SAPIENS_FUNCTIONAL = "homo_sapiens_funcgen_104_38";
-our $HOMO_SAPIENS_COMPARA = "homo_sapiens_compara_104_38";
+our $HOMO_SAPIENS_CORE = "homo_sapiens_core_110_38";
+our $HOMO_SAPIENS_VARIATION = "homo_sapiens_variation_110_38";
+our $HOMO_SAPIENS_FUNCTIONAL = "homo_sapiens_funcgen_110_38";
+our $HOMO_SAPIENS_COMPARA = "homo_sapiens_compara_110_38";
 #our $HOMO_SAPIENS_CORE = "homo_sapiens_core_78_38";
 #our $HOMO_SAPIENS_VARIATION = "homo_sapiens_variation_78_38";
 #our $HOMO_SAPIENS_FUNCTIONAL = "homo_sapiens_funcgen_78_38";

cellbase-app/app/scripts/gnomad_mt_prepare.py

@@ -0,0 +1,57 @@
+#!/usr/bin/env python3
+
+#  Copyright 2015-2020 OpenCB
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+
+import argparse
+import os
+import requests
+import sys
+import json
+import pathlib
+from pathlib import Path
+
+
+## Configure command-line options
+parser = argparse.ArgumentParser()
+parser.add_argument('-i', help="VCF file", required=True)
+
+
+## Parse command-line parameters and init basedir, tag and build_folder
+args = parser.parse_args()
+print(args.i)
+
+if os.path.isfile(args.i) == False:
+    print("no existe")
+
+
+# Opening file
+vcf_file = open(args.i, 'r')
+count = 0
+
+# Using for loop
+print("Using for loop")
+for line in vcf_file:
+    count += 1
+    if not line.startswith("#"):
+        line = line.strip()
+        cols = line.split("\t")
+        print(line)
+        info_cols = cols[7].split(";")
+        var = [x for x in info_cols if x.startswith("AN=")]
+        print("{}".format(var))
+
+
+# Closing files
+vcf_file.close()