Example #1
0
def run_rnaseq_variant_calling(data):
    """
    run RNA-seq variant calling, variation file is stored in `vrn_file`
    in the datadict
    """
    variantcaller = dd.get_variantcaller(data)
    if isinstance(variantcaller, list) and len(variantcaller) > 1:
        logger.error("Only one variantcaller can be run for RNA-seq at "
                     "this time. Post an issue here "
                     "(https://github.com/bcbio/bcbio-nextgen/issues) "
                     "if this is something you need to do.")
        sys.exit(1)

    if variantcaller:
        if "gatk-haplotype" in variantcaller:
            data = variation.rnaseq_gatk_variant_calling(data)
        if vardict.get_vardict_command(data):
            data = variation.rnaseq_vardict_variant_calling(data)
    if dd.get_vrn_file(data):
        ann_file = vcfanno.run_vcfanno(dd.get_vrn_file(data), ["rnaedit"],
                                       data)
        if ann_file:
            data = dd.set_vrn_file(data, ann_file)
        ann_file = population.run_vcfanno(dd.get_vrn_file(data), data,
                                          population.do_db_build([data]))
        if ann_file:
            data = dd.set_vrn_file(data, ann_file)
    return [[data]]
Example #2
0
def run_rnaseq_variant_calling(data):
    variantcaller = dd.get_variantcaller(data)
    if isinstance(variantcaller, list) and len(variantcaller) > 1:
        logger.error("Only one variantcaller can be run for RNA-seq at "
                     "this time. Post an issue here "
                     "(https://github.com/chapmanb/bcbio-nextgen/issues) "
                     "if this is something you need to do.")
        sys.exit(1)

    if variantcaller and "gatk" in variantcaller:
        data = variation.rnaseq_gatk_variant_calling(data)
    if vardict.get_vardict_command(data):
        data = variation.rnaseq_vardict_variant_calling(data)
    return [[data]]
Example #3
0
def run_rnaseq_variant_calling(data):
    variantcaller = dd.get_variantcaller(data)
    if isinstance(variantcaller, list) and len(variantcaller) > 1:
        logger.error("Only one variantcaller can be run for RNA-seq at "
                     "this time. Post an issue here "
                     "(https://github.com/chapmanb/bcbio-nextgen/issues) "
                     "if this is something you need to do.")
        sys.exit(1)

    if variantcaller and "gatk" in variantcaller:
        data = variation.rnaseq_gatk_variant_calling(data)
    if vardict.get_vardict_command(data):
        data = variation.rnaseq_vardict_variant_calling(data)
    return [[data]]
Example #4
0
def run_rnaseq_variant_calling(data):
    """
    run RNA-seq variant calling, variation file is stored in `vrn_file`
    in the datadict
    """
    variantcaller = dd.get_variantcaller(data)
    if isinstance(variantcaller, list) and len(variantcaller) > 1:
        logger.error("Only one variantcaller can be run for RNA-seq at "
                     "this time. Post an issue here "
                     "(https://github.com/bcbio/bcbio-nextgen/issues) "
                     "if this is something you need to do.")
        sys.exit(1)

    if variantcaller:
        if "gatk-haplotype" in variantcaller:
            data = variation.rnaseq_gatk_variant_calling(data)
        if vardict.get_vardict_command(data):
            data = variation.rnaseq_vardict_variant_calling(data)
        vrn_file = dd.get_vrn_file(data)
    return [[data]]
Example #5
0
def run_rnaseq_variant_calling(data):
    """
    run RNA-seq variant calling, variation file is stored in `vrn_file`
    in the datadict
    """
    variantcaller = dd.get_variantcaller(data)
    if isinstance(variantcaller, list) and len(variantcaller) > 1:
        logger.error("Only one variantcaller can be run for RNA-seq at "
                     "this time. Post an issue here "
                     "(https://github.com/chapmanb/bcbio-nextgen/issues) "
                     "if this is something you need to do.")
        sys.exit(1)

    if variantcaller and "gatk" in variantcaller:
        data = variation.rnaseq_gatk_variant_calling(data)
    if vardict.get_vardict_command(data):
        data = variation.rnaseq_vardict_variant_calling(data)
    # annotate RNA-editing events with vcfanno
    if dd.get_vrn_file(data):
        vrn_file = vcfanno.run_vcfanno(dd.get_vrn_file(data), "rnaedit", data)
        data = dd.set_vrn_file(data, vrn_file)
    return [[data]]