/tools/sr_mapping/lastz_wrapper.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 290 lines · 215 code · 9 blank · 66 comment · 32 complexity · b597014ae71612658adf9ac139a0957e MD5 · raw file
- #!/usr/bin/env python
- """
- Runs Lastz
- Written for Lastz v. 1.01.88.
- usage: lastz_wrapper.py [options]
- --ref_name: The reference name to change all output matches to
- --ref_source: Whether the reference is cached or from the history
- --source_select: Whether to used pre-set or cached reference file
- --input1: The name of the reference file if using history or reference base name if using cached
- --input2: The reads file to align
- --ref_sequences: The number of sequences in the reference file if using one from history
- --pre_set_options: Which of the pre set options to use, if using pre-sets
- --strand: Which strand of the read to search, if specifying all parameters
- --seed: Seeding settings, if specifying all parameters
- --gfextend: Whether to perform gap-free extension of seed hits to HSPs (high scoring segment pairs), if specifying all parameters
- --chain: Whether to perform chaining of HSPs, if specifying all parameters
- --transition: Number of transitions to allow in each seed hit, if specifying all parameters
- --O: Gap opening penalty, if specifying all parameters
- --E: Gap extension penalty, if specifying all parameters
- --X: X-drop threshold, if specifying all parameters
- --Y: Y-drop threshold, if specifying all parameters
- --K: Threshold for HSPs, if specifying all parameters
- --L: Threshold for gapped alignments, if specifying all parameters
- --entropy: Whether to involve entropy when filtering HSPs, if specifying all parameters
- --identity_min: Minimum identity (don't report matches under this identity)
- --identity_max: Maximum identity (don't report matches above this identity)
- --coverage: The minimum coverage value (don't report matches covering less than this)
- --unmask: Whether to convert lowercase bases to uppercase
- --out_format: The format of the output file (sam, diffs, or tabular (general))
- --output: The name of the output file
- --lastzSeqsFileDir: Directory of local lastz_seqs.loc file
- """
- import optparse, os, subprocess, shutil, sys, tempfile, threading, time
- from Queue import Queue
- from galaxy import eggs
- import pkg_resources
- pkg_resources.require( 'bx-python' )
- from bx.seq.twobit import *
- from bx.seq.fasta import FastaReader
- from galaxy.util.bunch import Bunch
- STOP_SIGNAL = object()
- WORKERS = 4
- SLOTS = 128
- def stop_err( msg ):
- sys.stderr.write( "%s" % msg )
- sys.exit()
- def stop_queues( lastz, combine_data ):
- # This method should only be called if an error has been encountered.
- # Send STOP_SIGNAL to all worker threads
- for t in lastz.threads:
- lastz.put( STOP_SIGNAL, True )
- combine_data.put( STOP_SIGNAL, True )
- class BaseQueue( object ):
- def __init__( self, num_threads, slots=-1 ):
- # Initialize the queue and worker threads
- self.queue = Queue( slots )
- self.threads = []
- for i in range( num_threads ):
- worker = threading.Thread( target=self.run_next )
- worker.start()
- self.threads.append( worker )
- def run_next( self ):
- # Run the next job, waiting until one is available if necessary
- while True:
- job = self.queue.get()
- if job is STOP_SIGNAL:
- return self.shutdown()
- self.run_job( job )
- time.sleep( 1 )
- def run_job( self, job ):
- stop_err( 'Not Implemented' )
- def put( self, job, block=False ):
- # Add a job to the queue
- self.queue.put( job, block )
- def shutdown( self ):
- return
- class LastzJobQueue( BaseQueue ):
- """
- A queue that runs commands in parallel. Blocking is done so the queue will
- not consume much memory.
- """
- def run_job( self, job ):
- # Execute the job's command
- proc = subprocess.Popen( args=job.command, shell=True, stderr=subprocess.PIPE, )
- proc.wait()
- stderr = proc.stderr.read()
- proc.wait()
- if stderr:
- stop_queues( self, job.combine_data_queue )
- stop_err( stderr )
- job.combine_data_queue.put( job )
- class CombineDataQueue( BaseQueue ):
- """
- A queue that concatenates files in serial. Blocking is not done since this
- queue is not expected to grow larger than the command queue.
