diff data_manager/malt_index_builder.py @ 1:787f1ca9045a draft default tip

Uploaded

--- a/data_manager/malt_index_builder.py	Tue Oct 12 14:15:35 2021 +0000
+++ b/data_manager/malt_index_builder.py	Wed Oct 13 20:12:48 2021 +0000
@@ -6,8 +6,6 @@
 import subprocess
 import sys
 
-DEFAULT_DATA_TABLE_NAME = "malt_indices"
-
 
 def get_id_name(params, dbkey, fasta_description=None):
     sequence_id = params['param_dict']['sequence_id']
@@ -22,29 +20,40 @@
     return sequence_id, sequence_name
 
 
-def build_malt_index(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, sequence_type, shapes, max_hits_per_seed, protein_reduct, data_table_name=DEFAULT_DATA_TABLE_NAME):
+def build_malt_index(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, sequence_type, shapes, max_hits_per_seed, protein_reduct):
+    # The malt-build program produces a directory of files,
+    # so the data table path entry will be a directory and
+    # not an index file.
     fasta_base_name = os.path.split(fasta_filename)[-1]
     sym_linked_fasta_filename = os.path.join(target_directory, fasta_base_name)
     os.symlink(fasta_filename, sym_linked_fasta_filename)
-    args = ['malt-build', '--input', sym_linked_fasta_filename, '--sequenceType', sequence_type, '--index', 'index']
+    args = ['malt-build', '--input', sym_linked_fasta_filename, '--sequenceType', sequence_type, '--index', target_directory]
     threads = os.environ.get('GALAXY_SLOTS')
     if threads:
         args.extend(['--threads', threads])
     if shapes is not None:
-        args.extend('--shapes', shapes)
+        args.extend(['--shapes', shapes])
     if max_hits_per_seed is not None:
-        args.extend('--maxHitsPerSeed', max_hits_per_seed)
+        args.extend(['--maxHitsPerSeed', max_hits_per_seed])
     if protein_reduct is not None:
-        args.extend('--proteinReduct', protein_reduct)
+        args.extend(['--proteinReduct', protein_reduct])
     proc = subprocess.Popen(args=args, shell=False, cwd=target_directory)
     return_code = proc.wait()
     if return_code:
         sys.exit('Error building index, return_code: %d' % return_code)
-    data_table_entry = dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name)
-    _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
+    # Remove unwanted files from the output directory.
+    os.remove(sym_linked_fasta_filename)
+    # The path entry here is the directory
+    # where the index files will be located,
+    # not a single index file (malt-build
+    # produces a directory if files, which
+    # is considered an index..
+    data_table_entry = dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=None)
+    _add_data_table_entry(data_manager_dict, data_table_entry)
 
 
-def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry):
+def _add_data_table_entry(data_manager_dict, data_table_entry):
+    data_table_name = "malt_indices"
     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, [])
     data_manager_dict['data_tables'][data_table_name].append(data_table_entry)
@@ -58,7 +67,7 @@
     parser.add_option('-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta description')
     parser.add_option('-e', '--sequence_type', dest='sequence_type', action='store', type="string", help='DNA or Protein sequences')
     parser.add_option('-p', '--shapes', dest='shapes', action='store', type="string", default=None, help='Comma-separated list of seed shapes')
-    parser.add_option('-m', '--max_hits_per_seed', dest='max_hits_per_seed', action='store', type="int", default=None, help='Maximum number of hits per seed')
+    parser.add_option('-m', '--max_hits_per_seed', dest='max_hits_per_seed', action='store', type="string", default=None, help='Maximum number of hits per seed')
     parser.add_option('-r', '--protein_reduct', dest='protein_reduct', action='store', type="string", default=None, help='Name or definition of protein alphabet reduction')
     (options, args) = parser.parse_args()
 
@@ -78,7 +87,7 @@
     sequence_id, sequence_name = get_id_name(params, dbkey=dbkey, fasta_description=options.fasta_description)
 
     # Build the index.
-    build_malt_index(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, options.sequence_type, options.shapes, options.max_hits_per_seed, options.protein_reduct, data_table_name=DEFAULT_DATA_TABLE_NAME)
+    build_malt_index(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, options.sequence_type, options.shapes, options.max_hits_per_seed, options.protein_reduct)
 
     # Save info to json file.
     with open(filename, 'w') as fh: