示例#1
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def runfn(*args):
    args = ipython.unzip_args(args)
    assert len(args) == 1
    fn_args = args[0][4:]
    with _setup_logging(fn_args):
        fn_name = args[0][0]
        dockerconf = args[0][1]
        cmd_args = args[0][2]
        parallel = args[0][3]
        return ipython.zip_args(run.do_runfn(fn_name, fn_args, cmd_args, parallel, dockerconf))
示例#2
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def run_stringtie_expression(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(rnaseq.run_stringtie_expression, *args))
示例#3
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def prep_align_inputs(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(alignprep.create_inputs, *args))
示例#4
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def cufflinks_merge(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(rnaseq.cufflinks_merge, *args))
示例#5
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def machine_info(*args):
    args = ipython.unzip_args(args)
    return ipython.zip_args(system.machine_info())
示例#6
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def compare_to_rm(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(validate.compare_to_rm, *args))
示例#7
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def merge_variant_files(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(vcfutils.merge_variant_files, *args))
示例#8
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def run_dexseq(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(rnaseq.run_dexseq, *args))
示例#9
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def merge_variant_files(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(vcfutils.merge_variant_files, *args))
示例#10
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def variantcall_sample(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(genotype.variantcall_sample, *args))
示例#11
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def combine_sample_regions(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(callable.combine_sample_regions, *args))
示例#12
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def combine_bam(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(shared.combine_bam, *args))
示例#13
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def run_dexseq(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(rnaseq.run_dexseq, *args))
示例#14
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def run_rnaseq_joint_genotyping(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(rnaseq.run_rnaseq_joint_genotyping, *args))
示例#15
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def run_rnaseq_variant_calling(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(rnaseq.run_rnaseq_variant_calling, *args))
示例#16
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def qsignature_summary(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(qcsummary.qsignature_summary, *args))
示例#17
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def run_cufflinks(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(rnaseq.run_cufflinks, *args))
示例#18
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def prep_gemini_db(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(population.prep_gemini_db, *args))
示例#19
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def combine_sample_regions(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(callable.combine_sample_regions, *args))
示例#20
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def call_hla(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(hla.call_hla, *args))
示例#21
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def detect_sv(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(structural.detect_sv, *args))
示例#22
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def finalize_sv(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(structural.finalize_sv, *args))
示例#23
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def run_disambiguate(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(disambiguate.run, *args))
示例#24
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def heterogeneity_estimate(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(heterogeneity.estimate, *args))
示例#25
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def archive_to_cram(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(archive.to_cram, *args))
示例#26
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def combine_calls(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(ensemble.combine_calls, *args))
示例#27
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 def wrapper(*args):
     args = ipython.unzip_args(args)
     with _setup_logging(args) as config:
         return ipython.zip_args(fn(*args))
示例#28
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def compare_to_rm(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(validate.compare_to_rm, *args))
示例#29
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def prep_samples(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(sample.prep_samples, *args))
示例#30
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def run_disambiguate(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(disambiguate.run, *args))
示例#31
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def pipeline_summary(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(qcsummary.pipeline_summary, *args))
示例#32
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def disambiguate_split(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(disambiguate.split, *args))
示例#33
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def generate_transcript_counts(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(rnaseq.generate_transcript_counts, *args))
示例#34
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def disambiguate_merge_extras(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(disambiguate.merge_extras, *args))
示例#35
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def run_rnaseq_variant_calling(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(rnaseq.run_rnaseq_variant_calling, *args))
示例#36
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def machine_info(*args):
    args = ipython.unzip_args(args)
    return ipython.zip_args(system.machine_info())
示例#37
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def combine_bam(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(shared.combine_bam, *args))
示例#38
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def clean_chipseq_alignment(*args):
    args = ipython.unzip_args(args)
    return ipython.zip_args(apply(chipseq.clean_chipseq_alignment, *args))
示例#39
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def variantcall_sample(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(genotype.variantcall_sample, *args))
示例#40
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def archive_to_cram(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(archive.to_cram, *args))
示例#41
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def prep_gemini_db(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(population.prep_gemini_db, *args))
示例#42
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def square_batch_region(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(joint.square_batch_region, *args))
示例#43
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def combine_calls(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(ensemble.combine_calls, *args))
示例#44
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def cufflinks_merge(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(rnaseq.cufflinks_merge, *args))
示例#45
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def coverage_summary(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(coverage.summary, *args))
示例#46
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def stringtie_merge(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(rnaseq.stringtie_merge, *args))
示例#47
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def disambiguate_split(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(disambiguate.split, *args))
示例#48
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def organize_samples(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(run_info.organize, *args))
示例#49
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def clean_chipseq_alignment(*args):
    args = ipython.unzip_args(args)
    return ipython.zip_args(chipseq.machine_info())
示例#50
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def prep_system(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(run_info.prep_system, *args))
示例#51
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def square_batch_region(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(joint.square_batch_region, *args))
示例#52
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def upload_samples_project(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(upload.project_from_sample, *args))
示例#53
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def organize_samples(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(run_info.organize, *args))
示例#54
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 def wrapper(*args):
     args = ipython.unzip_args(args)
     with _setup_logging(args) as config:
         return ipython.zip_args(fn(*args))
示例#55
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def run_sailfish(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args):
        return ipython.zip_args(apply(sailfish.run_sailfish, *args))
示例#56
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def prepare_bcbio_samples(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(sample.prepare_bcbio_samples, *args))
示例#57
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def postprocess_alignment(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(sample.postprocess_alignment, *args))
示例#58
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def trim_srna_sample(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(srna.trim_srna_sample, *args))
示例#59
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def merge_sample(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(sample.merge_sample, *args))
示例#60
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def run_cufflinks(*args):
    args = ipython.unzip_args(args)
    with _setup_logging(args) as config:
        return ipython.zip_args(apply(rnaseq.run_cufflinks, *args))