def get_rule_doc_snakemake(name):
"""Decode and return lines of the docstring(s) for the object."""
from sequana import Module
import snakemake
rule = Module(name)
wf = snakemake.Workflow(rule.path + "/%s.rules" % name)
wf.include(rule.path + "/%s.rules" % name)
docstring = list(wf.rules)[0].docstring
return docstring
def test_sequana_config():
s = snaketools.Module("compressor")
config = snaketools.SequanaConfig(s.config)
assert config.config.get("compressor")["source"] == "fastq.gz"
assert config.config.get("kraken:dummy") == None
# --------------------------------- tests different constructors
config = snaketools.SequanaConfig()
config = snaketools.SequanaConfig({"test": 1})
assert config.config.test == 1
# with a dictionary
config = snaketools.SequanaConfig(config.config)
# with a sequanaConfig instance
config = snaketools.SequanaConfig(config)
# with a non-yaml file
try:
json = sequana_data('test_summary_fastq_stats.json')
config = snaketools.SequanaConfig(json)
assert False
except:
assert True
try:
config = snaketools.SequanaConfig("dummy_dummy")
assert False
except:
assert True
# Test an exception
s = snaketools.Module("compressor")
config = snaketools.SequanaConfig(s.config)
config._recursive_update(config._yaml_code,
{"input_directory_dummy": "test"})
#config.check_config_with_schema(s.schema_config)
# loop over all pipelines, read the config, save it and check the content is
# identical. This requires to remove the templates. We want to make sure the
# empty strings are kept and that "no value" are kept as well
#
# field1: ""
# field2:
#
# is unchanged
from easydev import TempFile
output = TempFile(suffix=".yaml")
for pipeline in snaketools.pipeline_names:
config_filename = Module(pipeline)._get_config()
cfg1 = SequanaConfig(config_filename)
cfg1.cleanup() # remove templates and strip strings
cfg1.save(output.name)
cfg2 = SequanaConfig(output.name)
assert cfg2._yaml_code == cfg1._yaml_code
cfg2._update_config()
assert cfg1.config == cfg2.config
output.delete()
def get_rule_doc(name):
"""Decode and return the docstring(s) of a sequana/snakemake rule."""
url = "https://raw.githubusercontent.com/sequana/sequana_{}/master/README.rst".format(name)
data = urllib.request.urlopen(url).read().decode("utf8")
try:
from sequana import Module
m = Module(name)
version = m.version
except:
version = "?"
docstring = "**current version**:{}\n\n{}".format(version, data)
return docstring
def test_import_config_from_menu(qtbot):
widget = sequana_gui.SequanaGUI(ipython=True)
qtbot.addWidget(widget)
assert widget.sequana_factory._imported_config is None
# while an existing config file should
# First, we simulate selection of quality control pipeline
index = widget.sequana_factory._choice_button.findText("quality_control")
widget.sequana_factory._choice_button.setCurrentIndex(index)
widget.ui.tabs_pipeline.setCurrentIndex(0) # set sequana pipeline mode
widget._update_sequana("quality_control")
qc = Module("quality_control")
widget.menuImportConfig(qc.config)
assert widget.sequana_factory._imported_config is not None
widget.close()
def get_rule_doc(name):
"""Decode and return the docstring(s) of a sequana/snakemake rule."""
try:
from sequana import Module
rule = Module(name)
filename = rule.path + "/%s.rules" % name
data = open(filename, "r").read()
except ValueError:
# a local file ?
data = open(name, "r").read()
