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comparison lastz_wrapper.py @ 0:0801f8207d30 draft

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date Mon, 26 Nov 2012 09:47:51 -0500
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1 #!/usr/bin/env python
2
3 """
4 Runs Lastz
5 Written for Lastz v. 1.01.88.
6
7 usage: lastz_wrapper.py [options]
8 --ref_name: The reference name to change all output matches to
9 --ref_source: Whether the reference is cached or from the history
10 --source_select: Whether to used pre-set or cached reference file
11 --input1: The name of the reference file if using history or reference base name if using cached
12 --input2: The reads file to align
13 --ref_sequences: The number of sequences in the reference file if using one from history
14 --pre_set_options: Which of the pre set options to use, if using pre-sets
15 --strand: Which strand of the read to search, if specifying all parameters
16 --seed: Seeding settings, if specifying all parameters
17 --gfextend: Whether to perform gap-free extension of seed hits to HSPs (high scoring segment pairs), if specifying all parameters
18 --chain: Whether to perform chaining of HSPs, if specifying all parameters
19 --transition: Number of transitions to allow in each seed hit, if specifying all parameters
20 --O: Gap opening penalty, if specifying all parameters
21 --E: Gap extension penalty, if specifying all parameters
22 --X: X-drop threshold, if specifying all parameters
23 --Y: Y-drop threshold, if specifying all parameters
24 --K: Threshold for HSPs, if specifying all parameters
25 --L: Threshold for gapped alignments, if specifying all parameters
26 --entropy: Whether to involve entropy when filtering HSPs, if specifying all parameters
27 --identity_min: Minimum identity (don't report matches under this identity)
28 --identity_max: Maximum identity (don't report matches above this identity)
29 --coverage: The minimum coverage value (don't report matches covering less than this)
30 --unmask: Whether to convert lowercase bases to uppercase
31 --out_format: The format of the output file (sam, diffs, or tabular (general))
32 --output: The name of the output file
33 --lastzSeqsFileDir: Directory of local lastz_seqs.loc file
34 """
35 import optparse, os, subprocess, shutil, sys, tempfile, threading, time
36 from Queue import Queue
37
38 from galaxy import eggs
39 import pkg_resources
40 pkg_resources.require( 'bx-python' )
41 from bx.seq.twobit import *
42 from bx.seq.fasta import FastaReader
43 from galaxy.util.bunch import Bunch
44
45 STOP_SIGNAL = object()
46 WORKERS = 4
47 SLOTS = 128
48
49 def stop_err( msg ):
50 sys.stderr.write( "%s" % msg )
51 sys.exit()
52
53 def stop_queues( lastz, combine_data ):
54 # This method should only be called if an error has been encountered.
55 # Send STOP_SIGNAL to all worker threads
56 for t in lastz.threads:
57 lastz.put( STOP_SIGNAL, True )
58 combine_data.put( STOP_SIGNAL, True )
59
60 class BaseQueue( object ):
61 def __init__( self, num_threads, slots=-1 ):
62 # Initialize the queue and worker threads
63 self.queue = Queue( slots )
64 self.threads = []
65 for i in range( num_threads ):
66 worker = threading.Thread( target=self.run_next )
67 worker.start()
68 self.threads.append( worker )
69 def run_next( self ):
70 # Run the next job, waiting until one is available if necessary
71 while True:
72 job = self.queue.get()
73 if job is STOP_SIGNAL:
74 return self.shutdown()
75 self.run_job( job )
76 time.sleep( 1 )
77 def run_job( self, job ):
78 stop_err( 'Not Implemented' )
79 def put( self, job, block=False ):
80 # Add a job to the queue
81 self.queue.put( job, block )
82 def shutdown( self ):
83 return
84
85 class LastzJobQueue( BaseQueue ):
86 """
87 A queue that runs commands in parallel. Blocking is done so the queue will
88 not consume much memory.
89 """
90 def run_job( self, job ):
91 # Execute the job's command
92 proc = subprocess.Popen( args=job.command, shell=True, stderr=subprocess.PIPE, )
93 proc.wait()
94 stderr = proc.stderr.read()
95 proc.wait()
96 if stderr:
97 stop_queues( self, job.combine_data_queue )
98 stop_err( stderr )
99 job.combine_data_queue.put( job )
100
101 class CombineDataQueue( BaseQueue ):
102 """
103 A queue that concatenates files in serial. Blocking is not done since this
104 queue is not expected to grow larger than the command queue.
