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()
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",
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()
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():
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"