diff data_manager/kma_build_index.py @ 0:889cc43b72d6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/kma_build_index.py	Tue Feb 18 16:24:23 2020 -0500
@@ -0,0 +1,96 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+
+import argparse
+import errno
+import json
+import os
+import subprocess
+import uuid
+
+
+DATA_TABLE_NAME = "kma_index"
+
+
+def kma_build_index(kma_index_args, index_name, target_directory, data_table_name=DATA_TABLE_NAME):
+    UUID = str(uuid.uuid4())
+
+    os.mkdir(os.path.join(target_directory, UUID))
+
+    args = [
+        '-k', str(kma_index_args["k"]),
+        '-k_t', str(kma_index_args["k_t"]),
+        '-k_i', str(kma_index_args["k_i"]),
+        '-ML', str(kma_index_args["ML"]),
+        '-ht', str(kma_index_args["ht"]),
+        '-hq', str(kma_index_args["hq"]),
+        '-o', os.path.join(UUID, "index"),
+        '-i', " ".join(kma_index_args["fasta"]),
+    ]
+
+    subprocess.check_call(' '.join(['kma index'] + args), cwd=target_directory, shell=True)
+
+    data_table_entry = {
+        'data_tables': {
+            data_table_name: [
+                {
+                    "value": UUID,
+                    "name": index_name,
+                    "path": os.path.join(UUID, "index"),
+                }
+            ]
+        }
+    }
+
+    return data_table_entry
+
+
+def main(args):
+
+    data_manager_input = json.loads(open(args.data_manager_json).read())
+
+    target_directory = data_manager_input['output_data'][0]['extra_files_path']
+
+    try:
+        os.mkdir( target_directory )
+    except OSError as exc:
+        if exc.errno == errno.EEXIST and os.path.isdir( target_directory ):
+            pass
+        else:
+            raise
+
+    data_manager_output = {}
+
+    kma_index_args = {
+        "k": args.k,
+        "k_t": args.k_t,
+        "k_i": args.k_i,
+        "ML": args.ML,
+        "ht": args.ht,
+        "hq": args.hq,
+        "fasta": args.fasta,
+    }
+
+    data_manager_output = kma_build_index(
+        kma_index_args,
+        args.index_name,
+        target_directory,
+    )
+
+    open(args.data_manager_json, 'w').write(json.dumps(data_manager_output))
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('data_manager_json')
+    parser.add_argument('--k', dest='k', type=int, default=16, help='')
+    parser.add_argument('--k_t', dest='k_t', type=int, default=16, help='')
+    parser.add_argument('--k_i', dest='k_i', type=int, default=16, help='')
+    parser.add_argument('--ML', dest='ML', type=int, default=16, help='')
+    parser.add_argument('--ht', dest='ht', type=float, default=1.0, help='')
+    parser.add_argument('--hq', dest='hq', type=float, default=1.0, help='')
+    parser.add_argument('--name', dest='index_name', help='')
+    parser.add_argument('fasta', nargs='+', help='fasta file(s) to index')
+    args = parser.parse_args()
+    main(args)