# HG changeset patch
# User iuc
# Date 1491344189 14400
# Node ID 9946bc39c834637d8f83f2253e977106c4115b86
# Parent df883cc67fbdf7daa010841a95628c28ddf2a0ff
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 8652f36a3a3838dca989426961561e81432acf4f
diff -r df883cc67fbd -r 9946bc39c834 data_manager/twobit_builder.py
--- a/data_manager/twobit_builder.py Thu Jan 19 11:45:43 2017 -0500
+++ b/data_manager/twobit_builder.py Tue Apr 04 18:16:29 2017 -0400
@@ -1,19 +1,23 @@
#!/usr/bin/env python
-#Dan Blankenberg
+# Dan Blankenberg
+from __future__ import print_function
-import sys, os, tempfile, optparse, uuid, subprocess
+import optparse
+import os
+import subprocess
+import sys
+import tempfile
+from json import dumps, loads
-from json import loads, dumps
+CHUNK_SIZE = 2**20 # 1mb
-CHUNK_SIZE = 2**20 #1mb
-
def get_id_name( params, dbkey, fasta_description=None):
- #TODO: ensure sequence_id is unique and does not already appear in location file
+ # 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 #uuid.uuid4() generate and use an uuid
-
+ sequence_id = dbkey # uuid.uuid4() generate and use an uuid
+
sequence_name = params['param_dict']['sequence_name']
if not sequence_name:
sequence_name = fasta_description
@@ -21,18 +25,19 @@
sequence_name = dbkey
return sequence_id, sequence_name
+
def build_twobit( data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name ):
twobit_base_name = "%s.2bit" % ( sequence_id )
twobit_filename = os.path.join( target_directory, twobit_base_name )
-
+
args = [ 'faToTwoBit', fasta_filename, twobit_filename ]
- tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-twobit-builder-stderr" )
+ tmp_stderr = tempfile.NamedTemporaryFile( prefix="tmp-data-manager-twobit-builder-stderr" )
proc = subprocess.Popen( args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() )
return_code = proc.wait()
if return_code:
tmp_stderr.flush()
tmp_stderr.seek(0)
- print >> sys.stderr, "Error building index:"
+ print("Error building index:", file=sys.stderr)
while True:
chunk = tmp_stderr.read( CHUNK_SIZE )
if not chunk:
@@ -40,53 +45,55 @@
sys.stderr.write( chunk )
sys.exit( return_code )
tmp_stderr.close()
- #lastz_seqs
+ # lastz_seqs
data_table_entry = dict( value=sequence_id, name=sequence_name, path=twobit_base_name )
_add_data_table_entry( data_manager_dict, "lastz_seqs", data_table_entry )
- #twobit.loc
+ # twobit.loc
data_table_entry = dict( value=sequence_id, path=twobit_base_name )
_add_data_table_entry( data_manager_dict, "twobit", data_table_entry )
- #alignseq
+ # alignseq
data_table_entry = dict( type="seq", value=sequence_id, path=twobit_base_name )
_add_data_table_entry( data_manager_dict, "alignseq_seq", 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():
- #Parse Command Line
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' )
(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 = {}
-
+
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 )
-
- #build the index
+
+ # build the index
build_twobit( data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name )
-
- #save info to json file
+
+ # save info to json file
open( filename, 'wb' ).write( dumps( data_manager_dict ) )
-
-if __name__ == "__main__": main()
+
+if __name__ == "__main__":
+ main()
diff -r df883cc67fbd -r 9946bc39c834 data_manager/twobit_builder.xml
--- a/data_manager/twobit_builder.xml Thu Jan 19 11:45:43 2017 -0500
+++ b/data_manager/twobit_builder.xml Tue Apr 04 18:16:29 2017 -0400
@@ -3,14 +3,19 @@
ucsc-fatotwobit
builder
- twobit_builder.py "${out_file}" --fasta_filename "${all_fasta_source.fields.path}" --fasta_dbkey "${all_fasta_source.fields.dbkey}" --fasta_description "${all_fasta_source.fields.name}"
+
-
-
-
+
+
@@ -25,11 +30,9 @@
-
.. class:: infomark
-**Notice:** If you leave name, description, or id blank, it will be generated automatically.
-
+**Notice:** If you leave name, description, or id blank, it will be generated automatically.