# Try to identify the rule and therefore possible docstring
# It may be a standard rule or a dynamic rule !
# standard one
if name.endswith("_dynamic"):
name = name[:-8]
rulename_tag = "rule %s" % name
if rulename_tag in data:
data = data.split(rulename_tag, 1)[1]
else:
return "no docstring found for %s " % name
# Find first """ or ''' after the rule definition
single = data.find("'''")
double = data.find('"""')
if single > 0 and double > 0:
if single > double:
quotes = '"""'
else:
quotes = "'''"
elif single > 0:
quotes = "'''"
elif double > 0:
quotes = '"""'
else:
return "no docstring found for %s " % name
start = data.find(quotes)
end = data[start + 3:].find(quotes) + start + 3
if end == -1 or end < start:
return "no end of docstring found for %s " % name
docstring = data[start + 3:end]
return docstring
def test_pipeline_manager():
# test missing input_directory
cfg = SequanaConfig({})
try:
pm = snaketools.PipelineManager("custom", cfg)
assert False
except:
assert True
# normal behaviour but no input provided:
config = Module("quality_control")._get_config()
cfg = SequanaConfig(config)
cfg.cleanup() # remove templates
try:
pm = snaketools.PipelineManager("custome", cfg)
assert False
except:
assert True
cfg = SequanaConfig(config)
cfg.cleanup() # remove templates
file1 = sequana_data("Hm2_GTGAAA_L005_R1_001.fastq.gz")
file2 = sequana_data("Hm2_GTGAAA_L005_R2_001.fastq.gz")
cfg.config.input_samples['file1'] = file1
cfg.config.input_samples['file2'] = file2
pm = snaketools.PipelineManager("custome", cfg)
assert pm.paired == True
cfg = SequanaConfig(config)
cfg.cleanup() # remove templates
file1 = sequana_data("Hm2_GTGAAA_L005_R1_001.fastq.gz")
cfg.config.input_samples['file1'] = file1
pm = snaketools.PipelineManager("custome", cfg)
assert pm.paired == False
pm.getlogdir("fastqc")
pm.getwkdir("fastqc")
pm.getrawdata()
pm.getreportdir("test")
pm.getname("fastqc")
def sequana_init(options):
import sequana
from sequana.misc import textwrap
from sequana import SequanaConfig, sequana_data
sa = Tools(verbose=options.verbose)
# Check that the pipeline is well defined
module = Module(options.pipeline)
if os.path.exists(options.target_dir):
txt = "Will override the following files if present: %s.rules " +\
"config.yaml, runme.sh, ..."
sa.blue(txt % options.pipeline)
if options.force is True:
choice = "y"
else:
choice = input(
red("Do you want to proceed (to avoid this " +
" message, use --force)? [y]/n:"))
if choice == "n":
sys.exit(0)
# Copying snakefile
logger.info("Copying snakefile")
sa.mkdir(options.target_dir)
shutil.copy(module.snakefile,
options.target_dir + os.sep + options.pipeline + ".rules")
# Creating README to print on the screen and in a file
txt = "User command::\n\n"
txt += " %s \n\n" % " ".join(sys.argv)
txt += "You can now run snakemake yourself or type::"
txt += purple("""
snakemake -s %s.rules --stats stats.txt -p -j 4
""" % options.pipeline)
txt += """
# -j 4 means you will use 4 cores
# -p prints the commands used
# --stats stats.txt must be used since stats.txt is expected to be found.
or just run the bash script::
sh runme.sh
EDIT THE config.yaml if needed
Once finished with success, the report/ directory contains a summary.html
and relevant files (depends on the pipeline).
"""
logger.info("Creating README")
with open(options.target_dir + os.sep + "README", "w") as fh:
fh.write(txt.replace("\x1b[35m", "").replace("\x1b[39;49;00m", ""))
# Creating Config file
logger.info("Creating the config file")
# Create (if needed) and update the config file
config_filename = options.target_dir + os.sep + "config.yaml"
if options.config:
# full existing path
if os.path.exists(options.config):
shutil.copy(options.config, config_filename)
else: # or a sequana config file in the module path ?
