Python getpathの例

コード例 #1

def test_pipeline_manager():

    from sequana.pipelines_common import PipelineManager
    from sequana.pipelines_common import SequanaManager
    from sequana.pipelines_common import InputOptions
    from sequana.pipelines_common import SlurmOptions
    from sequana.pipelines_common import SnakemakeOptions
    from sequana.pipelines_common import GeneralOptions
    from sequana.pipelines_common import CutadaptOptions

    p = argparse.ArgumentParser()
    so = GeneralOptions()
    so.add_options(p)

    so = InputOptions()
    so.add_options(p)

    so = SnakemakeOptions()
    so.add_options(p)

    so = SlurmOptions()
    so.add_options(p)

    so = CutadaptOptions()
    so.add_options(p)

    from tempfile import TemporaryDirectory
    with TemporaryDirectory() as fout:
        options = p.parse_args(["--working-directory", fout, "--force"])

        pm = SequanaManager(options, "quality_control")

        from sequana.pipelines_common import get_pipeline_location as getpath
        sharedir = getpath('quality_control')

        pm.config.config.input_directory = sharedir
        pm.config.config.input_readtag = options.input_readtag
        pm.config.config.input_pattern = options.input_pattern
        pm.setup()
        pm.update_config(pm.config.config, options, "cutadapt")
        pm.teardown()

    options = p.parse_args([
        "--working-directory", fout, "--force", "--run-mode", "local",
        "--slurm-queue", "common"
    ])
    pm = PipelineManager(options, "quality_control")
    pm.setup()

    options = p.parse_args([
        "--working-directory", fout, "--force", "--run-mode", "slurm",
        "--slurm-queue", "common"
    ])
    pm = PipelineManager(options, "quality_control")
    pm.setup()

コード例 #2

ファイル: test_main.py プロジェクト: sequana/mapper

import easydev
import os
import tempfile
import subprocess
import sys
from sequana.pipelines_common import get_pipeline_location as getpath

sharedir = getpath('mapper')


def test_standalone_subprocess():
    directory = tempfile.TemporaryDirectory()
    cmd = """sequana_pipelines_mapper --input-directory {} 
            --working-directory {} --force""".format(sharedir, directory.name)
    subprocess.call(cmd.split())


def test_standalone_script():
    directory = tempfile.TemporaryDirectory()
    import sequana_pipelines.mapper.main as m
    sys.argv = ["test", "--input-directory", sharedir, 
            "--reference-file", sharedir + "/measles.fa",
            "--working-directory", directory.name, "--force"]
    m.main()


def test_standalone_script_minimap2():
    directory = tempfile.TemporaryDirectory()
    import sequana_pipelines.mapper.main as m
    sys.argv = ["test", "--input-directory", sharedir, 
            "--reference-file", sharedir + "/measles.fa",

コード例 #3

ファイル: test_main.py プロジェクト: minghao2016/rnaseq

import easydev
import os
import tempfile
import subprocess
import sys
from sequana.pipelines_common import get_pipeline_location as getpath

sharedir = getpath("rnaseq")
saccer3 = getpath("rnaseq") + "/Saccer3/"

#sequana_path = easydev.get_package_location('sequana_rnaseq')
#sharedir = os.sep.join([sequana_path , "sequana", 'data'])


def test_standalone_subprocess():
    directory = tempfile.TemporaryDirectory()
    cmd = """sequana_pipelines_rnaseq --input-directory {} --working-directory {} --rnadiff-mode one_factor""".format(
        sharedir, directory.name)
    subprocess.call(cmd.split())


def test_standalone_script():
    directory = tempfile.TemporaryDirectory()
    import sequana_pipelines.rnaseq.main as m
    sys.argv = [
        "test", "--input-directory", sharedir, "--genome-directory", saccer3,
        "--force", "--aligner", "bowtie2", "--rnadiff-mode", "one_factor",
        "--feature-counts-feature-type", 'gene,tRNA', "--rRNA-feature",
        "rRNA_gene"
    ]  # ideally should be rRNA but current
    m.main()

コード例 #4

import easydev
import os
import tempfile
import subprocess
import sys
from sequana.pipelines_common import get_pipeline_location as getpath

sharedir = getpath('merge_flowcells')
data1 = sharedir + "/flowcell1"
data2 = sharedir + "/flowcell2"


def test_standalone_subprocess():
    directory = tempfile.TemporaryDirectory()
    cmd = """sequana_pipelines_merge_flowcells --flowcells {} {}
            --working-directory {} --force""".format(data1, data2,
                                                     directory.name)
    subprocess.call(cmd.split())


def test_standalone_script():
    directory = tempfile.TemporaryDirectory()
    import sequana_pipelines.merge_flowcells.main as m
    sys.argv = [
        "test", "--flowcell-paths", data1, data2, "--working-directory",
        directory.name, "--force"
    ]
    m.main()


def test_full():

コード例 #5

ファイル: test_main.py プロジェクト: sequana/downsampling

import easydev
import os
import tempfile
import subprocess
import sys
from sequana.pipelines_common import get_pipeline_location as getpath

sharedir = getpath('downsampling')


def test_standalone_subprocess():
    directory = tempfile.TemporaryDirectory()
    cmd = """sequana_pipelines_downsampling --input-directory {}
            --working-directory {} --force""".format(sharedir, directory.name)
    subprocess.call(cmd.split())


def test_standalone_script():
    directory = tempfile.TemporaryDirectory()
    import sequana_pipelines.downsampling.main as m
    sys.argv = ["test", "--input-directory", sharedir, 
            "--working-directory", directory.name, "--force"]
    m.main()


def test_full():

    with tempfile.TemporaryDirectory() as directory:
        wk = directory
        cmd = "sequana_pipelines_downsampling --input-directory {} "
        cmd += "--working-directory {}  --force"