diff data_manager/install_primer_scheme_bedfiles.py @ 0:ae730ecdc7e7 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/install_primer_scheme_bedfiles.py	Sun Apr 19 09:22:19 2020 -0400
@@ -0,0 +1,141 @@
+#!/usr/bin/env python
+
+from __future__ import print_function, division
+
+import argparse
+import json
+import os
+import os.path
+import re
+import sys
+import shutil
+
+import requests
+
+DATA_TABLE_NAME = "primer_scheme_bedfiles"
+
+
+def fetch_artic_primers(output_directory, primers):
+    primer_sets = {
+        "ARTICv1": "https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V1/nCoV-2019.bed",
+        "ARTICv2": "https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V2/nCoV-2019.bed",
+        "ARTICv3": "https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V3/nCoV-2019.bed",
+    }
+
+    data = []
+    for name, url in primer_sets.items():
+        if name not in primers:
+            continue
+        response = requests.get(url)
+        if response.status_code != 200:
+            print(
+                "Error: download of",
+                url,
+                "failed with code",
+                response.status_code,
+                file=sys.stderr,
+            )
+            exit(response.status_code)
+        bed_output_filename = os.path.join(output_directory, name + ".bed")
+        open(bed_output_filename, "w").write(response.text)
+        description = name[:-2] + " " + name[-2:] + " primer set"
+        data.append(dict(value=name, path=bed_output_filename, description=description))
+    return data
+
+
+def install_primer_file(
+    output_directory, input_filename, primer_name, primer_description
+):
+    name = re.sub(r"\W", "", str(primer_name).replace(" ", "_"))
+    output_filename = os.path.join(output_directory, name + ".bed")
+    shutil.copyfile(input_filename, output_filename)
+    data = [dict(value=name, description=primer_description, path=output_filename)]
+    return data
+
+
+class SplitArgs(argparse.Action):
+    def __call__(self, parser, namespace, values, option_string=None):
+        setattr(namespace, self.dest, values.split(","))
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="Fetch ARTIC SARS-CoV-2 primer files for Galaxy/IRIDA use"
+    )
+    parser.add_argument(
+        "--output_directory", default="tmp", help="Directory to write output to"
+    )
+    primer_file = parser.add_argument_group()
+    primer_file.add_argument(
+        "--primer_file", help="BED format file containing primer scheme"
+    )
+    primer_file.add_argument(
+        "--primer_name",
+        help="Name of primer scheme (one word). Required if --primer_file is used",
+    )
+    primer_file.add_argument(
+        "--primer_description",
+        help="Description of primer scheme. Required if --primer_file is used",
+    )
+    artic = parser.add_argument_group()
+    artic.add_argument(
+        "--artic_primers",
+        action=SplitArgs,
+        help="Comma separated list of primers to fetch",
+    )
+    parser.add_argument(
+        "galaxy_datamanager_filename",
+        help="Galaxy JSON format file describing data manager inputs",
+    )
+    args = parser.parse_args()
+
+    if args.artic_primers is None and args.primer_file is None:
+        print(
+            "One of --artic_primers or --primer_file + --primer_name + --primer_description is required.",
+            file=sys.stderr,
+        )
+        exit(1)
+    elif args.primer_file is not None and (
+        args.primer_name is None or args.primer_description is None
+    ):
+        print(
+            "If --primer_file is used --primer_name and --primer_description is also required",
+            file=sys.stderr,
+        )
+        exit(1)
+    elif args.primer_file is not None and args.artic_primers is not None:
+        print(
+            "Only one of --artic_primers or --primer_file + --primer_name + --primer_description can be chosen"
+        )
+        exit(1)
+
+    config = json.load(open(args.galaxy_datamanager_filename))
+    output_directory = config.get("output_data", [{}])[0].get("extra_files_path", None)
+    if output_directory is None:
+        output_directory = args.output_directory
+
+    if not os.path.isdir(output_directory):
+        os.makedirs(output_directory)
+
+    data_manager_dict = {}
+    data_manager_dict["data_tables"] = json.load(
+        open(args.galaxy_datamanager_filename)
+    ).get("data_tables", {})
+    data_manager_dict["data_tables"] = data_manager_dict.get("data_tables", {})
+    data_manager_dict["data_tables"][DATA_TABLE_NAME] = data_manager_dict[
+        "data_tables"
+    ].get(DATA_TABLE_NAME, [])
+
+    if args.artic_primers:
+        data = fetch_artic_primers(output_directory, args.artic_primers)
+    else:
+        data = install_primer_file(
+            output_directory,
+            args.primer_file,
+            args.primer_name,
+            args.primer_description,
+        )
+
+    data_manager_dict["data_tables"][DATA_TABLE_NAME].extend(data)
+    print(data_manager_dict)
+    json.dump(data_manager_dict, open(args.galaxy_datamanager_filename, "w"))