当前位置: 首页>>代码示例>>Python>>正文


Python conftest.make_workdir函数代码示例

本文整理汇总了Python中tests.conftest.make_workdir函数的典型用法代码示例。如果您正苦于以下问题:Python make_workdir函数的具体用法?Python make_workdir怎么用?Python make_workdir使用的例子?那么恭喜您, 这里精选的函数代码示例或许可以为您提供帮助。


在下文中一共展示了make_workdir函数的15个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的Python代码示例。

示例1: test_programs

 def test_programs(self, data_dir):
     """Identify programs and versions used in analysis.
     """
     from bcbio.provenance import programs
     with make_workdir() as workdir:
         config = load_config(get_post_process_yaml(data_dir, workdir))
         print programs._get_versions(config)
开发者ID:DoaneAS,项目名称:bcbio-nextgen,代码行数:7,代码来源:test_pipeline.py

示例2: test_6_bamclean

def test_6_bamclean(install_test_files, data_dir):
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, os.pardir, "100326_FC6107FAAXX"),
              os.path.join(data_dir, "run_info-bamclean.yaml")]
        subprocess.check_call(cl)
开发者ID:biocyberman,项目名称:bcbio-nextgen,代码行数:7,代码来源:test_automated_analysis.py

示例3: test_1_parallel_vcf_combine

 def test_1_parallel_vcf_combine(self):
     """Parallel combination of VCF files, split by chromosome.
     """
     from bcbio.variation import vcfutils
     files = [
         os.path.join(self.var_dir, "S1-variants.vcf"),
         os.path.join(self.var_dir, "S2-variants.vcf")
     ]
     with make_workdir() as workdir:
         config = load_config(
             get_post_process_yaml(self.automated_dir, workdir))
         config["algorithm"] = {}
     region_dir = os.path.join(self.var_dir, "S1_S2-combined-regions")
     if os.path.exists(region_dir):
         shutil.rmtree(region_dir)
     if os.path.exists(self.combo_file):
         os.remove(self.combo_file)
     reqs = {"type": "local", "cores": 1}
     with prun.start(reqs, [[config]], config) as run_parallel:
         vcfutils.parallel_combine_variants(
             files, self.combo_file, self.ref_file, config, run_parallel)
     for fname in files:
         if os.path.exists(fname + ".gz"):
             subprocess.check_call(["gunzip", fname + ".gz"])
         if os.path.exists(fname + ".gz.tbi"):
             os.remove(fname + ".gz.tbi")
开发者ID:DoaneAS,项目名称:bcbio-nextgen,代码行数:26,代码来源:test_pipeline.py

示例4: test_10_umi

def test_10_umi(install_test_files, data_dir):
    """Allow BAM files as input to pipeline.
    """
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, "run_info-umi.yaml")]
        subprocess.check_call(cl)
开发者ID:biocyberman,项目名称:bcbio-nextgen,代码行数:8,代码来源:test_automated_analysis.py

示例5: test_7b_cancer_precall

def test_7b_cancer_precall(install_test_files, data_dir):
    """Test somatic prioritization and effects prediction with pre-called inputs.
    """
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, "run_info-cancer3.yaml")]
        subprocess.check_call(cl)
开发者ID:chapmanb,项目名称:bcbio-nextgen,代码行数:8,代码来源:test_automated_analysis.py

示例6: test_9_joint

def test_9_joint(install_test_files, data_dir):
    """Perform joint calling/backfilling/squaring off following variant calling.
    """
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, "run_info-joint.yaml")]
        subprocess.check_call(cl)
开发者ID:biocyberman,项目名称:bcbio-nextgen,代码行数:8,代码来源:test_automated_analysis.py

示例7: test_7_cancer

def test_7_cancer(install_test_files, data_dir):
    """Test paired tumor-normal calling using multiple
    calling approaches: MuTect, VarScan, FreeBayes.
    """
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, "run_info-cancer.yaml")]
        subprocess.check_call(cl)
开发者ID:biocyberman,项目名称:bcbio-nextgen,代码行数:9,代码来源:test_automated_analysis.py

