Mercurial > repos > fubar > data_manager_rnasta

changeset 3:2468ef56337a draft

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Deleted selected files
author fubar
date Fri, 03 Oct 2014 21:59:55 -0400
parents 8a2d16bfdae2
children 102bdfdda10b
files data_manager/rnastar_index_builder.py.orig data_manager/rnastar_index_builder.py.rej
diffstat 2 files changed, 0 insertions(+), 123 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/rnastar_index_builder.py.orig	Fri Oct 03 21:59:39 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,112 +0,0 @@
-#!/usr/bin/env python
-#Dan Blankenberg
-# adapted from Dan's BWA one for rna star
-# ross lazarus sept 2014
-#
-import sys
-import os
-import tempfile
-import optparse
-import subprocess
-
-from galaxy.util.json import from_json_string, to_json_string
-
-DEFAULT_DATA_TABLE_NAME = "rnastar_indexes"
-
-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_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}
-    
-    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
-    elif sjdbFileChrStartEnd:
-        cl += '--sjdbFileChrStartEnd %(sjdbFileChrStartEnd)s --sjdbOverhang %(sjdbOverhangs)s' % pdict
-    tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-rnastar-index-builder-stderr" )
-    args = cl.split(' ')
-    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: retcode=",retcode
-        while True:
-            chunk = tmp_stderr.read( CHUNK_SIZE )
-            if not chunk:
-                break
-            sys.stderr.write( chunk )
-    tmp_stderr.close()
-    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['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( '--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 )
-    (options, args) = parser.parse_args()
-    
-    filename = options.out_file
-    params = from_json_string( open( filename ).read() )
-    target_directory = options.out_index_path
-    os.mkdirs( 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_rnastar_index( data_manager_dict, options.fasta_filename, target_directory, dbkey, sequence_id, 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 )
-
-    
-    #save info to json file
-    open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
-        
-if __name__ == "__main__": main()
--- a/data_manager/rnastar_index_builder.py.rej	Fri Oct 03 21:59:39 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
---- rnastar_index_builder.py Mon Sep 29 20:47:45 2014 -0400
-+++ rnastar_index_builder.py Fri Oct 03 13:35:35 2014 -0400
-@@ -98,6 +89,7 @@
- 
- 
-     #save info to json file
--    open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
-+    open( filename, 'wb' ).write( dumps( data_manager_dict ) )
- 
- if __name__ == "__main__": main()
-+