raise (IOError("Config file %s not found locally" %
options.config))
else:
copy_config_from_sequana(module, "config.yaml", config_filename)
# Copy multiqc if it is available
multiqc_filename = options.target_dir + os.sep + "multiqc_config.yaml"
copy_config_from_sequana(module, "multiqc_config.yaml", multiqc_filename)
cluster_cfg_filename = options.target_dir + os.sep + "cluster_config.json"
copy_config_from_sequana(module, "cluster_config.json",
cluster_cfg_filename)
# The input
cfg = SequanaConfig(config_filename)
cfg.config.input_directory = options.input_directory
cfg.config.input_pattern = options.pattern
cfg.config.input_extension = options.extension
cfg.config.input_samples.file1 = options.file1
cfg.config.input_samples.file2 = options.file2
cfg.config.input_readtag = options.input_readtag
# Dedicated section for quality control section
if options.pipeline == "quality_control":
if options.design:
shutil.copy(options.design, options.target_dir + os.sep)
cfg.config['cutadapt'].design_file = os.path.basename(
options.design)
if options.kraken:
cfg.config.kraken.database_directory = os.path.abspath(
options.kraken)
cfg.config.kraken.do = True
else:
cfg.config.kraken.do = False
cfg.config['cutadapt'].fwd = options.adapter_fwd
cfg.config['cutadapt'].rev = options.adapter_rev
cfg.config['cutadapt'].adapter_type = options.adapters
# Foir all pipeline using BWA
if options.reference:
cfg.config.bwa_mem.reference = os.path.abspath(options.reference)
if options.pipeline == "variant_calling":
if options.reference:
cfg.config.bwa_mem_ref.reference = os.path.abspath(
options.reference)
if options.pipeline in ["rnaseq", "smallrnaseq"]:
if options.design:
shutil.copy(options.design, options.target_dir + os.sep)
cfg.config['cutadapt'].design_file = os.path.basename(
options.design)
cfg.config['cutadapt'].fwd = options.adapter_fwd
cfg.config['cutadapt'].rev = options.adapter_rev
cfg.config['cutadapt'].adapter_choice = options.adapters
cfg.copy_requirements(target=options.target_dir)
# FIXME If invalid, no error raised
if options.config_params:
params = [this.strip() for this in options.config_params.split(",")]
for param in params:
if param.count(":") not in [1, 2, 3]:
txt = "incorrect format following --config-params"
txt += "Expected at least one : sign or at most 2 of them"
txt += "Config file section such as :\n"
txt += "project: tutorial\n"
txt += "should be encoded project:tutorial"
raise ValueError(txt)
if param.count(":") == 1:
k, v = param.split(':')
cfg.config[k] = v
elif param.count(":") == 2:
k1, k2, v = param.split(":")
cfg.config[k1][k2] = v
elif param.count(":") == 3:
k1, k2, k3, v = param.split(":")
cfg.config[k1][k2][k3] = v
# important to update yaml with content of config
cfg._update_yaml()
cfg.save(config_filename)
# Creating a unique runme.sh file
runme_filename = options.target_dir + os.sep + "runme.sh"
with open(runme_filename, "w") as fout:
cmd = "#!/bin/sh\n"
cmd += "# generated with sequana version %s with this command:\n" % sequana.version
cmd += "# %s\n" % " ".join(sys.argv)
cmd += "snakemake -s %(project)s.rules --stats stats.txt -p -j %(jobs)s --nolock"
if options.forceall:
cmd += " --forceall "
if options.cluster:
# Do we want to include the cluster config option ?
cluster_config = Module(options.pipeline).cluster_config
if options.ignore_cluster_config is True:
cluster_config = None
if cluster_config is None:
cmd += ' --cluster "%s"' % options.cluster
else:
cmd += ' --cluster "%s" --cluster-config %s' %\
(options.cluster, os.path.basename(cluster_config))
if options.redirection:
cmd += " 1>run.out 2>run.err"
fout.write(
cmd % {
'project': options.pipeline,
'jobs': options.jobs,
"version": sequana.version
})
# change permission of runme.sh to 755
st = os.stat(runme_filename)
os.chmod(runme_filename, st.st_mode | 0o755)
sa.green("Initialisation of %s succeeded" % options.target_dir)
sa.green("Please, go to the project directory ")
sa.purple("\n cd %s\n" % options.target_dir)
sa.green("Check out the README and config.yaml files")
sa.green("A basic script to run the analysis is named runme.sh ")
sa.purple("\n sh runme.sh\n")
sa.purple("On a slurm cluster, you may type:")
sa.purple("\n srun --qos normal runme.sh\n")
sa.green(
"In case of trouble, please post an issue on https://github.com/sequana/sequana/issue "
)
sa.green(
"or type sequana --issue and fill a post with the error and the config file (NO DATA PLEASE)"
)
# Change permission
try: #python 3
os.chmod(runme_filename, 0o755)
except:
logger.info(
"Please use Python3. Change the mode of %s manually to 755" %
runme_filename)
def main(args=None):
"""Mostly checking the options provided by the user and then call
:func:`sequana_init` function to create the pre-filled config file +
snakemake + README +runme.sh in a dedicated project directory.
