def testNbSeq(self):
nb_seq = FastaIO.nbSeq(self.tmp_mono_line)
self.assertEqual(4, nb_seq)
nb_seq = FastaIO.nbSeq(self.tmp_multi_line)
self.assertEqual(4, nb_seq)
nb_seq = FastaIO.nbSeq(self.tmp_multi_line_gz)
self.assertEqual(4, nb_seq)
def writeTargetReads(out_R1_path, out_R2_path, reads_pairs):
"""
"""
with FastaIO(out_R1_path, "a") as FH_out_R1:
with FastaIO(out_R2_path, "a") as FH_out_R2:
for R1, R2 in reads_pairs:
FH_out_R1.write(R1)
FH_out_R2.write(R2)
def addStartTag(in_path, out_path):
FH_in = FastaIO(in_path)
FH_out = FastaIO(out_path, "w")
for record in FH_in:
record.string = "^" + record.string
FH_out.write(record)
FH_in.close()
FH_out.close()
def testNbSeqAndNt(self):
nb_seq, nb_nt = FastaIO.nbSeqAndNt(self.tmp_mono_line)
self.assertEqual(nb_seq, 4)
self.assertEqual(nb_nt, 104)
nb_seq, nb_nt = FastaIO.nbSeqAndNt(self.tmp_multi_line)
self.assertEqual(nb_seq, 4)
self.assertEqual(nb_nt, 104)
nb_seq, nb_nt = FastaIO.nbSeqAndNt(self.tmp_multi_line_gz)
self.assertEqual(nb_seq, 4)
self.assertEqual(nb_nt, 104)
def testIsValid(self):
# Valid
self.assertTrue(FastaIO.isValid(self.tmp_mono_line))
self.assertTrue(FastaIO.isValid(self.tmp_multi_line))
self.assertTrue(FastaIO.isValid(self.tmp_multi_line_gz))
# Valid long file
content = ">seq1\nATGC\n>seq2\nATGC\n>seq3\nATGC\n>seq4\nATGC\n>seq5\nATGC\n>seq6\nATGC\n>seq7\nATGC\n>seq8\nATGC\n>seq9\nATGC\n>seq10\nATGC\n>seq11\nATGC\n>seq12\nATGC"
with open(self.tmp_out, "w") as FH_out:
FH_out.write(content)
self.assertTrue(FastaIO.isValid(self.tmp_out))
# Valid empty file
content = ""
with open(self.tmp_out, "w") as FH_out:
FH_out.write(content)
self.assertTrue(FastaIO.isValid(self.tmp_out))
# Valid empty sequence
content = ">seq1\n"
with open(self.tmp_out, "w") as FH_out:
FH_out.write(content)
self.assertTrue(FastaIO.isValid(self.tmp_out))
# Invalid file (two headers)
content = ">seq1\nATGC\n>seq2\n>seq3\nATGC"
with open(self.tmp_out, "w") as FH_out:
FH_out.write(content)
self.assertTrue(not FastaIO.isValid(self.tmp_out))
# Invalid file (no header at the first line)
content = "seq1\nATGC\n>seq2\nATGC"
with open(self.tmp_out, "w") as FH_out:
FH_out.write(content)
self.assertTrue(not FastaIO.isValid(self.tmp_out))
# Invalid file (fastq)
content = "@seq1\nATGC\n+\n####"
with open(self.tmp_out, "w") as FH_out:
FH_out.write(content)
self.assertTrue(not FastaIO.isValid(self.tmp_out))
def getSeqByChr(genome_path):
"""
Return by chromosome name the sequence of this chromosome.
:param genome_path: Path to the genome file (format: fasta).
:type genome_path: str
:return: By chromosome name the sequence of this chromosome in uppercase.
:rtype: dict
"""
genome_by_chr = dict()
FH_seq = FastaIO(genome_path)
for record in FH_seq:
genome_by_chr[record.id] = record.string.upper()
FH_seq.close()
return genome_by_chr
def getChrSeq(in_ref, chrom_id):
"""
"""
chrom_seq = None
with FastaIO(in_ref) as FH_seq:
for record in FH_seq:
if record.id == chrom_id:
chrom_seq = record.string
return chrom_seq
def testIter(self):
with FastaIO(self.tmp_mono_line) as FH_in:
for idx, record in enumerate(FH_in):
self.assertTrue(cmpSequences(record, self.expected_rec[idx]))
self.assertEqual(idx + 1, 4)
with FastaIO(self.tmp_multi_line) as FH_in:
for idx, record in enumerate(FH_in):
self.assertTrue(cmpSequences(record, self.expected_rec[idx]))
self.assertEqual(idx + 1, 4)
with FastaIO(self.tmp_multi_line_gz) as FH_in:
for idx, record in enumerate(FH_in):
self.assertTrue(cmpSequences(record, self.expected_rec[idx]))
self.assertEqual(idx + 1, 4)
with FastaIO(self.tmp_mono_line) as FH_in_mono:
with FastaIO(self.tmp_multi_line) as FH_in_multi:
idx = 0
for rec_expected, rec_mono_line, rec_multi_line in zip(
self.expected_rec, FH_in_mono, FH_in_multi):
self.assertTrue(cmpSequences(rec_mono_line, rec_expected))
self.assertTrue(cmpSequences(rec_multi_line, rec_expected))
idx += 1
self.assertEqual(idx, 4)
def getSeqRecord(in_seq, selected_id):
"""
@summary: Returns the selected sequence object from the sequences file.
