diff data_manager/homer_genome_preparse.py @ 0:5d2e5fddec81 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_homer_preparse commit e49d856e0181edc6120220a1b819cba2466a4289"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/homer_genome_preparse.py	Sun Aug 08 10:57:48 2021 +0000
@@ -0,0 +1,94 @@
+#!/usr/bin/env python
+# Dan Blankenberg for bowtie2
+# Modified by Lucille Delisle for homer
+from __future__ import print_function
+
+import json
+import optparse
+import os
+import subprocess
+import sys
+
+DEFAULT_DATA_TABLE_NAME = "homer_preparse"
+
+
+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 homer_preparse(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id,
+                   sequence_name, size, mask, version,
+                   data_table_name=DEFAULT_DATA_TABLE_NAME):
+    args = ['preparseGenome.pl', fasta_filename, '-size', str(size), '-preparsedDir', target_directory]
+    if mask:
+        args.append('-mask')
+    proc = subprocess.Popen(args=args, shell=False, cwd=target_directory)
+    return_code = proc.wait()
+    if return_code:
+        print("Error preparsing genome.", file=sys.stderr)
+        sys.exit(return_code)
+    mask_suffix = 'r' if mask else ''
+    mask_suffix_name = ' masked' if mask else ''
+    data_table_entry = dict(value=sequence_id + mask_suffix + '_' + str(size), dbkey=dbkey,
+                            mask=str(mask), size=str(size), name=sequence_name + mask_suffix_name + ' (' + str(size) + 'bp)',
+                            path=sequence_id + mask_suffix + '_' + str(size),
+                            path_fasta=fasta_filename,
+                            version=version)
+    _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
+
+
+def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry):
+    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)
+    return data_manager_dict
+
+
+def main():
+    parser = optparse.OptionParser()
+    parser.add_option('-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename')
+    parser.add_option('-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey')
+    parser.add_option('-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description')
+    parser.add_option('-s', '--size', dest='size', action='store', type="int", default=200, help='fragment size')
+    parser.add_option('-m', '--mask', dest='mask', action='store_true', default=False, help='mask the lower case bases (repeats)')
+    parser.add_option('-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name')
+    parser.add_option('--index_version', dest='index_version', action='store', type="string", default=None, help='index version')
+    (options, args) = parser.parse_args()
+
+    filename = args[0]
+
+    with open(filename) as fh:
+        params = json.load(fh)
+    target_directory = params['output_data'][0]['extra_files_path']
+    os.mkdir(target_directory)
+    data_manager_dict = {}
+
+    dbkey = options.fasta_dbkey
+
+    if dbkey in [None, '', '?']:
+        raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (dbkey))
+
+    sequence_id, sequence_name = get_id_name(params, dbkey=dbkey, fasta_description=options.fasta_description)
+
+    # preparse the genome
+    homer_preparse(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id,
+                   sequence_name, options.size, options.mask, options.index_version,
+                   data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME)
+
+    # save info to json file
+    with open(filename, 'w') as fh:
+        json.dump(data_manager_dict, fh, sort_keys=True)
+
+
+if __name__ == "__main__":
+    main()