Mercurial > repos > devteam > data_manager_gatk_picard_index_builder
comparison data_manager/data_manager_gatk_picard_index_builder.py @ 0:619dd9e9c09c draft
Imported from capsule None
author | devteam |
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date | Tue, 01 Apr 2014 10:48:03 -0400 |
parents | |
children | b31f1fcb203c |
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-1:000000000000 | 0:619dd9e9c09c |
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1 #!/usr/bin/env python | |
2 # Dave B. | |
3 # Uses fasta sorting functions written by Dan Blankenberg. | |
4 | |
5 import json | |
6 import optparse | |
7 import os | |
8 import shutil | |
9 import subprocess | |
10 import sys | |
11 import tempfile | |
12 | |
13 CHUNK_SIZE = 2**20 | |
14 | |
15 DEFAULT_DATA_TABLE_NAME = "fasta_indexes" | |
16 | |
17 def get_id_name( params, dbkey, fasta_description=None): | |
18 #TODO: ensure sequence_id is unique and does not already appear in location file | |
19 sequence_id = params['param_dict']['sequence_id'] | |
20 if not sequence_id: | |
21 sequence_id = dbkey | |
22 | |
23 sequence_name = params['param_dict']['sequence_name'] | |
24 if not sequence_name: | |
25 sequence_name = fasta_description | |
26 if not sequence_name: | |
27 sequence_name = dbkey | |
28 return sequence_id, sequence_name | |
29 | |
30 def build_picard_index( data_manager_dict, fasta_filename, target_directory, dbkey, sequence_id, sequence_name, jar, data_table_name=DEFAULT_DATA_TABLE_NAME ): | |
31 fasta_base_name = os.path.split( fasta_filename )[-1] | |
32 gatk_sorted_fasta_filename = os.path.join( target_directory, fasta_base_name ) | |
33 shutil.copy( fasta_filename, gatk_sorted_fasta_filename ) | |
34 _sort_fasta_gatk( gatk_sorted_fasta_filename ) | |
35 sam_index_filename = '%s.fai' % gatk_sorted_fasta_filename | |
36 if not os.path.exists( sam_index_filename ): | |
37 sam_command = [ 'samtools', 'faidx', gatk_sorted_fasta_filename ] | |
38 _run_command( sam_command, target_directory ) | |
39 args = [ 'java', '-jar', jar, 'R=%s' % gatk_sorted_fasta_filename, 'O=%s.dict' % sequence_id ] | |
40 _run_command( args, target_directory ) | |
41 data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_name ) | |
42 _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ) | |
43 | |
44 def _run_command( command, target_directory ): | |
45 tmp_stderr = tempfile.NamedTemporaryFile( prefix = "tmp-data-manager-gatk_picard_index_builder-stderr" ) | |
46 proc = subprocess.Popen( args=command, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno() ) | |
47 return_code = proc.wait() | |
48 if return_code: | |
49 tmp_stderr.flush() | |
50 tmp_stderr.seek( 0 ) | |
51 sys.stderr.write( "Error building index:\n" ) | |
52 while True: | |
53 chunk = tmp_stderr.read( CHUNK_SIZE ) | |
54 if not chunk: | |
55 break | |
56 sys.stderr.write( chunk ) | |
57 sys.exit( return_code ) | |
58 tmp_stderr.close() | |
59 | |
60 def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ): | |
61 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) | |
62 data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] ) | |
63 data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry ) | |
64 return data_manager_dict | |
65 | |
66 def _move_and_index_fasta_for_sorting( fasta_filename ): | |
67 unsorted_filename = tempfile.NamedTemporaryFile().name | |
68 shutil.move( fasta_filename, unsorted_filename ) | |
69 fasta_offsets = {} | |
70 unsorted_fh = open( unsorted_filename ) | |
71 while True: | |
72 offset = unsorted_fh.tell() | |
73 line = unsorted_fh.readline() | |
74 if not line: | |
75 break | |
76 if line.startswith( ">" ): | |
77 line = line.split( None, 1 )[0][1:] | |
78 fasta_offsets[ line ] = offset | |
79 unsorted_fh.close() | |
80 current_order = map( lambda x: x[1], sorted( map( lambda x: ( x[1], x[0] ), fasta_offsets.items() ) ) ) | |
81 return ( unsorted_filename, fasta_offsets, current_order ) | |
82 | |
83 def _write_sorted_fasta( sorted_names, fasta_offsets, sorted_fasta_filename, unsorted_fasta_filename ): | |
84 unsorted_fh = open( unsorted_fasta_filename ) | |