105 """
106 def __init__( self, output_filename, num_threads=1 ):
107 BaseQueue.__init__( self, num_threads )
108 self.CHUNK_SIZE = 2**20 # 1Mb
109 self.output_file = open( output_filename, 'wb' )
110 def run_job( self, job ):
111 in_file = open( job.output, 'rb' )
112 while True:
113 chunk = in_file.read( self.CHUNK_SIZE )
114 if not chunk:
115 in_file.close()
116 break
117 self.output_file.write( chunk )
118 for file_name in job.cleanup:
119 os.remove( file_name )
120 def shutdown( self ):
121 self.output_file.close()
122 return
123
124 def __main__():
125 #Parse Command Line
126 parser = optparse.OptionParser()
127 parser.add_option( '', '--ref_name', dest='ref_name', help='The reference name to change all output matches to' )
128 parser.add_option( '', '--ref_source', dest='ref_source', help='Whether the reference is cached or from the history' )
129 parser.add_option( '', '--ref_sequences', dest='ref_sequences', help='Number of sequences in the reference dataset' )
130 parser.add_option( '', '--source_select', dest='source_select', help='Whether to used pre-set or cached reference file' )
131 parser.add_option( '', '--input1', dest='input1', help='The name of the reference file if using history or reference base name if using cached' )
132 parser.add_option( '', '--input2', dest='input2', help='The reads file to align' )
133 parser.add_option( '', '--pre_set_options', dest='pre_set_options', help='Which of the pre set options to use, if using pre-sets' )
134 parser.add_option( '', '--strand', dest='strand', help='Which strand of the read to search, if specifying all parameters' )
135 parser.add_option( '', '--seed', dest='seed', help='Seeding settings, if specifying all parameters' )
136 parser.add_option( '', '--transition', dest='transition', help='Number of transitions to allow in each seed hit, if specifying all parameters' )
137 parser.add_option( '', '--gfextend', dest='gfextend', help='Whether to perform gap-free extension of seed hits to HSPs (high scoring segment pairs), if specifying all parameters' )
138 parser.add_option( '', '--chain', dest='chain', help='Whether to perform chaining of HSPs, if specifying all parameters' )
139 parser.add_option( '', '--O', dest='O', help='Gap opening penalty, if specifying all parameters' )
140 parser.add_option( '', '--E', dest='E', help='Gap extension penalty, if specifying all parameters' )
141 parser.add_option( '', '--X', dest='X', help='X-drop threshold, if specifying all parameters' )
142 parser.add_option( '', '--Y', dest='Y', help='Y-drop threshold, if specifying all parameters' )
143 parser.add_option( '', '--K', dest='K', help='Threshold for HSPs, if specifying all parameters' )
144 parser.add_option( '', '--L', dest='L', help='Threshold for gapped alignments, if specifying all parameters' )
145 parser.add_option( '', '--entropy', dest='entropy', help='Whether to involve entropy when filtering HSPs, if specifying all parameters' )
146 parser.add_option( '', '--identity_min', dest='identity_min', help="Minimum identity (don't report matches under this identity)" )
147 parser.add_option( '', '--identity_max', dest='identity_max', help="Maximum identity (don't report matches above this identity)" )
148 parser.add_option( '', '--coverage', dest='coverage', help="The minimum coverage value (don't report matches covering less than this)" )
149 parser.add_option( '', '--unmask', dest='unmask', help='Whether to convert lowercase bases to uppercase' )
150 parser.add_option( '', '--out_format', dest='format', help='The format of the output file (sam, diffs, or tabular (general))' )
151 parser.add_option( '', '--output', dest='output', help='The output file' )
152 parser.add_option( '', '--lastzSeqsFileDir', dest='lastzSeqsFileDir', help='Directory of local lastz_seqs.loc file' )
153 ( options, args ) = parser.parse_args()
154
155 # output version # of tool
156 try:
157 tmp = tempfile.NamedTemporaryFile().name
158 tmp_stdout = open( tmp, 'wb' )
159 proc = subprocess.Popen( args='lastz -v', shell=True, stdout=tmp_stdout )
160 tmp_stdout.close()
161 returncode = proc.wait()
162 stdout = None
163 for line in open( tmp_stdout.name, 'rb' ):
164 if line.lower().find( 'version' ) >= 0:
165 stdout = line.strip()
166 break
167 if stdout:
168 sys.stdout.write( '%s\n' % stdout )
169 else:
170 raise Exception
171 except:
172 sys.stdout.write( 'Could not determine Lastz version\n' )
173
174 if options.unmask == 'yes':
175 unmask = '[unmask]'
176 else:
177 unmask = ''
178 if options.ref_name:
179 ref_name = '[nickname=%s]' % options.ref_name
180 else:
181 ref_name = ''
182 # Prepare for commonly-used preset options
183 if options.source_select == 'pre_set':
184 set_options = '--%s' % options.pre_set_options
185 # Prepare for user-specified options
186 else:
187 set_options = '--%s --%s --gapped --strand=%s --seed=%s --%s O=%s E=%s X=%s Y=%s K=%s L=%s --%s' % \
188 ( options.gfextend, options.chain, options.strand, options.seed, options.transition,
189 options.O, options.E, options.X, options.Y, options.K, options.L, options.entropy )
190 # Specify input2 and add [fullnames] modifier if output format is diffs
191 if options.format == 'diffs':
192 input2 = '%s[fullnames]' % options.input2
193 else:
194 input2 = options.input2
195 if options.format == 'tabular':
196 # Change output format to general if it's tabular and add field names for tabular output
197 format = 'general-'
198 tabular_fields = ':score,name1,strand1,size1,start1,zstart1,end1,length1,text1,name2,strand2,size2,start2,zstart2,end2,start2+,zstart2+,end2+,length2,text2,diff,cigar,identity,coverage,gaprate,diagonal,shingle'
199 elif options.format == 'sam':
200 # We currently ALWAYS suppress SAM headers.
