# HG changeset patch
# User fubar
# Date 1420757594 18000
# Node ID 102bdfdda10bd2bb3aa8999d78067af17be0411f
# Parent 2468ef56337a189625bdd757adf0c2f97e30896e
Uploaded
diff -r 2468ef56337a -r 102bdfdda10b data_manager/rnastar_index_builder.py
--- a/data_manager/rnastar_index_builder.py Fri Oct 03 21:59:55 2014 -0400
+++ b/data_manager/rnastar_index_builder.py Thu Jan 08 17:53:14 2015 -0500
@@ -11,7 +11,8 @@
from json import loads, dumps
-DEFAULT_DATA_TABLE_NAME = "rnastar_indexes"
+DEFAULT_DATA_TABLE_NAME = "rnastar_index"
+CHUNK_SIZE = 2**20
def get_id_name( params, dbkey, fasta_description=None):
#TODO: ensure sequence_id is unique and does not already appear in location file
@@ -26,71 +27,85 @@
sequence_name = dbkey
return sequence_id, sequence_name
-def build_rnastar_index( data_manager_dict, fasta_filename, target_directory, dbkey, sequence_id, sequence_name, data_table_name,
+
+def _run_command( command, target_directory ):
+ tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-rnastar_index_builder-stderr" )
+ return_code = subprocess.call( command, shell=False, stdout=sys.stdout, stderr=tmp_stderr.fileno() )
+ if return_code:
+ tmp_stderr.flush()
+ tmp_stderr.seek( 0 )
+ sys.stderr.write( "### star reports an error:\n" )
+ while True:
+ chunk = tmp_stderr.read( CHUNK_SIZE )
+ if not chunk:
+ break
+ sys.stderr.write( chunk )
+ sys.exit( return_code )
+ tmp_stderr.close()
+ return return_code
+
+
+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
- #tmp_dir = tempfile.mkdtemp( prefix='tmp-data-manager-bwa-index-builder-' )
- 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 )
- pdict={'target_directory':target_directory,'n_threads':n_threads, 'sjdbFileChrStartEnd':sjdbFileChrStartEnd,
- 'sjdbGTFtagExonParentTranscript':sjdbGTFtagExonParentTranscript, 'sjdbGTFfeatureExon':sjdbGTFfeatureExon,
- 'sjdbGTFchrPrefix':sjdbGTFchrPrefix,'sjdbOverhang':sjdbOverhang, 'sjdbGTFfile':sjdbGTFfile,
- 'sym_linked_fasta_filename':sym_linked_fasta_filename}
+ fasta_base_name = os.path.basename( fasta_filename )
+ #sym_linked_fasta_filename = os.path.join( tmp_dir, fasta_base_name )
+ #os.symlink( fasta_filename, sym_linked_fasta_filename )
+ #print >> sys.stdout,'made',sym_linked_fasta_filename
+ cl = ['STAR','--runMode', 'genomeGenerate', '--genomeFastaFiles', fasta_filename, '--genomeDir', target_directory, '--runThreadN',n_threads ]
- cl = 'STAR --runMode genomeGenerate --genomeFastaFiles %(sym_linked_fasta_filename)s --genomeDir %(target_directory)s --runThreadN %(n_threads)s' % pdict
if sjdbGTFfile:
- cl += '''--sjdbGTFchrPrefix %(sjdbGTFchrPrefix)s --sjdbGTFfeatureExon %(sjdbGTFfeatureExon)s --sjdbOverhang %(sjdbOverhang)s
- --sjdbGTFfile %(sjdbGTFfile)s --sjdbGTFtagExonParentTranscript %(sjdbGTFtagExonParentTranscript)s''' % pdict
+ cl += [ '--sjdbGTFfeatureExon', sjdbGTFfeatureExon,'--sjdbGTFtagExonParentTranscript',sjdbGTFtagExonParentTranscript]
+ if (sjdbGTFchrPrefix > ''):
+ cl += ['--sjdbGTFchrPrefix', sjdbGTFchrPrefix]
+ cl += ['--sjdbOverhang', sjdbOverhang, '--sjdbGTFfile', sjdbGTFfile]
elif sjdbFileChrStartEnd:
- cl += '--sjdbFileChrStartEnd %(sjdbFileChrStartEnd)s --sjdbOverhang %(sjdbOverhangs)s' % pdict
- args = cl.split(' ')
- proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