"""
import sequana
if args is None:
args = sys.argv[:]
user_options = Options(prog="sequana")
# If --help or no options provided, show the help
if len(args) == 1:
sa = Tools()
sa.purple("Welcome to Sequana standalone application")
logger.critical("You must use --pipeline <valid pipeline name>\nuse "
"--show-pipelines or --help for more information. ")
return
else:
options = user_options.parse_args(args[1:])
# these imports must be local. This also speed up the --help
sa = Tools(verbose=options.verbose)
sa.purple("Welcome to Sequana standalone application")
# Those options are mutually exclusive
flag = int(
"%s%s%s%s%s%s" %
(int(bool(options.issue)), int(bool(options.version)),
int(bool(options.info)), int(bool(options.show_pipelines)),
int(bool(options.pipeline)), int(bool(options.get_config))), 2)
if flag not in [1, 2, 4, 8, 16, 3, 32]:
logger.critical("You must use one of --pipeline, --info, "
"--show-pipelines, --issue, --version, --get-config")
sys.exit(1)
# OPTIONS that gives info and exit
if options.issue:
onweb('https://github.com/sequana/sequana/issues')
return
if options.version:
sa.purple("Sequana version %s" % sequana.version)
return
if options.show_pipelines:
sa.purple("Valid pipeline names:")
for this in sorted(valid_pipelines):
m = Module(this)
sa.green(" - " + this)
print(textwrap(m.overview, indent=8))
return
if options.info:
module = Module(options.info)
module.onweb()
return
if options.pipeline:
# check validity of the pipeline name
if options.pipeline not in valid_pipelines:
txt = "".join([" - %s\n" % this for this in valid_pipelines])
logger.critical("%s not a valid pipeline name. Use of one:\n" %
options.pipeline + txt)
sys.exit(1)
# copy locally the request config file from a specific pipeline
if flag == 3: #--get-config and --pipeline used
module = Module(options.pipeline)
copy_config_from_sequana(module)
return
# pipeline should be defined by now. Let us start the real work here
Module("dag").check("warning")
Module(options.pipeline).check("warning")
# If user provides file1 and/or file2, check the files exist
if options.file1 and os.path.exists(options.file1) is False:
raise ValueError("%s does not exist" % options.file1)
if options.file2 and os.path.exists(options.file2) is False:
raise ValueError("%s does not exist" % options.file2)
if options.kraken and os.path.exists(options.kraken) is False:
raise ValueError("%s does not exist" % options.kraken)
if options.input_directory and os.path.exists(
options.input_directory) is False:
raise ValueError("%s does not exist" % options.input_directory)
# check valid combo of arguments
flag = int(
"%s%s%s%s%s" % (
int(bool(options.pattern)),
int(bool(options.input_directory)),
int(bool(options.file1)),
int(bool(options.file2)),
int(bool(options.config)),
), 2)
# config file has flag 1, others have flag 2,4,8,16
# config file alone : 1
# --input-directory alone: 2
# --file1 alone: 4
# --file1 + --file2 : 2+4=6
# --input-pattern alone: 16
# none of those options redirect to input_directory=local
if flag not in [0, 1, 2, 4, 6, 8, 16]:
logger.critical(help_input + "\n\nUse --help for more information")
sys.exit(1)
assert options.extension in ["fastq", "fq", "fastq.gz", "fq.gz", "bam"]
# Note that we use abspath to make it more robust and easier to debug
# If no options, we use input_directory and set it to "."
if flag == 0 or options.input_directory:
if flag == 0:
options.input_directory = "."
