def test_duplicated_design():
filename = sequana_data("test_expdesign_hiseq_duplicated_index.csv")
ss = FindAdaptersFromDesign(filename, "Small")
res = ss.get_adapters_from_sample("VB-22")
assert res['index1']['fwd'].identifier == "Small_Adapter_5|name:small5|seq:ACAGTG"
assert res['index1']['fwd'].sequence == "CAAGCAGAAGACGGCATACGAGATACAGTGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA"
def test_wrong_design():
design = sequana_data("test_expdesign_wrong.csv")
ad = FindAdaptersFromDesign(design, "NEXTFlex48_DNA")
try:
ad.check()
assert False
except:
assert True
def test_wrong_design():
design = sequana_data("test_expdesign_wrong.csv")
ad = FindAdaptersFromDesign(design, "PCRFree")
try:
ad.check()
assert False
except:
assert True
def test_nextera():
# simple indexing
design = sequana_data("test_index_mapper.csv")
ad = FindAdaptersFromDesign(design, "Nextera")
results = ad.get_adapters_from_sample("C4405-M1-EC1")
assert results['index1']['fwd'][0].identifier == 'Nextera_index_N703|name:N703|seq:AGGCAGAA'
ad.check() # all samples are used in get_adapters_from_sample
ad.sample_names
fwd, rev = ad.save_adapters_to_fasta("C4405-M1-EC1")
os.remove(fwd)
os.remove(rev)
# double indexing
design = sequana_data("test_expdesign_hiseq_doubleindex.csv")
fa = FindAdaptersFromDesign(design, "Nextera")
fa.check()
def test_all_adapters():
# test all adapters using a dummy design file.
design = sequana_data("test_index_mapper.csv")
"""TODO
adapters_NEBNext2_fwd.fa
adapters_NEBNext_fwd.fa
dapters_Small_fwd.fa
adapters_NEBNextOligos_fwd.fa
adapters_SMARTer_fwd.f
adapters_Nextera_2_fwd.fa
"""
for this in ['TruSeq', 'Nextera', 'NEXTFlex48_DNA', 'Small', 'NEBNext']:
#'NEXTFlex96_DNA', 'TruSeqCD_DNA', 'TruSeqUD']:
fa = FindAdaptersFromDesign(design, this)
res = fa.get_adapters_from_sample("C1152-S2-EC1")
_check_content(res)
# Nextera
fa = FindAdaptersFromDesign(design, "Nextera")
res = fa.get_adapters_from_sample("C1152-S2-EC1")
assert "revc" in res['universal']
assert "seq:TAAGGCGA" in res['index1']['fwd'][0].identifier
assert "transposase_seq_1" in res.keys()
assert "transposase_seq_2" in res.keys()
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_wrong_sample():
design = sequana_data("test_index_mapper.csv")
ad = FindAdaptersFromDesign(design, "TruSeq")
res = ad.get_adapters_from_sample("C4405-M1-EC1")
assert res['index1']['fwd'] is None
assert res['index1']['revc'] is None
def test_nextflex48():
design = sequana_data("test_index_mapper.csv")
try:
ad = FindAdaptersFromDesign(design, "error")
assert False
except Exception:
assert True
# Other input from PCRFree NextFlex48
ad = FindAdaptersFromDesign(design, "NEXTFlex48_DNA")
# Test the index1/2_seq with 3 cases
# index1 present only,
# no index at all (None)
# index1 and index2 present
design1 = sequana_data("test_expdesign_hiseq.csv")
ad1 = FindAdaptersFromDesign(design1, "NEXTFlex48_DNA")
ad1.check()
res1 = ad1.get_adapters_from_sample("553-iH2-1")
res2 = ad1.get_adapters_from_sample("539-st2")
res3 = ad1.get_adapters_from_sample("107-st2")
assert res1['index1'][
'fwd'].identifier == "NEXTFlex48_DNA|name:8|seq:TTAGGC"
assert res1['index1']['fwd'].name == "8"
assert res1['index1']['revc'].name == "8"
assert list(res2.keys()) == ["universal"]
assert res3['index1']['fwd'].name == "9"
assert res3['index1']['revc'].name == "9"
assert res3['index2']['fwd'].name == "10"
assert res3['index2']['revc'].name == "10"
# double indexing
# This is a double indexing for PCRFree, which has not been tested
# since it requires 16S adapters not yet in sequana
"""design2 = sequana_data("test_expdesign_miseq_illumina2.csv")
ad2 = FindAdaptersFromDesign(design2, "PCRFree")
assert ad2.get_adapters_from_sample('M2')['index1']['fwd'].identifier == \
'NextFlex_PCR_Free_adapter2|name:2|seq:TGACCA'
assert ad2.get_adapters_from_sample('M2')['index2']['fwd'].identifier == \
'NextFlex_PCR_Free_adapter13|name:13|seq:AGTCAA'
"""
design = sequana_data("test_expdesign_miseq_illumina.csv")
ad = FindAdaptersFromDesign(design, "NEXTFlex48_DNA")
res = ad.get_adapters_from_sample("CR81-L1236-P1")
assert res['index1'][
'fwd'].identifier == 'NEXTFlex48_DNA|name:1|seq:CGATGT'
design1 = sequana_data("test_expdesign_miseq_illumina_1.csv")
ad = FindAdaptersFromDesign(design1, "NEXTFlex48_DNA")
ad.check() # all sample names must be found
res = ad.get_adapters_from_sample("CM-2685")['index1']['fwd']
assert res.name == "3"
def test_all_adapters():
