Ejemplo n.º 1
0
def cactusPrepare(options, project):
    """ annotate a SeqFile with ancestral names as well as paths for output sequences."""

    # read the input
    seqFile = SeqFile(options.seqFile)
    configNode = ET.parse(options.configFile).getroot()
    config = ConfigWrapper(configNode)

    # prepare output sequence directory
    # todo: support remote (ie s3) output directory
    try:
        os.makedirs(options.outSeqDir)
    except:
        pass
    if not os.path.isdir(options.outSeqDir):
        raise RuntimeError('Unable to create output sequence directory \'{}\''.format(options.outSeqDir))
    if not os.access(options.outSeqDir, os.W_OK):
        logger.warning('Output sequence directory is not writeable: \'{}\''.format(options.outSeqDir))

    # hack the configfile to skip preprocessing and write it to the output dir
    if options.preprocessOnly:
        config.removePreprocessors()
        options.configFile = os.path.join(options.outSeqDir, 'config.xml')
        config.writeXML(options.configFile)
        
    # pass through the config file to the options
    # todo (don't like second hard-code check of .xml path)
    if options.configFile != os.path.join(cactusRootPath(), "cactus_progressive_config.xml"):
        options.cactusOptions += ' --configFile {}'.format(options.configFile)

    # get the ancestor names
    tree = MultiCactusTree(seqFile.tree)
    tree.nameUnlabeledInternalNodes(prefix = config.getDefaultInternalNodePrefix())

    # make the output
    outSeqFile = SeqFile()
    outSeqFile.tree= tree
    outSeqFile.pathMap = seqFile.pathMap
    outSeqFile.outgroups = seqFile.outgroups

    # update paths for preprocessed leaves or inferred ancestors
    for node in outSeqFile.tree.breadthFirstTraversal():
        name = outSeqFile.tree.getName(node)
        leaf = outSeqFile.tree.isLeaf(node)
        if leaf or (not leaf and name not in seqFile.pathMap and not options.preprocessOnly):
            out_basename = seqFile.pathMap[name] if name in seqFile.pathMap else '{}.fa'.format(name)
            outSeqFile.pathMap[name] = os.path.join(options.outSeqDir, os.path.basename(out_basename))

    # write the output
    with open(options.outSeqFile, 'w') as out_sf:
        out_sf.write(str(outSeqFile))

    # write the instructions
    print(get_plan(options, project, outSeqFile))
Ejemplo n.º 2
0
def cactusPrepare(options, project):
    """ annotate a SeqFile with ancestral names as well as paths for output sequences."""

    # read the input
    seqFile = SeqFile(options.seqFile)
    configNode = ET.parse(options.configFile).getroot()
    config = ConfigWrapper(configNode)

    if not options.wdl:
        # prepare output sequence directory
        # todo: support remote (ie s3) output directory
        try:
            os.makedirs(options.outDir)
        except:
            pass
        if not os.path.isdir(options.outDir):
            raise RuntimeError('Unable to create output sequence directory \'{}\''.format(options.outDir))
        if not os.access(options.outDir, os.W_OK):
            logger.warning('Output sequence directory is not writeable: \'{}\''.format(options.outDir))

    if options.preprocessOnly or options.gpu:
        if options.preprocessOnly:
            # hack the configfile to skip preprocessing and write it to the output dir
            config.removePreprocessors()
        if options.gpu:
            # hack the configfile to toggle on gpu lastz
            cafNode = findRequiredNode(config.xmlRoot, "caf")
            cafNode.attrib["gpuLastz"] = "true"
            # realigning doesn't mix well with lastz so we make sure it's off
            # https://github.com/ComparativeGenomicsToolkit/cactus/issues/271
            cafNode.attrib["realign"] = "0"
        options.configFile = os.path.join(options.outDir, 'config-prepared.xml')
        sys.stderr.write("configuration saved in {}\n".format(options.configFile))
        config.writeXML(options.configFile)
        
    # pass through the config file to the options
    # todo (don't like second hard-code check of .xml path)
    if options.configFile != os.path.join(cactusRootPath(), "cactus_progressive_config.xml") and not options.wdl:
        options.cactusOptions += ' --configFile {}'.format(options.configFile)

    # get the ancestor names
    tree = MultiCactusTree(seqFile.tree)
    tree.nameUnlabeledInternalNodes(prefix = config.getDefaultInternalNodePrefix())

    # make the output
    outSeqFile = SeqFile()
    outSeqFile.tree= tree
    outSeqFile.pathMap = copy.deepcopy(seqFile.pathMap)
    outSeqFile.outgroups = copy.deepcopy(seqFile.outgroups)

    # update paths for preprocessed leaves or inferred ancestors
    for node in outSeqFile.tree.breadthFirstTraversal():
        name = outSeqFile.tree.getName(node)
        leaf = outSeqFile.tree.isLeaf(node)
        if leaf or (not leaf and name not in seqFile.pathMap and not options.preprocessOnly):
            out_basename = seqFile.pathMap[name] if name in seqFile.pathMap else '{}.fa'.format(name)
            outSeqFile.pathMap[name] = os.path.join(options.outDir, os.path.basename(out_basename))
            if options.wdl:
                # uniquify name in wdl to prevent collisions
                outSeqFile.pathMap[name] += '.pp'

    # write the output
    if options.outSeqFile:
        with open(options.outSeqFile, 'w') as out_sf:
            out_sf.write(str(outSeqFile))

    # write the instructions
    print(get_plan(options, project, seqFile, outSeqFile))