options.input_directory = os.path.abspath(options.input_directory)
data = options.input_directory + os.sep + "*" + options.extension
options.file1 = ""
options.file2 = ""
options.pattern = ""
if options.verbose:
logger.info("Looking for sample files matching %s" % data)
elif options.pattern:
options.pattern = os.path.abspath(options.pattern)
data = os.path.abspath(options.pattern)
options.input_directory = ""
options.extension = ""
options.file1 = ""
options.file2 = ""
elif options.config:
pass
elif options.file1:
data = [options.file1]
options.file1 = os.path.abspath(options.file1)
if options.file2:
data = [options.file2]
options.file2 = os.path.abspath(options.file2)
options.input_directory = ""
options.pattern = ""
options.extension = ""
if options.extension == 'bam' or options.pattern.endswith('bam') or \
options.pattern.endswith('bed'):
ff = FileFactory(data)
else:
ff = FastQFactory(data,
read_tag=options.input_readtag,
verbose=options.verbose)
if options.pipeline == 'quality_control' or options.pipeline == 'rnaseq':
# check combo
flag = int(
"%s%s%s%s%s" %
(int(bool(options.no_adapters)), int(bool(options.design)),
int(bool(options.adapters)), int(bool(
options.adapter_fwd)), int(bool(options.adapter_rev))), 2)
if flag not in [16, 12, 6, 4, 2, 3]:
logger.critical(
"You must use a design experimental file using --design"
" and --adapters to indicate the type of adapters (PCRFree"
" or Nextera), or provide the adapters directly as a "
" string (or a file) using --adapter_fwd (AND --adapter_"
"rev for paired-end data). A third way is to set --adapters"
" to either Nextera, PCRFree, Rubicon or universal in which case "
" all adapters will be used (slower). Finally, you may use "
" --no-adapters for testing purpose or if you know there "
" is no adapters")
sys.exit(1)
# flag 12 (design + adapters when wrong args provided)
if options.design and options.adapters not in adapters_choice:
raise ValueError(
"When using --design, you must also "
"provide the type of adapters using --adapters (set to "
"one of %s )" % adapters_choice)
if options.design and options.adapters:
from sequana import FindAdaptersFromDesign
fa = FindAdaptersFromDesign(options.design, options.adapters)
fa.check()
# flag 12 (design + adapters with correct args)
elif options.design and options.adapters in adapters_choice:
options.adapters_fwd = options.adapters
options.adapters_rev = options.adapters
elif options.no_adapters:
options.adapter_fwd = "XXXX"
options.adapter_rev = "XXXX"
else:
if options.adapter_fwd is None:
if options.adapters not in ["universal"] + adapters_choice:
msg = "Incorrect adapter choice %s. " % options.adapters
msg += "Correct values are :\n"
for this in ['universal'] + adapters_choice:
msg += " - {}\n ".format(this)
logger.error(msg)
raise ValueError
# flag 4
if options.adapters == "universal":
options.adapter_fwd = "GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGC"
options.adapter_rev = "TCTAGCCTTCTCGCAGCACATCCCTTTCTCACATCTAGAGCCACCAGCGGCATAGTAA"
# flag 4
else:
# Let the pipeline handle the names
options.adapter_fwd = options.adapters
options.adapter_rev = options.adapters
# flag 2/3
else:
if options.adapter_fwd:
# Could be a string or a file. If a file, check the format
if os.path.exists(options.adapter_fwd):
AdapterReader(options.adapter_fwd)
options.adapter_fwd = "file:%s" % options.adapter_fwd
if options.adapter_rev:
# Could be a string or a file. If a file, check the format
if os.path.exists(options.adapter_rev):
AdapterReader(options.adapter_rev)
options.adapter_rev = "file:%s" % options.adapter_rev
if options.design:
# Just check the format
adapter_finder = FindAdaptersFromDesign(options.design,
options.adapters)
# If all options are valid, we can now create the tree structure
sequana_init(options)
def test_md5():
from sequana import Module
m = Module("quality_control")
data = m.md5()
def main(args=None):
user_options = Options(prog="sequana")
if args is None:
args = sys.argv
# If --help or no options provided, show the help
if len(args) == 1:
user_options.parse_args(["prog", "--help"])
else:
options = user_options.parse_args(args[1:])
if options.version:
import sequana
print(sequana.version)
sys.exit()
if options.jobs > 20 and options.bypass is False:
raise ValueError('The number of jobs is limited to 20. You can ' +
'force this limit by using --bypass-job-limit')
if misc.on_cluster("tars-") and options.unlock is False:
if options.cluster is None:
raise ValueError("You are on TARS (Institut Pasteur). You " +
" must use --cluster option to provide the scheduler " +
" options (typically ' --cluster 'sbatch --qos normal' )")
# valid codecs:
valid_extensions = [("fastq." + ext2).rstrip(".")
