diff data_manager/mash_sketch_builder.py @ 0:2af9137ba067 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit c6efcbece52dec310253537b35419839746fff7f"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/mash_sketch_builder.py	Wed Feb 26 17:06:21 2020 -0500
@@ -0,0 +1,95 @@
+#!/usr/bin/env python
+
+import argparse
+import errno
+import json
+import os
+import subprocess
+import uuid
+
+
+DATA_TABLE_NAME = "mash_sketches"
+
+
+def mash_sketch(mash_sketch_args, sketch_name, target_directory, data_table_name=DATA_TABLE_NAME):
+    UUID = str(uuid.uuid4())
+
+    os.mkdir(os.path.join(target_directory, UUID))
+
+    sketch_path = os.path.join(target_directory, UUID, "sketch")
+
+    args = [
+        '-k', str(mash_sketch_args["kmer_size"]),
+        '-s', str(mash_sketch_args["sketch_size"]),
+        '-w', str(mash_sketch_args["probability_threshold"]),
+        '-o', str(sketch_path),
+        '-p', str(mash_sketch_args["threads"]),
+        str(mash_sketch_args["fasta"]),
+    ]
+
+    if mash_sketch_args["individual_sequences"]:
+        args = args + ["-i"]
+
+    subprocess.check_call(['mash', 'sketch'] + args, cwd=target_directory)
+
+    data_table_entry = {
+        'data_tables': {
+            data_table_name: [
+                {
+                    "value": UUID,
+                    "name": sketch_name,
+                    "path": UUID,
+                }
+            ]
+        }
+    }
+
+    return data_table_entry
+
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('data_manager_json')
+    parser.add_argument('--kmer-size', dest='kmer_size', type=int, default=35, help='kmer length')
+    parser.add_argument('--sketch-size', dest='sketch_size', type=int, default=31, help='minimizer length')
+    parser.add_argument('--probability-threshold', dest='probability_threshold', type=float, default=0.01, help='Probability threshold for warning about low k-mer size')
+    parser.add_argument('--individual-sequences', dest='individual_sequences', action='store_true', default=False, help='Sketch individual sequences (for multi-fasta files)')
+    parser.add_argument('--fasta', dest='fasta', help='Fasta file to sketch')
+    parser.add_argument('--threads', dest='threads', default=1, help='threads')
+    parser.add_argument('--sketch-name', dest='sketch_name', help='Name for sketch')
+    args = parser.parse_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 = {}
+
+    mash_sketch_args = {
+        "kmer_size": args.kmer_size,
+        "sketch_size": args.sketch_size,
+        "probability_threshold": args.probability_threshold,
+        "fasta": args.fasta,
+        "individual_sequences": args.individual_sequences,
+        "threads": args.threads,
+    }
+
+    data_manager_output = mash_sketch(
+        mash_sketch_args,
+        args.sketch_name,
+        target_directory,
+    )
+
+    open(args.data_manager_json, 'w').write(json.dumps(data_manager_output, sort_keys=True))
+
+
+if __name__ == "__main__":
+    main()