- """
- def __init__( self, output_filename, num_threads=1 ):
- BaseQueue.__init__( self, num_threads )
- self.CHUNK_SIZE = 2**20 # 1Mb
- self.output_file = open( output_filename, 'wb' )
- def run_job( self, job ):
- in_file = open( job.output, 'rb' )
- while True:
- chunk = in_file.read( self.CHUNK_SIZE )
- if not chunk:
- in_file.close()
- break
- self.output_file.write( chunk )
- for file_name in job.cleanup:
- os.remove( file_name )
- def shutdown( self ):
- self.output_file.close()
- return
- def __main__():
- #Parse Command Line
- parser = optparse.OptionParser()
- parser.add_option( '', '--ref_name', dest='ref_name', help='The reference name to change all output matches to' )
- parser.add_option( '', '--ref_source', dest='ref_source', help='Whether the reference is cached or from the history' )
- parser.add_option( '', '--ref_sequences', dest='ref_sequences', help='Number of sequences in the reference dataset' )
- parser.add_option( '', '--source_select', dest='source_select', help='Whether to used pre-set or cached reference file' )
- parser.add_option( '', '--input1', dest='input1', help='The name of the reference file if using history or reference base name if using cached' )
- parser.add_option( '', '--input2', dest='input2', help='The reads file to align' )
- parser.add_option( '', '--pre_set_options', dest='pre_set_options', help='Which of the pre set options to use, if using pre-sets' )
- parser.add_option( '', '--strand', dest='strand', help='Which strand of the read to search, if specifying all parameters' )
- parser.add_option( '', '--seed', dest='seed', help='Seeding settings, if specifying all parameters' )
- parser.add_option( '', '--transition', dest='transition', help='Number of transitions to allow in each seed hit, if specifying all parameters' )
- 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' )
- parser.add_option( '', '--chain', dest='chain', help='Whether to perform chaining of HSPs, if specifying all parameters' )
- parser.add_option( '', '--O', dest='O', help='Gap opening penalty, if specifying all parameters' )
- parser.add_option( '', '--E', dest='E', help='Gap extension penalty, if specifying all parameters' )
- parser.add_option( '', '--X', dest='X', help='X-drop threshold, if specifying all parameters' )
- parser.add_option( '', '--Y', dest='Y', help='Y-drop threshold, if specifying all parameters' )
- parser.add_option( '', '--K', dest='K', help='Threshold for HSPs, if specifying all parameters' )
- parser.add_option( '', '--L', dest='L', help='Threshold for gapped alignments, if specifying all parameters' )
- parser.add_option( '', '--entropy', dest='entropy', help='Whether to involve entropy when filtering HSPs, if specifying all parameters' )
- parser.add_option( '', '--identity_min', dest='identity_min', help="Minimum identity (don't report matches under this identity)" )
- parser.add_option( '', '--identity_max', dest='identity_max', help="Maximum identity (don't report matches above this identity)" )
- parser.add_option( '', '--coverage', dest='coverage', help="The minimum coverage value (don't report matches covering less than this)" )
- parser.add_option( '', '--unmask', dest='unmask', help='Whether to convert lowercase bases to uppercase' )
- parser.add_option( '', '--out_format', dest='format', help='The format of the output file (sam, diffs, or tabular (general))' )
- parser.add_option( '', '--output', dest='output', help='The output file' )
- parser.add_option( '', '--lastzSeqsFileDir', dest='lastzSeqsFileDir', help='Directory of local lastz_seqs.loc file' )
- ( options, args ) = parser.parse_args()
- # output version # of tool
- try:
- tmp = tempfile.NamedTemporaryFile().name
- tmp_stdout = open( tmp, 'wb' )
- proc = subprocess.Popen( args='lastz -v', shell=True, stdout=tmp_stdout )
- tmp_stdout.close()
- returncode = proc.wait()
- stdout = None
- for line in open( tmp_stdout.name, 'rb' ):
- if line.lower().find( 'version' ) >= 0:
- stdout = line.strip()
- break
- if stdout:
- sys.stdout.write( '%s\n' % stdout )
- else:
- raise Exception
- except:
- sys.stdout.write( 'Could not determine Lastz version\n' )
- if options.unmask == 'yes':
- unmask = '[unmask]'
- else:
- unmask = ''
- if options.ref_name:
- ref_name = '[nickname=%s]' % options.ref_name
- else:
- ref_name = ''
- # Prepare for commonly-used preset options
- if options.source_select == 'pre_set':
- set_options = '--%s' % options.pre_set_options
- # Prepare for user-specified options
- else:
- set_options = '--%s --%s --gapped --strand=%s --seed=%s --%s O=%s E=%s X=%s Y=%s K=%s L=%s --%s' % \
- ( options.gfextend, options.chain, options.strand, options.seed, options.transition,
- options.O, options.E, options.X, options.Y, options.K, options.L, options.entropy )
- # Specify input2 and add [fullnames] modifier if output format is diffs
- if options.format == 'diffs':
- input2 = '%s[fullnames]' % options.input2
- else:
- input2 = options.input2
- if options.format == 'tabular':
- # Change output format to general if it's tabular and add field names for tabular output
- format = 'general-'
- 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'
- elif options.format == 'sam':
- # We currently ALWAYS suppress SAM headers.
