/usr/lib/python2.7/dist-packages/pbalign/pbalignrunner.py is in python-pbalign 0.3.0-1.
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###############################################################################
# Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# * Neither the name of Pacific Biosciences nor the names of its
# contributors may be used to endorse or promote products derived from
# this software without specific prior written permission.
#
# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
# THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT
# NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
###############################################################################
"""This script defines class PBAlignRunner.
PBAlignRunner uses AlignService to align PacBio reads in FASTA/BASE/PULSE/FOFN
formats to reference sequences, then uses FilterServices to filter out
alignments that do not satisfy filtering criteria, and finally generates a SAM
or BAM file.
"""
# Author: Yuan Li
import functools
import logging
import time
import sys
import shutil
from pbcommand.cli import pbparser_runner
from pbcommand.utils import setup_log
from pbcore.util.ToolRunner import PBToolRunner
from pbcore.io import (AlignmentSet, ConsensusAlignmentSet)
from pbalign.__init__ import get_version
from pbalign.options import (ALGORITHM_CANDIDATES, get_contract_parser,
resolved_tool_contract_to_args)
from pbalign.alignservice.blasr import BlasrService
from pbalign.alignservice.bowtie import BowtieService
from pbalign.alignservice.gmap import GMAPService
from pbalign.utils.fileutil import getFileFormat, FILE_FORMATS, real_ppath
from pbalign.utils.tempfileutil import TempFileManager
from pbalign.pbalignfiles import PBAlignFiles
from pbalign.filterservice import FilterService
from pbalign.bampostservice import BamPostService
class PBAlignRunner(PBToolRunner):
"""Tool runner."""
def __init__(self, args=None, argumentList=(),
output_dataset_type=AlignmentSet):
"""Initialize a PBAlignRunner object.
argumentList is a list of arguments, such as:
['--debug', '--maxHits', '10', 'in.fasta', 'ref.fasta', 'out.sam']
"""
desc = "Utilities for aligning PacBio reads to reference sequences."
if args is None: # FIXME unit testing hack
args = get_contract_parser().arg_parser.parser.parse_args(argumentList)
self.args = args
# args.verbosity is computed by counting # of 'v's in '-vv...'.
# However in parseOptions, arguments are parsed twice to import config
# options and then overwrite them with argumentList (e.g. command-line)
# options.
#self.args.verbosity = 1 if (self.args.verbosity is None) else \
# (int(self.args.verbosity) / 2 + 1)
super(PBAlignRunner, self).__init__(desc)
self._output_dataset_type = output_dataset_type
self._alnService = None
self._filterService = None
self.fileNames = PBAlignFiles()
self._tempFileManager = TempFileManager()
def _setupParsers(self, description):
pass
def _addStandardArguments(self):
pass
def getVersion(self):
"""Return version."""
return get_version()
def _createAlignService(self, name, args, fileNames, tempFileManager):
"""
Create and return an AlignService by algorithm name.
Input:
name : an algorithm name such as blasr
fileNames : an PBAlignFiles object
args : pbalign options
tempFileManager: a temporary file manager
Output:
an object of AlignService subclass (such as BlasrService).
"""
if name not in ALGORITHM_CANDIDATES:
errMsg = "ERROR: unrecognized algorithm {algo}".format(algo=name)
logging.error(errMsg)
raise ValueError(errMsg)
service = None
if name == "blasr":
service = BlasrService(args, fileNames, tempFileManager)
elif name == "bowtie":
service = BowtieService(args, fileNames, tempFileManager)
elif name == "gmap":
service = GMAPService(args, fileNames, tempFileManager)
else:
errMsg = "Service for {algo} is not implemented.".\
format(algo=name)
logging.error(errMsg)
raise ValueError(errMsg)
service.checkAvailability()
return service
def _makeSane(self, args, fileNames):
"""
Check whether the input arguments make sense or not.
"""
errMsg = ""
if args.useccs == "useccsdenovo":
args.readType = "CCS"
if fileNames.inputFileFormat == FILE_FORMATS.CCS:
args.readType = "CCS"
if args.forQuiver:
logging.warning("Option --forQuiver has been deprecated in 3.0")
outFormat = getFileFormat(fileNames.outputFileName)
if outFormat == FILE_FORMATS.CMP:
errMsg = "pbalign no longer supports CMP.H5 Output in 3.0."
raise IOError(errMsg)
if outFormat == FILE_FORMATS.BAM or outFormat == FILE_FORMATS.XML:
if args.algorithm != "blasr":
errMsg = "Must choose blasr in order to output a bam file."
raise ValueError(errMsg)
if args.filterAdapterOnly:
errMsg = "-filterAdapter does not work when out format is BAM."
raise ValueError(errMsg)
def _parseArgs(self):
"""Overwrite ToolRunner.parseArgs(self).
Parse PBAlignRunner arguments considering both args in argumentList and
args in a config file (specified by --configFile).
"""
pass
def _output(self, inSam, refFile, outFile, readType=None):
"""Generate a SAM, BAM file.
