diff data_manager/rnastar_index_builder.py @ 0:2883a3b7dc56 draft

planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/rnastar_index_builder.py	Mon Feb 08 03:23:34 2016 -0500
@@ -0,0 +1,71 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+import argparse
+from subprocess import check_call, CalledProcessError
+from json import load, dump
+from os import environ, mkdir
+from os.path import isdir, exists
+import shlex
+import sys
+
+def get_id_name( params, dbkey, fasta_description=None):
+    #TODO: ensure sequence_id is unique and does not already appear in location file
+    sequence_id = params['param_dict']['sequence_id']
+    if not sequence_id:
+        sequence_id = dbkey
+
+    sequence_name = params['param_dict']['sequence_name']
+    if not sequence_name:
+        sequence_name = fasta_description
+        if not sequence_name:
+            sequence_name = dbkey
+    return sequence_id, sequence_name
+
+def make_rnastar_index(output_directory, fasta_filename):
+#     STAR
+#         --runMode genomeGenerate
+#         --genomeDir tempstargenomedir
+#         --genomeFastaFiles $input1
+#         --runThreadsN \${GALAXY_SLOTS:-1}
+#         --genomeChrBinNbits $advanced_options.chr_bin_nbits
+
+    if exists(output_directory) and not isdir(output_directory):
+        print("Output directory path already exists but is not a directory: {}".format(output_directory), file=sys.stderr)
+    elif not exists(output_directory):
+        mkdir(output_directory)
+
+    if 'GALAXY_SLOTS' in environ:
+        nslots = environ['GALAXY_SLOTS']
+    else:
+        nslots = 1
+
+    # cmdline_str = 'STAR --runMode genomeGenerate --genomeDir {} --genomeFastaFiles {} --runThreadsN {}'.format(output_directory,
+    #                                                                                                            fasta_filename,
+    #                                                                                                            nslots)
+    # cmdline = shlex.split(cmdline_str)
+    cmdline = ('touch', '{}/foo'.format(output_directory))
+    try:
+        check_call(cmdline)
+    except CalledProcessError:
+        print("Error building RNA STAR index", file=sys.stderr)
+    return(output_directory)
+
+parser = argparse.ArgumentParser(description="Generate RNA STAR genome index and JSON describing this")
+parser.add_argument('output_filename')
+parser.add_argument('--fasta_filename')
+parser.add_argument('--fasta_dbkey')
+parser.add_argument('--fasta_description', default=None)
+parser.add_argument('--data_table_name', default='rnastar_indexes')
+args = parser.parse_args()
+
+params = load(open(args.output_filename, 'rb'))
+
+output_directory = params['output_data'][0]['extra_files_path']
+
+make_rnastar_index(output_directory, args.fasta_filename)
+(sequence_id, sequence_name) = get_id_name(params, args.fasta_dbkey, args.fasta_description)
+data_table_entry = dict(value=sequence_id, dbkey=args.fasta_dbkey, name=sequence_name, path=output_directory)
+output_datatable_dict = dict('data_tables', dict(args.data_table_name, [data_table_entry]))
+
+dump(output_datatable_dict(open(args.output_file, 'wb')))
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