# test all adapters using a dummy design file.
design = sequana_data("test_index_mapper.csv")
# Rubicon
fa = FindAdaptersFromDesign(design, "Rubicon")
res = fa.get_adapters_from_sample("C1152-S2-EC1")
assert "PolyA" not in res.keys()
assert "PolyT" not in res.keys()
assert "universal" in res.keys()
assert "fwd" in res['universal']
assert "rev" in res['universal']
# TruSeq
fa = FindAdaptersFromDesign(design, "TruSeq")
res = fa.get_adapters_from_sample("C1152-S2-EC1")
assert "PolyA" in res.keys()
assert "PolyT" in res.keys()
assert "universal" in res
assert "fwd" in res['universal']
assert "rev" in res['universal']
# Nextera
fa = FindAdaptersFromDesign(design, "Nextera")
res = fa.get_adapters_from_sample("C1152-S2-EC1")
assert res['index1']['fwd'][0].identifier == "Nextera_index_N701|name:N701|seq:TAAGGCGA"
assert "transposase_seq_1" in res.keys()
assert "transposase_seq_2" in res.keys()
assert "universal" in res.keys()
assert "fwd" in res['universal']
assert "rev" in res['universal']
# PCRFree
fa = FindAdaptersFromDesign(design, "PCRFree")
res = fa.get_adapters_from_sample("C1152-S2-EC1")
assert "universal" in res.keys()
assert "fwd" in res['universal']
assert "rev" in res['universal']
# let us be more precise for PCRFree only for a regression bug where
# res['universal']
assert res["universal"]["fwd"].identifier == "Universal_Adapter|name:universal"
assert res["universal"]["fwd"].sequence == "AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT"
# NEBNext
fa = FindAdaptersFromDesign(design, "NEBNext")
res = fa.get_adapters_from_sample("C1152-S2-EC1")
assert "universal" in res.keys()
assert "fwd" in res['universal']
assert "rev" in res['universal']
# Small
fa = FindAdaptersFromDesign(design, "Small")
res = fa.get_adapters_from_sample("C1152-S2-EC1")
assert "universal" in res.keys()
assert "fwd" in res['universal']
assert "rev" in res['universal']
def test_wrong_sample():
design = sequana_data("test_index_mapper.csv")
ad = FindAdaptersFromDesign(design, "Rubicon")
res = ad.get_adapters_from_sample("C4405-M1-EC1")
assert res['index1']['fwd'] is None
assert res['index1']['rev'] is None
def test_rubicon():
design = sequana_data("test_expdesign_rubicon.csv")
fa = FindAdaptersFromDesign(design, "Rubicon")
fa.check()
def test_pcrfree():
design = sequana_data("test_index_mapper.csv")
try:
ad = FindAdaptersFromDesign(design, "error")
assert False
except Exception:
assert True
# Other input from PCRFree
ad = FindAdaptersFromDesign(design, "PCRFree")
# Test the index1/2_seq with 3 cases
# index1 present only,
# no index at all (None)
# index1 and index2 present
design1 = sequana_data("test_expdesign_hiseq.csv")
ad1 = FindAdaptersFromDesign(design1, "PCRFree")
ad1.check()
res1 = ad1.get_adapters_from_sample("553-iH2-1")
res2 = ad1.get_adapters_from_sample("539-st2")
res3 = ad1.get_adapters_from_sample("107-st2")
assert res1['index1']['fwd'].identifier == "NextFlex_PCR_Free_adapter8|name:8|seq:TTAGGC"
assert res1['index1']['fwd'].name == "8"
assert res1['index1']['rev'].name == "8"
assert list(res2.keys()) == ["universal"]
assert res3['index1']['fwd'].name == "9"
assert res3['index1']['rev'].name == "9"
assert res3['index2']['fwd'].name == "10"
assert res3['index2']['rev'].name == "10"
# double indexing
# This is a double indexing for PCRFree, which has not been tested
# since it requires 16S adapters not yet in sequana
"""design2 = sequana_data("test_expdesign_miseq_illumina2.csv")
ad2 = FindAdaptersFromDesign(design2, "PCRFree")
assert ad2.get_adapters_from_sample('M2')['index1']['fwd'].identifier == \
'NextFlex_PCR_Free_adapter2|name:2|seq:TGACCA'
assert ad2.get_adapters_from_sample('M2')['index2']['fwd'].identifier == \
'NextFlex_PCR_Free_adapter13|name:13|seq:AGTCAA'
"""
design = sequana_data("test_expdesign_miseq_illumina.csv")
ad = FindAdaptersFromDesign(design, "PCRFree")
res = ad.get_adapters_from_sample("CR81-L1236-P1")
assert res['index1']['fwd'].identifier == 'NextFlex_PCR_Free_adapter1|name:1|seq:CGATGT'
design1 = sequana_data("test_expdesign_miseq_illumina_1.csv")
ad = FindAdaptersFromDesign(design1, "PCRFree")
ad.check() # all sample names must be found
res = ad.get_adapters_from_sample("CM-2685")['index1']['fwd']
assert res.name == "3"