Input:
inSam : an input SAM/BAM file. (e.g. fileName.filteredSam)
refFile : the reference file. (e.g. fileName.targetFileName)
outFile : the output SAM/BAM file
(i.e. fileName.outputFileName)
readType: standard or cDNA or CCS (can be None if not specified)
Output:
output, errCode, errMsg
"""
output, errCode, errMsg = "", 0, ""
outFormat = getFileFormat(outFile)
if outFormat == FILE_FORMATS.BAM:
pass # Nothing to be done
if outFormat == FILE_FORMATS.SAM:
logging.info("OutputService: Genearte the output SAM file.")
logging.debug("OutputService: Move %s as %s", inSam, outFile)
try:
shutil.move(real_ppath(inSam), real_ppath(outFile))
except shutil.Error as e:
output, errCode, errMsg = "", 1, "Exited with error: " + str(e)
logging.error(errMsg)
raise RuntimeError(errMsg)
elif outFormat == FILE_FORMATS.CMP:
errMsg = "pbalign no longer supports CMP.H5 Output in 3.0."
logging.error(errMsg)
raise IOError(errMsg)
elif outFormat == FILE_FORMATS.XML:
logging.info("OutputService: Generating the output XML file %s %s",
inSam, outFile)
# Create {out}.xml, given {out}.bam
outBam = str(outFile[0:-3]) + "bam"
aln = None
# FIXME This should really be more automatic
if readType == "CCS":
self._output_dataset_type = ConsensusAlignmentSet
aln = self._output_dataset_type(real_ppath(outBam))
for res in aln.externalResources:
res.reference = refFile
aln.write(outFile)
return output, errCode, errMsg
def _cleanUp(self, realDelete=False):
""" Clean up temporary files and intermediate results. """
logging.debug("Clean up temporary files and directories.")
self._tempFileManager.CleanUp(realDelete)
def run(self):
"""
The main function, it is called by PBToolRunner.start().
"""
startTime = time.time()
logging.info("pbalign version: %s", get_version())
#logging.debug("Original arguments: " + str(self._argumentList))
# Create an AlignService by algorithm name.
self._alnService = self._createAlignService(self.args.algorithm,
self.args,
self.fileNames,
self._tempFileManager)
# Make sane.
self._makeSane(self.args, self.fileNames)
# Run align service.
self._alnService.run()
# Create a temporary filtered SAM/BAM file as output for FilterService.
outFormat = getFileFormat(self.fileNames.outputFileName)
suffix = ".bam" if outFormat in \
[FILE_FORMATS.BAM, FILE_FORMATS.XML] else ".sam"
self.fileNames.filteredSam = self._tempFileManager.\
RegisterNewTmpFile(suffix=suffix)
# Call filter service on SAM or BAM file.
self._filterService = FilterService(self.fileNames.alignerSamOut,
self.fileNames.targetFileName,
self.fileNames.filteredSam,
self.args.algorithm,
#self._alnService.name,
self._alnService.scoreSign,
self.args,
self.fileNames.adapterGffFileName)
self._filterService.run()
# Sort bam before output
if outFormat in [FILE_FORMATS.BAM, FILE_FORMATS.XML]:
# Sort/make index for BAM output.
BamPostService(self.fileNames).run()
# Output all hits in SAM, BAM.
self._output(
inSam=self.fileNames.filteredSam,
refFile=self.fileNames.targetFileName,
outFile=self.fileNames.outputFileName,
readType=self.args.readType)
# Delete temporay files anyway to make
self._cleanUp(False if (hasattr(self.args, "keepTmpFiles") and
self.args.keepTmpFiles is True) else True)
endTime = time.time()
logging.info("Total time: {:.2f} s.".format(float(endTime - startTime)))
return 0
def args_runner(args, output_dataset_type=AlignmentSet):
"""args runner"""
# PBAlignRunner inherits PBToolRunner. So PBAlignRunner.start() parses args,
# sets up logging and finally returns run().
return PBAlignRunner(args, output_dataset_type=output_dataset_type).start()
def _resolved_tool_contract_runner(output_dataset_type,
resolved_tool_contract):
"""
Template function for running from a tool contract with an explicitly
specified output dataset type.
"""
args = resolved_tool_contract_to_args(resolved_tool_contract)
return args_runner(args, output_dataset_type=output_dataset_type)
resolved_tool_contract_runner = functools.partial(
_resolved_tool_contract_runner, AlignmentSet)
resolved_tool_contract_runner_ccs = functools.partial(
_resolved_tool_contract_runner, ConsensusAlignmentSet)
def main(argv=sys.argv, get_parser_func=get_contract_parser,
contract_runner_func=resolved_tool_contract_runner):
"""Main, supporting both args runner and tool contract runner."""
return pbparser_runner(
argv=argv[1:],
parser=get_parser_func(),
args_runner_func=args_runner,
contract_runner_func=contract_runner_func,
alog=logging.getLogger(__name__),
setup_log_func=setup_log)
if __name__ == "__main__":
sys.exit(main())
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