for ext2 in ['', 'bz2', 'gz', 'dsrc']]
valid_extensions += [("fq." + ext2).rstrip(".")
for ext2 in ['', 'bz2', 'gz', 'dsrc']]
valid_combos = [(x, y) for x in valid_extensions
for y in valid_extensions
if x!=y]
if (options.source, options.target) not in valid_combos:
raise ValueError("""--target and --source combo not valid.
Must be one of fastq, fastq.gz, fastq.bz2 or fastq.dsrc""")
# Create the config file locally
module = Module("compressor")
with TempFile(suffix=".yaml", dir=".") as temp:
cfg = SequanaConfig(module.config)
cfg.config.compressor.source = options.source
cfg.config.compressor.target = options.target
cfg.config.compressor.recursive = options.recursive
cfg.config.compressor.verbose = options.verbose
cfg.config.compressor.threads = options.threads
cfg._update_yaml()
cfg.save(filename=temp.name)
# The Snakefile can stay in its original place:
rule = module.path + os.sep + "compressor.rules"
# Run the snakemake command itself.
cmd = 'snakemake -s %s --configfile %s -j %s ' % \
(rule, temp.name, options.jobs)
if options.dryrun:
cmd += " --dryrun "
if options.verbose is False:
cmd += " --quiet "
else:
cmd += " -p "
# for slurm only: --cores-per-socket
if options.cluster:
cluster = ' --cluster "%s" ' % options.cluster
cmd += cluster
if options.snakemake:
if " -s " in options.snakemake or " -j " in options.snakemake:
raise ValueError("-s or -j cannot be used in " +
" --snakemake-options (already used internally")
cmd += options.snakemake
if options.unlock:
cmd += " --unlock "
if options.verbose:
print(cmd)
# On travis, snakemake.shell command from snakemake fails.
# Most probably because travis itself uses a subprocess.
# excute from easydev uses pexpect.spawn, which seems to work well
from easydev import execute
execute(cmd, showcmd=False)
def module():
return Module("quality_control")
def test_md5():
from sequana import Module
m = Module("compressor")
data = m.md5()
def test_pipeline_manager():
# test missing input_directory
cfg = SequanaConfig({})
try:
pm = snaketools.PipelineManager("custom", cfg)
assert False
except:
assert True
# normal behaviour but no input provided:
config = Module("compressor")._get_config()
cfg = SequanaConfig(config)
cfg.cleanup() # remove templates
try:
pm = snaketools.PipelineManager("custome", cfg)
assert False
except:
assert True
cfg = SequanaConfig(config)
cfg.cleanup() # remove templates
file1 = sequana_data("Hm2_GTGAAA_L005_R1_001.fastq.gz")
cfg.config.input_directory, cfg.config.input_pattern = os.path.split(file1)
#file2 = sequana_data("Hm2_GTGAAA_L005_R2_001.fastq.gz")
pm = snaketools.PipelineManager("custom", cfg)
assert pm.paired == False
cfg = SequanaConfig(config)
cfg.cleanup() # remove templates
cfg.config.input_directory, cfg.config.input_pattern = os.path.split(file1)
cfg.config.input_pattern = "Hm*gz"
#file1 = sequana_data("Hm2_GTGAAA_L005_R1_001.fastq.gz")
pm = snaketools.PipelineManager("custom", cfg)
pm.plot_stats()
assert pm.paired == True