85 sorted_fh = open( sorted_fasta_filename, 'wb+' ) | |
86 | |
87 for name in sorted_names: | |
88 offset = fasta_offsets[ name ] | |
89 unsorted_fh.seek( offset ) | |
90 sorted_fh.write( unsorted_fh.readline() ) | |
91 while True: | |
92 line = unsorted_fh.readline() | |
93 if not line or line.startswith( ">" ): | |
94 break | |
95 sorted_fh.write( line ) | |
96 unsorted_fh.close() | |
97 sorted_fh.close() | |
98 | |
99 def _int_to_roman( integer ): | |
100 if not isinstance( integer, int ): | |
101 raise TypeError, "expected integer, got %s" % type( integer ) | |
102 if not 0 < integer < 4000: | |
103 raise ValueError, "Argument must be between 1 and 3999, got %s" % str( integer ) | |
104 ints = ( 1000, 900, 500, 400, 100, 90, 50, 40, 10, 9, 5, 4, 1 ) | |
105 nums = ( 'M', 'CM', 'D', 'CD', 'C', 'XC', 'L', 'XL', 'X', 'IX', 'V', 'IV', 'I' ) | |
106 result = "" | |
107 for i in range( len( ints ) ): | |
108 count = int( integer / ints[ i ] ) | |
109 result += nums[ i ] * count | |
110 integer -= ints[ i ] * count | |
111 return result | |
112 | |
113 def _sort_fasta_gatk( fasta_filename ): | |
114 ( unsorted_filename, fasta_offsets, current_order ) = _move_and_index_fasta_for_sorting( fasta_filename ) | |
115 sorted_names = map( str, range( 1, 100 ) ) + map( _int_to_roman, range( 1, 100 ) ) + [ 'X', 'Y', 'M' ] | |
116 #detect if we have chrN, or just N | |
117 has_chr = False | |
118 for chrom in sorted_names: | |
119 if "chr%s" % chrom in current_order: | |
120 has_chr = True | |
121 break | |
122 | |
123 if has_chr: | |
124 sorted_names = map( lambda x: "chr%s" % x, sorted_names) | |
125 else: | |
126 sorted_names.insert( 0, "MT" ) | |
127 sorted_names.extend( map( lambda x: "%s_random" % x, sorted_names ) ) | |
128 | |
129 existing_sorted_names = [] | |
130 for name in sorted_names: | |
131 # Append each chromosome only once. | |
132 if name in current_order and name not in existing_sorted_names: | |
133 existing_sorted_names.append( name ) | |
134 for name in current_order: | |
135 #TODO: confirm that non-canonical names do not need to be sorted specially | |
136 if name not in existing_sorted_names: | |
137 existing_sorted_names.append( name ) | |
138 | |
139 if existing_sorted_names == current_order: | |
140 shutil.move( unsorted_filename, fasta_filename ) | |
141 else: | |
142 _write_sorted_fasta( existing_sorted_names, fasta_offsets, fasta_filename, unsorted_filename ) | |
143 | |
144 def main(): | |
145 #Parse Command Line | |
146 parser = optparse.OptionParser() | |
147 parser.add_option( '-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename' ) | |
148 parser.add_option( '-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey' ) | |
149 parser.add_option( '-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description' ) | |
150 parser.add_option( '-n', '--data_table_name', dest='data_table_name', action='store', type="string", default=None, help='data_table_name' ) | |
151 parser.add_option( '-j', '--jar', dest='jar', action='store', type="string", default=None, help='GATK .jar file' ) | |
152 (options, args) = parser.parse_args() | |
153 | |
154 filename = args[0] | |
155 | |
156 params = json.loads( open( filename ).read() ) | |
157 target_directory = params[ 'output_data' ][0]['extra_files_path'] | |
158 os.mkdir( target_directory ) | |
159 data_manager_dict = {} | |
160 | |
161 if options.fasta_dbkey in [ None, '', '?' ]: | |
162 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( options.fasta_dbkey ) ) | |
163 | |
164 sequence_id, sequence_name = get_id_name( params, dbkey=options.fasta_dbkey, fasta_description=options.fasta_description ) | |
165 | |
166 #build the index | |
167 build_picard_index( data_manager_dict, | |
168 options.fasta_filename, | |
169 target_directory, | |
170 options.fasta_dbkey, | |
171 sequence_id, | |
172 sequence_name, | |
173 options.jar, | |
174 data_table_name=options.data_table_name or DEFAULT_DATA_TABLE_NAME ) | |
175 | |
176 #save info to json file | |
177 open( filename, 'wb' ).write( json.dumps( data_manager_dict ) ) | |
178 | |
179 if __name__ == "__main__": main() |