diff data_manager/rnastar_index_builder.py @ 0:cc25c735cae1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 3265247e909410db2a6d6087a2c0d3a9885c120c

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/rnastar_index_builder.py	Wed Nov 23 17:41:18 2016 -0500
@@ -0,0 +1,121 @@
+#!/usr/bin/env python
+# Dan Blankenberg
+# adapted from Dan's BWA one for rna star
+# ross lazarus sept 2014
+# fixed some stupid bugs January 2015
+import json
+import optparse
+import os
+import subprocess
+import sys
+import tempfile
+
+CHUNK_SIZE = 2**20
+ONE_GB = 2**30
+
+DEFAULT_DATA_TABLE_NAME = "rnastar_index"
+
+
+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 _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 build_rnastar_index(data_manager_dict, fasta_filename, target_directory,
+                        dbkey, sequence_id, sequence_name, data_table_name,
+                        sjdbOverhang, sjdbGTFfile, sjdbFileChrStartEnd,
+                        sjdbGTFtagExonParentTranscript, sjdbGTFfeatureExon,
+                        sjdbGTFchrPrefix, n_threads):
+    # TODO: allow multiple FASTA input files
+    fasta_base_name = os.path.basename( fasta_filename )
+    sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name )
+    os.symlink( fasta_filename, sym_linked_fasta_filename )
+    # print >> sys.stdout,'made',sym_linked_fasta_filename
+    cl = ['STAR', '--runMode', 'genomeGenerate', '--genomeFastaFiles', sym_linked_fasta_filename, '--genomeDir', target_directory, '--runThreadN', n_threads ]
+
+    if sjdbGTFfile:
+        cl += [ '--sjdbGTFfeatureExon', sjdbGTFfeatureExon, '--sjdbGTFtagExonParentTranscript', sjdbGTFtagExonParentTranscript]
+        if (sjdbGTFchrPrefix > ''):
+            cl += ['--sjdbGTFchrPrefix', sjdbGTFchrPrefix]
+        cl += ['--sjdbOverhang', sjdbOverhang, '--sjdbGTFfile', sjdbGTFfile]
+    elif sjdbFileChrStartEnd:
+        cl += ['--sjdbFileChrStartEnd', sjdbFileChrStartEnd, '--sjdbOverhang', sjdbOverhang]
+
+    tmp_stderr = tempfile.NamedTemporaryFile( prefix="tmp-data-manager-rnastar-index-builder-stderr" )
+    proc = subprocess.Popen( args=cl, 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:"
+        while True:
+            chunk = tmp_stderr.read( CHUNK_SIZE )
+            if not chunk:
+                break
+            sys.stderr.write( chunk )
+        sys.exit( return_code )
+    tmp_stderr.close()
+    data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name )
+    data_manager_dict = _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
+    return data_manager_dict
+
+
+def main():
+    # Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option( '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' )
+    parser.add_option( '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' )
+    parser.add_option( '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' )
+    parser.add_option( '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name' )
+    parser.add_option( '--sjdbGTFfile', type="string", default=None )
+    parser.add_option( '--sjdbGTFchrPrefix', type="string", default=None )
+    parser.add_option( '--sjdbGTFfeatureExon', type="string", default=None )
+    parser.add_option( '--sjdbGTFtagExonParentTranscript', type="string", default=None )
+    parser.add_option( '--sjdbFileChrStartEnd', type="string", default=None )
+    parser.add_option( '--sjdbOverhang', type="string", default='100' )
+    parser.add_option( '--runThreadN', type="string", default='4' )
+    (options, args) = parser.parse_args()
+    filename = args[0]
+    params = json.loads( open( filename ).read() )
+    target_directory = params[ 'output_data' ][0]['extra_files_path'].encode('ascii', 'replace')
+    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 )
+
+    try:
+        os.mkdir( target_directory )
+    except OSError:
+        pass
+    # build the index
+    data_manager_dict = build_rnastar_index(
+        data_manager_dict={}, fasta_filename=options.fasta_filename,
+        target_directory=target_directory, dbkey=dbkey, sequence_id=sequence_id,
+        sequence_name=sequence_name, data_table_name=options.data_table_name,
+        sjdbOverhang=options.sjdbOverhang, sjdbGTFfile=options.sjdbGTFfile,
+        sjdbFileChrStartEnd=options.sjdbFileChrStartEnd,
+        sjdbGTFtagExonParentTranscript=options.sjdbGTFtagExonParentTranscript,
+        sjdbGTFfeatureExon=options.sjdbGTFfeatureExon,
+        sjdbGTFchrPrefix=options.sjdbGTFchrPrefix, n_threads=options.runThreadN)
+    open( filename, 'wb' ).write( json.dumps( data_manager_dict ) )
+
+
+if __name__ == "__main__":
+    main()