コード例 #1
0
ファイル: rnaseq.py プロジェクト: apastore/bcbio-nextgen
def quantitate_expression_noparallel(samples, run_parallel):
    """
    run transcript quantitation for algorithms that don't run in parallel
    """
    data = samples[0][0]
    if "express" in dd.get_expression_caller(data):
        samples = run_parallel("run_express", samples)
    samples = run_parallel("run_dexseq", samples)
    if "rmats" in dd.get_splicecaller(data):
        samples = run_parallel("run_rmats", samples)
    return samples
コード例 #2
0
ファイル: splice.py プロジェクト: apastore/bcbio-nextgen
def splicecall_prepare(data, run_parallel):
    """Entry point for doing alternative splice callers"""
    gtf_file = dd.get_gtf_file(data)
    caller_fns = get_callers()
    to_process = []
    caller = "rmats"
    for sample in data:
        if dd.get_replicate(sample[0]) == 1:
            mimic = copy.copy(sample[0])
            if caller in dd.get_splicecaller(sample[0]):
                if caller in caller_fns and dd.get_phenotype(mimic) != "control":
                    mimic["rmats_fn"] = caller
                    name = dd.get_sample_name(mimic)
                    rep_mimic = _get_replicate_samples(mimic, data)
                    mimic = _get_paired_samples(mimic, data)
                    if mimic:
                        to_process.append(mimic)
                    else:
                        logger.info("Skipping alternative splice calling. No input sample for %s" % name)
    if to_process:
        after_process = run_parallel("splicecalling", to_process)
        data = _sync(data, after_process)
    return data
コード例 #3
0
ファイル: rnaseq.py プロジェクト: apastore/bcbio-nextgen
def run_rmats(data):
    """Detect differential alternative splicing by rMATS"""
    splicecaller =  dd.get_splicecaller(data)
    if "rmats" in splicecaller:
    	data = splice.peakcall_prepare(data)
    return [[data]]
コード例 #4
0
ファイル: __init__.py プロジェクト: apastore/bcbio-nextgen
def _get_splice_file(x, fn_name):
    """Get peak caller for this file name."""
    for caller in dd.get_splicecaller(x):
        if fn_name.find(caller) > -1:
            return caller
    return os.path.basename(fn_name)