src/toil_lib/tools/variant_manipulation.py
def gatk_variant_filtration(job, vcf_id, filter_name, filter_expression, ref_fasta, ref_fai, ref_dict):
    """
    Filters VCF file using GATK VariantFiltration. Fixes extra pair of quotation marks in VCF header that
    may interfere with other VCF tools.

    :param JobFunctionWrappingJob job: passed automatically by Toil
    :param str vcf_id: FileStoreID for input VCF file
    :param str filter_name: Name of filter for VCF header
    :param str filter_expression: JEXL filter expression
    :param str ref_fasta: FileStoreID for reference genome fasta
    :param str ref_fai: FileStoreID for reference genome index file
    :param str ref_dict: FileStoreID for reference genome sequence dictionary file
    :return: FileStoreID for filtered VCF file
    :rtype: str
    """
    inputs = {'genome.fa': ref_fasta,
              'genome.fa.fai': ref_fai,
              'genome.dict': ref_dict,
              'input.vcf': vcf_id}

    work_dir = job.fileStore.getLocalTempDir()
    for name, file_store_id in inputs.iteritems():
        job.fileStore.readGlobalFile(file_store_id, os.path.join(work_dir, name))

    command = ['-T', 'VariantFiltration',
               '-R', 'genome.fa',
               '-V', 'input.vcf',
               '--filterName', filter_name,   # Documents filter name in header
               '--filterExpression', filter_expression,
               '-o', 'filtered_variants.vcf']

    job.fileStore.logToMaster('Running GATK VariantFiltration using {name}: '
                              '{expression}'.format(name=filter_name, expression=filter_expression))

    docker_parameters = ['--rm', 'log-driver', 'none',
                         '-e', 'JAVA_OPTS=-Djava.io.tmpdir=/data/ -Xmx{}'.format(job.memory)]
    dockerCall(job=job, workDir=work_dir,
               parameters=command,
               tool='quay.io/ucsc_cgl/gatk:3.5--dba6dae49156168a909c43330350c6161dc7ecc2',
               dockerParameters=docker_parameters)

    # Remove extra quotation marks around filter expression.
    malformed_header = os.path.join(work_dir, 'filtered_variants.vcf')
    fixed_header = os.path.join(work_dir, 'fixed_header.vcf')
    filter_regex = re.escape('"%s"' % filter_expression)
    with open(malformed_header, 'r') as f, open(fixed_header, 'w') as g:
        for line in f:
            g.write(re.sub(filter_regex, filter_expression, line))

    return job.fileStore.writeGlobalFile(fixed_header)
def gatk_variant_filtration(job, vcf_id, filter_name, filter_expression, ref_fasta, ref_fai, ref_dict):
    inputs = {'genome.fa': ref_fasta,
              'genome.fa.fai': ref_fai,
              'genome.dict': ref_dict,
              'input.vcf': vcf_id}

    work_dir = job.fileStore.getLocalTempDir()
    for name, file_store_id in inputs.iteritems():
        job.fileStore.readGlobalFile(file_store_id, os.path.join(work_dir, name))

    command = ['-T', 'VariantFiltration',
               '-R', 'genome.fa',
               '-V', 'input.vcf',
               '--filterName', filter_name,   # Documents filter name in header
               '--filterExpression', filter_expression,
               '-o', 'filtered_variants.vcf']

    job.fileStore.logToMaster('Running GATK VariantFiltration using {name}: '
                              '{expression}'.format(name=filter_name, expression=filter_expression))

    docker_parameters = ['--rm', 'log-driver', 'none',
                         '-e', 'JAVA_OPTS=-Djava.io.tmpdir=/data/ -Xmx{}'.format(job.memory)]
    dockerCall(job=job, workDir=work_dir,
               parameters=command,
               tool='quay.io/ucsc_cgl/gatk:3.5--dba6dae49156168a909c43330350c6161dc7ecc2',
               dockerParameters=docker_parameters)

    # Remove extra quotation marks around filter expression.
    malformed_header = os.path.join(work_dir, 'filtered_variants.vcf')
    fixed_header = os.path.join(work_dir, 'fixed_header.vcf')
    filter_regex = re.escape('"%s"' % filter_expression)
    with open(malformed_header, 'r') as f, open(fixed_header, 'w') as g:
        for line in f:
            g.write(re.sub(filter_regex, filter_expression, line))

    return job.fileStore.writeGlobalFile(fixed_header)
def gatk_variant_filtration ( job , vcf_id , filter_name , filter_expression , ref_fasta , ref_fai , ref_dict ) : inputs = { 'genome.fa' : ref_fasta , 'genome.fa.fai' : ref_fai , 'genome.dict' : ref_dict , 'input.vcf' : vcf_id } work_dir = job . fileStore . getLocalTempDir ( ) for name , file_store_id in inputs . iteritems ( ) : job . fileStore . readGlobalFile ( file_store_id , os . path . join ( work_dir , name ) ) command = [ '-T' , 'VariantFiltration' , '-R' , 'genome.fa' , '-V' , 'input.vcf' , '--filterName' , filter_name , # Documents filter name in header '--filterExpression' , filter_expression , '-o' , 'filtered_variants.vcf' ] job . fileStore . logToMaster ( 'Running GATK VariantFiltration using {name}: ' '{expression}' . format ( name = filter_name , expression = filter_expression ) ) docker_parameters = [ '--rm' , 'log-driver' , 'none' , '-e' , 'JAVA_OPTS=-Djava.io.tmpdir=/data/ -Xmx{}' . format ( job . memory ) ] dockerCall ( job = job , workDir = work_dir , parameters = command , tool = 'quay.io/ucsc_cgl/gatk:3.5--dba6dae49156168a909c43330350c6161dc7ecc2' , dockerParameters = docker_parameters ) # Remove extra quotation marks around filter expression. malformed_header = os . path . join ( work_dir , 'filtered_variants.vcf' ) fixed_header = os . path . join ( work_dir , 'fixed_header.vcf' ) filter_regex = re . escape ( '"%s"' % filter_expression ) with open ( malformed_header , 'r' ) as f , open ( fixed_header , 'w' ) as g : for line in f : g . write ( re . sub ( filter_regex , filter_expression , line ) ) return job . fileStore . writeGlobalFile ( fixed_header )
Filters VCF file using GATK VariantFiltration. Fixes extra pair of quotation marks in VCF header that
    may interfere with other VCF tools.

    :param JobFunctionWrappingJob job: passed automatically by Toil
    :param str vcf_id: FileStoreID for input VCF file
    :param str filter_name: Name of filter for VCF header
    :param str filter_expression: JEXL filter expression
    :param str ref_fasta: FileStoreID for reference genome fasta
    :param str ref_fai: FileStoreID for reference genome index file
    :param str ref_dict: FileStoreID for reference genome sequence dictionary file
    :return: FileStoreID for filtered VCF file
    :rtype: str
Filters VCF file using GATK VariantFiltration . Fixes extra pair of quotation marks in VCF header that may interfere with other VCF tools .