示例8: test_srnaseq_bowtie

def test_srnaseq_bowtie(install_test_files, data_dir):
    """Run an sRNA-seq analysis.
    """
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, os.pardir, "test_srnaseq"),
              os.path.join(data_dir, "run_info-srnaseq_bowtie.yaml")]
        subprocess.check_call(cl)
开发者ID:biocyberman,项目名称:bcbio-nextgen,代码行数:9,代码来源:test_automated_analysis.py

示例9: test_7_cancer_nonormal

def test_7_cancer_nonormal(install_test_files, data_dir):
    """Test cancer calling without normal samples or with normal VCF panels.
    Requires MuTect and GATK.
    """
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, "run_info-cancer2.yaml")]
        subprocess.check_call(cl)
开发者ID:biocyberman,项目名称:bcbio-nextgen,代码行数:9,代码来源:test_automated_analysis.py

示例10: test_2_rnaseq

def test_2_rnaseq(install_test_files, data_dir):
    """Run an RNA-seq analysis with TopHat and generate gene-level counts.
    """
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, os.pardir, "110907_ERP000591"),
              os.path.join(data_dir, "run_info-rnaseq.yaml")]
        subprocess.check_call(cl)
开发者ID:biocyberman,项目名称:bcbio-nextgen,代码行数:9,代码来源:test_automated_analysis.py

示例11: test_3_full_pipeline

def test_3_full_pipeline(install_test_files, data_dir):
    """Run full automated analysis pipeline with multiplexing.
    """
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, os.pardir, "110106_FC70BUKAAXX"),
              os.path.join(data_dir, "run_info.yaml")]
        subprocess.check_call(cl)
开发者ID:biocyberman,项目名称:bcbio-nextgen,代码行数:9,代码来源:test_automated_analysis.py

示例12: test_2_scrnaseq

def test_2_scrnaseq(install_test_files, data_dir):
    """Run a single-cell RNA-seq analysis
    """
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, os.pardir, "Harvard-inDrop"),
              os.path.join(data_dir, "run_info-scrnaseq.yaml")]
        subprocess.check_call(cl)
开发者ID:biocyberman,项目名称:bcbio-nextgen,代码行数:9,代码来源:test_automated_analysis.py

示例13: test_2_star

def test_2_star(install_test_files, data_dir):
    """Run an RNA-seq analysis with STAR and generate gene-level counts.
    """
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, os.pardir, "test_fusion"),
              os.path.join(data_dir, "run_info-star.yaml")]
        subprocess.check_call(cl)
开发者ID:biocyberman,项目名称:bcbio-nextgen,代码行数:9,代码来源:test_automated_analysis.py

示例14: test_2_fastrnaseq

def test_2_fastrnaseq(install_test_files, data_dir):
    """Run a fast RNA-seq analysis
    """
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, os.pardir, "test_fusion"),
              os.path.join(data_dir, "run_info-fastrnaseq.yaml")]
        subprocess.check_call(cl)
开发者ID:biocyberman,项目名称:bcbio-nextgen,代码行数:9,代码来源:test_automated_analysis.py

示例15: test_4_empty_fastq

def test_4_empty_fastq(install_test_files, data_dir):
    """Handle analysis of empty fastq inputs from failed runs.
    """
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, os.pardir, "110221_empty_FC12345AAXX"),
              os.path.join(data_dir, "run_info-empty.yaml")]
        subprocess.check_call(cl)
开发者ID:biocyberman,项目名称:bcbio-nextgen,代码行数:9,代码来源:test_automated_analysis.py


注:本文中的tests.conftest.make_workdir函数示例由纯净天空整理自Github/MSDocs等开源代码及文档管理平台,相关代码片段筛选自各路编程大神贡献的开源项目,源码版权归原作者所有,传播和使用请参考对应项目的License;未经允许,请勿转载。