201 format = 'sam-'
202 tabular_fields = ''
203 else:
204 format = options.format
205 tabular_fields = ''
206
207 # Set up our queues
208 lastz_job_queue = LastzJobQueue( WORKERS, slots=SLOTS )
209 combine_data_queue = CombineDataQueue( options.output )
210
211 if options.ref_source == 'history':
212 # Reference is a fasta dataset from the history, so split job across
213 # the number of sequences in the dataset ( this could be a HUGE number )
214 try:
215 # Ensure there is at least 1 sequence in the dataset ( this may not be necessary ).
216 error_msg = "The reference dataset is missing metadata, click the pencil icon in the history item and 'auto-detect' the metadata attributes."
217 ref_sequences = int( options.ref_sequences )
218 if ref_sequences < 1:
219 stop_queues( lastz_job_queue, combine_data_queue )
220 stop_err( error_msg )
221 except:
222 stop_queues( lastz_job_queue, combine_data_queue )
223 stop_err( error_msg )
224 seqs = 0
225 fasta_reader = FastaReader( open( options.input1 ) )
226 while True:
227 # Read the next sequence from the reference dataset
228 seq = fasta_reader.next()
229 if not seq:
230 break
231 seqs += 1
232 # Create a temporary file to contain the current sequence as input to lastz
233 tmp_in_fd, tmp_in_name = tempfile.mkstemp( suffix='.in' )
234 tmp_in = os.fdopen( tmp_in_fd, 'wb' )
235 # Write the current sequence to the temporary input file
236 tmp_in.write( '>%s\n%s\n' % ( seq.name, seq.text ) )
237 tmp_in.close()
238 # Create a 2nd temporary file to contain the output from lastz execution on the current sequence
239 tmp_out_fd, tmp_out_name = tempfile.mkstemp( suffix='.out' )
240 os.close( tmp_out_fd )
241 # Generate the command line for calling lastz on the current sequence
242 command = 'lastz %s%s%s %s %s --ambiguousn --nolaj --identity=%s..%s --coverage=%s --format=%s%s > %s' % \
243 ( tmp_in_name, unmask, ref_name, input2, set_options, options.identity_min,
244 options.identity_max, options.coverage, format, tabular_fields, tmp_out_name )
245 # Create a job object
246 job = Bunch()
247 job.command = command
248 job.output = tmp_out_name
249 job.cleanup = [ tmp_in_name, tmp_out_name ]
250 job.combine_data_queue = combine_data_queue
251 # Add another job to the lastz_job_queue. Execution
252 # will wait at this point if the queue is full.
253 lastz_job_queue.put( job, block=True )
254 # Make sure the value of sequences in the metadata is the same as the
255 # number of sequences read from the dataset ( this may not be necessary ).
256 if ref_sequences != seqs:
257 stop_queues( lastz_job_queue, combine_data_queue )
258 stop_err( "The value of metadata.sequences (%d) differs from the number of sequences read from the reference (%d)." % ( ref_sequences, seqs ) )
259 else:
260 # Reference is a locally cached 2bit file, split job across number of chroms in 2bit file
261 tbf = TwoBitFile( open( options.input1, 'r' ) )
262 for chrom in tbf.keys():
263 # Create a temporary file to contain the output from lastz execution on the current chrom
264 tmp_out_fd, tmp_out_name = tempfile.mkstemp( suffix='.out' )
265 os.close( tmp_out_fd )
266 command = 'lastz %s/%s%s%s %s %s --ambiguousn --nolaj --identity=%s..%s --coverage=%s --format=%s%s >> %s' % \
267 ( options.input1, chrom, unmask, ref_name, input2, set_options, options.identity_min,
268 options.identity_max, options.coverage, format, tabular_fields, tmp_out_name )
269 # Create a job object
270 job = Bunch()
271 job.command = command
272 job.output = tmp_out_name
273 job.cleanup = [ tmp_out_name ]
274 job.combine_data_queue = combine_data_queue
275 # Add another job to the lastz_job_queue. Execution
276 # will wait at this point if the queue is full.
277 lastz_job_queue.put( job, block=True )
278
279 # Stop the lastz_job_queue
280 for t in lastz_job_queue.threads:
281 lastz_job_queue.put( STOP_SIGNAL, True )
282 # Although all jobs are submitted to the queue, we can't shut down the combine_data_queue
283 # until we know that all jobs have been submitted to its queue. We do this by checking
284 # whether all of the threads in the lastz_job_queue have terminated.
285 while threading.activeCount() > 2:
286 time.sleep( 1 )
287 # Now it's safe to stop the combine_data_queue
288 combine_data_queue.put( STOP_SIGNAL )
289
290 if __name__=="__main__": __main__()