- return_code = proc.wait()
- if return_code:
- sys.exit( return_code )
+ cl += ['--sjdbFileChrStartEnd', sjdbFileChrStartEnd, '--sjdbOverhang', sjdbOverhang]
+ return_code = _run_command(command=cl,target_directory=target_directory)
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 )
-
-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.setdefault('data_tables',{})
+ data_manager_dict['data_tables'].setdefault(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' )
- parser.add_option( '-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name' )
- parser.add_option( '--out_file', default=None)
- parser.add_option( '--out_index_path', default=None)
+ 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="int", default=100 )
- parser.add_option( '--runThreadN', type="int", default=4 )
+ parser.add_option( '--sjdbOverhang', type="string", default='100' )
+ parser.add_option( '--runThreadN', type="string", default='4' )
(options, args) = parser.parse_args()
-
- filename = options.out_file
+ filename = args[0]
+ # this is passed as an positional parameter in the original wrapper with the extra_files_path from the params
params = loads( open( filename ).read() )
- target_directory = options.out_index_path
- os.mkdirs( target_directory )
+ target_directory = params[ 'output_data' ][0]['extra_files_path'].encode('ascii','replace')
+ try:
+ os.mkdir( target_directory )
+ except OSError:
+ pass
+
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 ) )
+ raise Exception( 'dbkey "%s" does not specify any locally known genome to be indexed.' % ( dbkey ) )
sequence_id, sequence_name = get_id_name( params, dbkey=dbkey, fasta_description=options.fasta_description )
#build the index
- build_rnastar_index( data_manager_dict, options.fasta_filename, target_directory, dbkey, sequence_id, sequence_name, data_table_name=options.data_table_name,
+ data_manager_dict = build_rnastar_index( data_manager_dict = 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,
diff -r 2468ef56337a -r 102bdfdda10b data_manager/rnastar_index_builder.xml
--- a/data_manager/rnastar_index_builder.xml Fri Oct 03 21:59:55 2014 -0400
+++ b/data_manager/rnastar_index_builder.xml Thu Jan 08 17:53:14 2015 -0500
@@ -4,10 +4,11 @@
rnastar
-rnastar_index_builder.py --out_file "${out_file}" --fasta_filename "${all_fasta_source.fields.path}"
+rnastar_index_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}"
---data_table_name "rnastar_indexes" --out_index_path "${out_file.extra_files_path}" --runThreadN 1
+--runThreadN 1
#if $genemodel.modelformat=="gff3":
+ --sjdbGTFchrPrefix "${genemodel.sjdbGTFchrPrefix}"
--sjdbOverhang "${genemodel.sjdbOverhang}"
--sjdbGTFfile "${genemodel.sjdbGTFfile}"
--sjdbGTFtagExonParentTranscript "${genemodel.sjdbGTFtagExonParentTranscript}"
@@ -20,7 +21,9 @@
#if $genemodel.modelformat=="None":
--sjdbOverhang 0
#end if
+--data_table_name "rnastar_index"
+
@@ -50,7 +53,7 @@
-
@@ -58,7 +61,7 @@
+ help="GTF tag name to be used as exons' parents for building transcripts - use what's in your gene model file eg parent for gff3">
diff -r 2468ef56337a -r 102bdfdda10b data_manager_conf.xml
--- a/data_manager_conf.xml Fri Oct 03 21:59:55 2014 -0400
+++ b/data_manager_conf.xml Thu Jan 08 17:53:14 2015 -0500
@@ -2,7 +2,7 @@
-
+