def to_js(self, output="krona.html", onweb=False):
if self._data_created == False:
status = self.kraken_to_krona()
execute("ktImportText %s -o %s" % (self.output_filename, output))
if onweb is True:
import easydev
easydev.onweb(output)
def to_js(self, output="krona.html", onweb=False):
if self._data_created == False:
status = self.kraken_to_krona()
execute("ktImportText %s -o %s" % (self.output_filename, output))
if onweb is True:
import easydev
easydev.onweb(output)
def gdsctools_help(name=None):
if name is None:
easydev.onweb('http://gdsctools.readthedocs.org')
else:
url = "http://gdsctools.readthedocs.org/en/master/references.html"
try:
url += '#module-' + name.__module__
except:
print("Not a known gdsctools class or function")
easydev.onweb(url)
def gdsctools_help(name=None):
import easydev
if name is None:
easydev.onweb('http://gdsctools.readthedocs.org')
else:
url = "http://gdsctools.readthedocs.org/en/master/references.html"
try:
url += '#module-' + name.__module__
except:
print("Not a known gdsctools class or function")
easydev.onweb(url)
def on_web(self, identifier):
"""Open a tab related to the COSMIC identifier (in your browser)"""
from easydev import onweb
url = self._get_url(identifier)
onweb(url)
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 main(args=None):
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:
user_options.parse_args(["prog", "--help"])
else:
options = user_options.parse_args(args[1:])
sequana_debug_level(options.logging_level)
if options.download_reference:
logger.info("Downloading reference %s from %s\n" %
(options.download_reference, options.database))
from bioservices.apps import download_fasta as df
df.download_fasta(options.download_reference, method=options.database)
if options.download_genbank is None:
return
if options.download_genbank:
logger.info("Downloading genbank %s from %s\n" %
(options.download_reference, options.database))
from sequana.snpeff import download_fasta_and_genbank
download_fasta_and_genbank(options.download_genbank,
options.download_genbank,
genbank=True, fasta=False)
return
if options.genbank:
assert os.path.exists(options.genbank), \
"%s does not exists" % options.genbank
if options.verbose:
logger.info("Reading %s. This may take time depending on "
"your input file" % options.input)
# Convert BAM to BED
if options.input.endswith(".bam"):
bedfile = options.input.replace(".bam", ".bed")
if options.verbose:
logger.info("Converting BAM into BED file")
shellcmd("bedtools genomecov -d -ibam %s > %s" % (options.input, bedfile))
elif options.input.endswith(".bed"):
bedfile = options.input
else:
raise ValueError("Input file must be a BAM or BED file")
# Set the thresholds
if options.low_threshold is None:
options.low_threshold = -options.threshold
if options.high_threshold is None:
options.high_threshold = options.threshold
# and output directory
config.output_dir = options.output_directory
config.sample_name = os.path.basename(options.input).split('.')[0]
# Now we can create the instance of GenomeCoverage
gc = GenomeCov(bedfile, options.genbank, options.low_threshold,
options.high_threshold, 0.5, 0.5)
# if we have the reference, let us use it
if options.reference:
logger.info('Computing GC content')
gc.compute_gc_content(options.reference, options.w_gc,
options.circular)
# Now we scan the chromosomes,
if len(gc.chr_list) == 1:
if options.verbose:
logger.warning("There is only one chromosome. Selected automatically.")
chrom = gc.chr_list[0]
chromosomes = [chrom]
run_analysis(chrom, options, gc.feature_dict)
elif options.chromosome <=-1 or options.chromosome > len(gc.chr_list):
raise ValueError("invalid chromosome index ; must be in [1-{}]".format(len(gc.chr_list)+1))
else: # chromosome index is zero
# For user, we start at position 1 but in python, we start at zero
if options.chromosome:
chromosomes = [gc[options.chromosome-1]]
else:
chromosomes = gc
if options.verbose:
print("There are %s chromosomes/contigs." % len(gc))
for this in gc.chr_list:
print(" {}".format(this.chrom_name))
for i, chrom in enumerate(chromosomes):
if options.verbose:
print("==================== analysing chrom/contig %s/%s (%s)"
% (i + options.chromosome, len(gc),
chrom.chrom_name))
run_analysis(chrom, options, gc.feature_dict)
if options.verbose:
logger.info("Creating report in %s. Please wait" % config.output_dir)
if options.chromosome:
cc = options.chromosome - 1
datatable = CoverageModule.init_roi_datatable(gc[cc])
ChromosomeCoverageModule(chromosomes[0], datatable, None)
page = "{0}{1}{2}.cov.html".format(config.output_dir, os.sep,
chrom.chrom_name)
else:
CoverageModule(gc)
page = "{0}{1}coverage.html".format(config.output_dir, os.sep)
if options.show_html:
from easydev import onweb
onweb(page)
def show(self):
"""Opens the filename defined in the constructor"""
from easydev import onweb
onweb(self.output)
def onweb(self):
from easydev import onweb
onweb(self.settings.directory + os.sep + 'index.html')
def onweb(self):
"""Open the HTML document in a browser"""
from easydev import onweb
onweb(self.abspath)
def onweb(self):
from easydev import onweb
onweb(self.settings.directory + os.sep + 'index.html')
def onweb(self):
"""Open the HTML document in a browser"""
from easydev import onweb
onweb(self.abspath)
def show(self):
"""Opens the filename defined in the constructor"""
from easydev import onweb
onweb(self.output)
def on_web(self, identifier):
"""Open a tab related to the COSMIC identifier (in your browser)"""
from easydev import onweb
url = self._get_url(identifier)
onweb(url)