- format = 'sam-'
- tabular_fields = ''
- else:
- format = options.format
- tabular_fields = ''
- # Set up our queues
- lastz_job_queue = LastzJobQueue( WORKERS, slots=SLOTS )
- combine_data_queue = CombineDataQueue( options.output )
- if options.ref_source == 'history':
- # Reference is a fasta dataset from the history, so split job across
- # the number of sequences in the dataset ( this could be a HUGE number )
- try:
- # Ensure there is at least 1 sequence in the dataset ( this may not be necessary ).
- error_msg = "The reference dataset is missing metadata, click the pencil icon in the history item and 'auto-detect' the metadata attributes."
- ref_sequences = int( options.ref_sequences )
- if ref_sequences < 1:
- stop_queues( lastz_job_queue, combine_data_queue )
- stop_err( error_msg )
- except:
- stop_queues( lastz_job_queue, combine_data_queue )
- stop_err( error_msg )
- seqs = 0
- fasta_reader = FastaReader( open( options.input1 ) )
- while True:
- # Read the next sequence from the reference dataset
- seq = fasta_reader.next()
- if not seq:
- break
- seqs += 1
- # Create a temporary file to contain the current sequence as input to lastz
- tmp_in_fd, tmp_in_name = tempfile.mkstemp( suffix='.in' )
- tmp_in = os.fdopen( tmp_in_fd, 'wb' )
- # Write the current sequence to the temporary input file
- tmp_in.write( '>%s\n%s\n' % ( seq.name, seq.text ) )
- tmp_in.close()
- # Create a 2nd temporary file to contain the output from lastz execution on the current sequence
- tmp_out_fd, tmp_out_name = tempfile.mkstemp( suffix='.out' )
- os.close( tmp_out_fd )
- # Generate the command line for calling lastz on the current sequence
- command = 'lastz %s%s%s %s %s --ambiguousn --nolaj --identity=%s..%s --coverage=%s --format=%s%s > %s' % \
- ( tmp_in_name, unmask, ref_name, input2, set_options, options.identity_min,
- options.identity_max, options.coverage, format, tabular_fields, tmp_out_name )
- # Create a job object
- job = Bunch()
- job.command = command
- job.output = tmp_out_name
- job.cleanup = [ tmp_in_name, tmp_out_name ]
- job.combine_data_queue = combine_data_queue
- # Add another job to the lastz_job_queue. Execution
- # will wait at this point if the queue is full.
- lastz_job_queue.put( job, block=True )
- # Make sure the value of sequences in the metadata is the same as the
- # number of sequences read from the dataset ( this may not be necessary ).
- if ref_sequences != seqs:
- stop_queues( lastz_job_queue, combine_data_queue )
- stop_err( "The value of metadata.sequences (%d) differs from the number of sequences read from the reference (%d)." % ( ref_sequences, seqs ) )
- else:
- # Reference is a locally cached 2bit file, split job across number of chroms in 2bit file
- tbf = TwoBitFile( open( options.input1, 'r' ) )
- for chrom in tbf.keys():
- # Create a temporary file to contain the output from lastz execution on the current chrom
- tmp_out_fd, tmp_out_name = tempfile.mkstemp( suffix='.out' )
- os.close( tmp_out_fd )
- command = 'lastz %s/%s%s%s %s %s --ambiguousn --nolaj --identity=%s..%s --coverage=%s --format=%s%s >> %s' % \
- ( options.input1, chrom, unmask, ref_name, input2, set_options, options.identity_min,
- options.identity_max, options.coverage, format, tabular_fields, tmp_out_name )
- # Create a job object
- job = Bunch()
- job.command = command
- job.output = tmp_out_name
- job.cleanup = [ tmp_out_name ]
- job.combine_data_queue = combine_data_queue
- # Add another job to the lastz_job_queue. Execution
- # will wait at this point if the queue is full.
- lastz_job_queue.put( job, block=True )
- # Stop the lastz_job_queue
- for t in lastz_job_queue.threads:
- lastz_job_queue.put( STOP_SIGNAL, True )
- # Although all jobs are submitted to the queue, we can't shut down the combine_data_queue
- # until we know that all jobs have been submitted to its queue. We do this by checking
- # whether all of the threads in the lastz_job_queue have terminated.
- while threading.activeCount() > 2:
- time.sleep( 1 )
- # Now it's safe to stop the combine_data_queue
- combine_data_queue.put( STOP_SIGNAL )
- if __name__=="__main__": __main__()