# HG changeset patch
# User dave
# Date 1530399130 14400
# Node ID 125b8ae43807432073e1a34c42d5e36d54d89a92
# Parent 3da261f8ac9095653eca634cb3070a9ee5e31d5a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit db8f5e7fadc3bf752951b837a977919f8409e4b6-dirty
diff -r 3da261f8ac90 -r 125b8ae43807 data_manager/.data_manager_make_blastn_dbs.py.swp
Binary file data_manager/.data_manager_make_blastn_dbs.py.swp has changed
diff -r 3da261f8ac90 -r 125b8ae43807 data_manager/.data_manager_make_blastn_dbs.xml.swp
Binary file data_manager/.data_manager_make_blastn_dbs.xml.swp has changed
diff -r 3da261f8ac90 -r 125b8ae43807 data_manager/data_manager_make_blastn_database.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_make_blastn_database.py Sat Jun 30 18:52:10 2018 -0400
@@ -0,0 +1,65 @@
+#!/usr/bin/env python
+# Dan Blankenberg
+from __future__ import print_function
+
+import optparse
+import os
+import subprocess
+import sys
+from json import dumps, loads
+
+DEFAULT_DATA_TABLE_NAMES = ["blastn_databases"]
+
+
+def build_blastn_index(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=DEFAULT_DATA_TABLE_NAMES):
+ # TODO: allow multiple FASTA input files
+ 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 = ['makeblastdb', '-in', sym_linked_fasta_filename, '-dbtype', 'nucl', '-out', sequence_id]
+ proc = subprocess.Popen(args=args, shell=False, cwd=target_directory)
+ return_code = proc.wait()
+ if return_code:
+ print("Error building index.", file=sys.stderr)
+ sys.exit(return_code)
+ data_table_entry = dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=sequence_id)
+ for data_table_name in data_table_names:
+ _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('-i', '--input', dest='input', action='store', type="string", default=None, help='Input FASTA')
+ parser.add_option('-d', '--dbkey', dest='dbkey', action='store', type="string", default=None, help='Unique identifier')
+ parser.add_option('-n', '--name', dest='name', action='store', type="string", default=None, help='Name')
+ (options, args) = parser.parse_args()
+
+ filename = args[0]
+
+ params = loads(open(filename).read())
+ #raise NameError(dumps(params, indent=2, sort_keys=True))
+ target_directory = params['output_data'][0]['extra_files_path']
+ os.mkdir(target_directory)
+ data_manager_dict = {}
+
+ if options.dbkey in [None, '', '?']:
+ raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (options.dbkey))
+
+ sequence_id, sequence_name = (options.dbkey, options.name)
+
+ # build the index
+ build_blastn_index(data_manager_dict, options.input, params, target_directory, options.dbkey, sequence_id, sequence_name, data_table_names=['blastn_databases'])
+
+ # save info to json file
+ open(filename, 'wb').write(dumps(data_manager_dict))
+
+
+if __name__ == "__main__":
+ main()
diff -r 3da261f8ac90 -r 125b8ae43807 data_manager/data_manager_make_blastn_database.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_make_blastn_database.xml Sat Jun 30 18:52:10 2018 -0400
@@ -0,0 +1,61 @@
+
+ from fasta file
+
+ blast
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**What it does**
+
+Fetches a reference genomes or sequences from various sources (URL, Galaxy History, or a server directory) and populates the "blastn_db" data table.
+
+------
+
+.. class:: infomark
+
+**Notice:** If you leave name, description, or id blank, it will be generated automatically.
+
+
diff -r 3da261f8ac90 -r 125b8ae43807 data_manager/data_manager_make_blastn_dbs.py
--- a/data_manager/data_manager_make_blastn_dbs.py Sat Jun 30 16:19:53 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,78 +0,0 @@
-#!/usr/bin/env python
-# Dan Blankenberg
-from __future__ import print_function
-
-import optparse
-import os
-import subprocess
-import sys
-from json import dumps, loads
-
-DEFAULT_DATA_TABLE_NAMES = ["blastn_dbs"]
-
-
-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 build_blastn_index(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=DEFAULT_DATA_TABLE_NAMES):
- # TODO: allow multiple FASTA input files
- 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 = ['makeblastdb', '-in', sym_linked_fasta_filename, '-dbtype', "'nucl'", '-out', sequence_id]
- proc = subprocess.Popen(args=args, shell=False, cwd=target_directory)
- return_code = proc.wait()
- if return_code:
- print("Error building index.", file=sys.stderr)
- sys.exit(return_code)
- data_table_entry = dict(value=sequence_id, dbkey=dbkey, name=sequence_name, path=sequence_id)
- for data_table_name in data_table_names:
- _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('-i', '--input', dest='input', action='store', type="string", default=None, help='Input FASTA')
- parser.add_option('-d', '--dbkey', dest='dbkey', action='store', type="string", default=None, help='Unique identifier')
- parser.add_option('-n', '--name', dest='name', action='store', type="string", default=None, help='Name')
- (options, args) = parser.parse_args()
-
- filename = args[0]
-
- params = loads(open(filename).read())
- target_directory = params['output_data'][0]['extra_files_path']
- os.mkdir(target_directory)
- data_manager_dict = {}
-
- 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=options.dbkey, fasta_description=options.name)
-
- # build the index
- build_blastn_index(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=options.data_table_name or DEFAULT_DATA_TABLE_NAMES)
-
- # save info to json file
- open(filename, 'wb').write(dumps(data_manager_dict))
-
-
-if __name__ == "__main__":
- main()
diff -r 3da261f8ac90 -r 125b8ae43807 data_manager/data_manager_make_blastn_dbs.xml
--- a/data_manager/data_manager_make_blastn_dbs.xml Sat Jun 30 16:19:53 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,61 +0,0 @@
-
- for fasta and blastdbs
-
- blast
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-**What it does**
-
-Fetches a reference genomes or sequences from various sources (URL, Galaxy History, or a server directory) and populates the "blastn_db" data table.
-
-------
-
-.. class:: infomark
-
-**Notice:** If you leave name, description, or id blank, it will be generated automatically.
-
-
diff -r 3da261f8ac90 -r 125b8ae43807 data_manager_conf.xml
--- a/data_manager_conf.xml Sat Jun 30 16:19:53 2018 -0400
+++ b/data_manager_conf.xml Sat Jun 30 18:52:10 2018 -0400
@@ -1,6 +1,6 @@
-
+