Commit 1211bfa6 authored by Afif Elghraoui's avatar Afif Elghraoui
Browse files

New upstream version 2.2.2

parent db3cde28

.gitignore

+1 −0
Original line number Diff line number Diff line
@@ -11,3 +11,4 @@ dist/ 
TAGS

evidence_dump/

nosetests.xml

_deps/

GenomicConsensus/ResultCollector.py

+16 −33
Original line number Diff line number Diff line 
#################################################################################

# 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.

#################################################################################



# Author: David Alexander, Jim Drake



import cProfile, logging, os.path, sys
@@ -37,6 +7,7 @@ from collections import OrderedDict, defaultdict 
from .options import options

from GenomicConsensus import reference, consensus, utils, windows

from .io.VariantsGffWriter import VariantsGffWriter

from .io.VariantsVcfWriter import VariantsVcfWriter

from pbcore.io import FastaWriter, FastqWriter



class ResultCollector(object):
@@ -84,7 +55,10 @@ class ResultCollector(object): 
        self.consensusChunksByRefId      = defaultdict(list)



        # open file writers

        self.fastaWriter = self.fastqWriter = self.gffWriter = None

        self.fastaWriter = None

        self.fastqWriter = None

        self.gffWriter   = None

        self.vcfWriter   = None

        if options.fastaOutputFilename:

            self.fastaWriter = FastaWriter(options.fastaOutputFilename)

        if options.fastqOutputFilename:
@@ -93,6 +67,10 @@ class ResultCollector(object): 
            self.gffWriter = VariantsGffWriter(options.gffOutputFilename,

                                               vars(options),

                                               reference.byName.values())

        if options.vcfOutputFilename:

            self.vcfWriter = VariantsVcfWriter(options.vcfOutputFilename,

                                               vars(options),

                                               reference.byName.values())



    def onResult(self, result):

        window, cssAndVariants = result
@@ -105,6 +83,7 @@ class ResultCollector(object): 
        if self.fastaWriter: self.fastaWriter.close()

        if self.fastqWriter: self.fastqWriter.close()

        if self.gffWriter:   self.gffWriter.close()

        if self.vcfWriter:   self.vcfWriter.close()

        logging.info("Output files completed.")



    def _recordNewResults(self, window, css, variants):
@@ -122,8 +101,12 @@ class ResultCollector(object): 
        if basesProcessed == requiredBases:

            # This contig is done, so we can dump to file and delete

            # the data structures.

            if self.gffWriter or self.vcfWriter:

                variants = sorted(self.variantsByRefId[refId])

                if self.gffWriter:

                self.gffWriter.writeVariants(sorted(self.variantsByRefId[refId]))

                    self.gffWriter.writeVariants(variants)

                if self.vcfWriter:

                    self.vcfWriter.writeVariants(variants)

            del self.variantsByRefId[refId]



            #

GenomicConsensus/Worker.py

+0 −30
Original line number Diff line number Diff line 
#################################################################################

# 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.

#################################################################################



# Author: David Alexander, Jim Drake



import cProfile, logging, os.path

GenomicConsensus/__init__.py

+2 −32
Original line number Diff line number Diff line 
#################################################################################

# 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.

#################################################################################

# Author: David Alexander, David Seifert



# Author: David Alexander



__VERSION__ = "2.1.0"
 
__VERSION__ = '2.2.2'  # don't forget to update setup.py and doc/conf.py too

GenomicConsensus/algorithmSelection.py

+0 −31
Original line number Diff line number Diff line 
#!/usr/bin/env python

#################################################################################

# Copyright (c) 2011-2016, 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.

#################################################################################



# Author: David Alexander



from .utils import die