pm.getlogdir("fastqc")
pm.getwkdir("fastqc")
pm.getrawdata()
pm.getreportdir("test")
pm.getname("fastqc")
# Test different configuration of input_directory, input_readtag,
# input_pattern
# Test the _R[12]_ paired
with tempfile.TemporaryDirectory() as tmpdir:
cfg = SequanaConfig()
cfgname = tmpdir + "/config.yaml"
cfg.config.input_pattern = "*fastq.gz"
cfg.config.input_directory = tmpdir
cfg.config.input_readtag = "_R[12]_"
cfg._update_yaml()
cfg.save(cfgname)
cmd = "touch {}/test_R1_.fastq.gz".format(tmpdir)
subprocess.call(cmd.split())
cmd = "touch {}/test_R2_.fastq.gz".format(tmpdir)
subprocess.call(cmd.split())
pm = snaketools.PipelineManager("test", cfgname)
assert pm.paired == True
# Test the _[12]_ paired
with tempfile.TemporaryDirectory() as tmpdir:
cfg = SequanaConfig()
cfgname = tmpdir + "/config.yaml"
cfg.config.input_pattern = "*fastq.gz"
cfg.config.input_directory = tmpdir
cfg.config.input_readtag = "_[12]."
cfg._update_yaml()
cfg.save(cfgname)
cmd = "touch {}/test_1.fastq.gz".format(tmpdir)
subprocess.call(cmd.split())
cmd = "touch {}/test_2.fastq.gz".format(tmpdir)
subprocess.call(cmd.split())
pm = snaketools.PipelineManager("test", cfgname)
assert pm.paired is True
# Test the _R[12]_ single end
with tempfile.TemporaryDirectory() as tmpdir:
cfg = SequanaConfig()
cfgname = tmpdir + "/config.yaml"
cfg.config.input_pattern = "*fastq.gz"
cfg.config.input_directory = tmpdir
cfg.config.input_readtag = "_R[12]_"
cfg._update_yaml()
cfg.save(cfgname)
cmd = "touch {}/test_R1_.fastq.gz".format(tmpdir)
subprocess.call(cmd.split())
pm = snaketools.PipelineManager("test", cfgname)
assert pm.paired is False
# Test the _R[12]_ single end
with tempfile.TemporaryDirectory() as tmpdir:
cfg = SequanaConfig()
cfgname = tmpdir + "/config.yaml"
cfg.config.input_pattern = "*fq.gz" # wrong on purpose
cfg.config.input_directory = tmpdir
cfg.config.input_readtag = "_R[12]_"
cfg._update_yaml()
cfg.save(cfgname)
cmd = "touch {}/test_R1_.fastq.gz".format(tmpdir)
subprocess.call(cmd.split())
try:
pm = snaketools.PipelineManager("test", cfgname)
assert False
except:
assert True
# Test the _R[12]_ single end
with tempfile.TemporaryDirectory() as tmpdir:
cfg = SequanaConfig()
cfgname = tmpdir + "/config.yaml"
cfg.config.input_pattern = "*fastq.gz"
cfg.config.input_directory = tmpdir
cfg.config.input_readtag = "R[12]_"
cfg._update_yaml()
cfg.save(cfgname)
cmd = "touch {}/testR1_.fastq.gz".format(tmpdir)
subprocess.call(cmd.split())
cmd = "touch {}/testR2_.fastq.gz".format(tmpdir)
subprocess.call(cmd.split())
try:
pm = snaketools.PipelineManager("test", cfgname)
assert False
except:
assert True
def test_module_version():
Module("snpeff/1.0").version == "1.0"
def test_check_config_with_schema():
schema = Module("compressor").schema_config
SequanaConfig(Module("compressor").config).check_config_with_schema(schema)
def test_md5():
from sequana import Module
m = Module("quality_control")
data = m.md5()