@param in_seq: [str] Path to the sequences file (format: fasta).
@param selected_id: [str] The ID of the selected sequence.
@return: [Sequence] The selected sequence object.
"""
selected_record = None
with FastaIO(in_seq) as FH_in:
for record in FH_in:
if record.id == selected_id:
selected_record = record
return selected_record
def getChromSeq(chrom_name, in_fasta):
"""
Return the sequence corresponding to the chromosome.
:param chrom_name: The name of the selected chromosome.
:type chrom_name: str
:param in_fasta: The path to the file sequences file (format: fasta).
:type in_fasta: str
:return: the sequence corresponding to the chromosome.
:rtype: str
"""
seq = None
with FastaIO(in_fasta) as FH_ref:
for record in FH_ref:
if record.id == chrom_name:
seq = record.string
if seq is None:
raise Exception(
'The chromosome "{}" cannot be rertrieved from "{}".'.format(
chrom_name, in_fasta))
return seq
def getBEDRecords(ref_path, amplicons):
for ampl in amplicons:
ampl["found"] = False
bed_ampl = []
with FastaIO(ref_path) as FH_seq:
for record in FH_seq:
chr_id = record.id
chr_str = record.string.upper()
for ampli in amplicons:
# Primers are on strand +
up_primer = ampli["f_primer"].upper()
down_primer = ampli["r_primer"].upper()
start, end = findPosOnSequence(chr_id, chr_str, up_primer,
down_primer)
if start is not None:
ampli["found"] = True
bed_ampl.append(
BEDRecord(chr_id, start, end, ampli["name"], 0, "+",
start + len(up_primer),
end - len(down_primer)))
# Primers are on strand -
up_primer = revcom(ampli["r_primer"].upper())
down_primer = revcom(ampli["f_primer"].upper())
start, end = findPosOnSequence(chr_id, chr_str, up_primer,
down_primer)
if start is not None:
ampli["found"] = True
bed_ampl.append(
BEDRecord(chr_id, start, end, ampli["name"], 0, "-",
start + len(up_primer),
end - len(down_primer)))
for ampl in amplicons:
if not ampl["found"]:
warnings.warn(
'The amplicons {} with primers fwd:{}, rvs:{} cannot be found in {}.'
.format(ampl["name"], ampl["f_primer"], ampl["r_primer"],
ref_path))
return (bed_ampl)
def setUp(self):
tmp_folder = tempfile.gettempdir()
unique_id = str(uuid.uuid1())
# Temporary files
self.tmp_sequences = os.path.join(tmp_folder, unique_id + ".fasta")
self.tmp_regions = os.path.join(tmp_folder, unique_id + ".bed")
self.tmp_variants = os.path.join(tmp_folder, unique_id + ".vcf")
self.tmp_output = os.path.join(tmp_folder, unique_id + "_out.vcf")
# Exec command
self.cmd = [
"filterVCFPrimers.py",
"--input-variants", self.tmp_variants,
"--input-regions", self.tmp_regions,
"--input-sequences", self.tmp_sequences,
"--output-variants", self.tmp_output
]
# Create fasta
with FastaIO(self.tmp_sequences, "w") as FH_seq:
FH_seq.write(Sequence("artificial_chr1", "NNNAAAATTTGGGGGGGGGGTTTAAANNN"))
# 123456789| | | | | | | | | |
# 10| 14| 18| 22| 26|
# 12 16 20 24 28
FH_seq.write(Sequence("artificial_chr2", "CGATNNNCGAT"))
# 123456789|
# 10
# Create VCF
with VCFIO(self.tmp_variants, "w") as FH_var:
FH_var.info = {"ZOI": HeaderInfoAttr("ZOI", "If the variant can be in interest area.", type="String", number="1")}
FH_var.writeHeader()
self.variants = [
VCFRecord("artificial_chr1", 6, "alt_0", "A", ["AA"], None, None, {"ZOI": "no"}),
VCFRecord("artificial_chr1", 8, "alt_1", "TT", ["T"], None, None, {"ZOI": "no"}),
VCFRecord("artificial_chr1", 8, "alt_2", "T", ["TT"], None, None, {"ZOI": "yes"}),
VCFRecord("artificial_chr1", 9, "alt_3", "TTGG", ["TT"], None, None, {"ZOI": "yes"}),
VCFRecord("artificial_chr1", 14, "alt_4", "G", ["GG"], None, None, {"ZOI": "yes"}),
VCFRecord("artificial_chr1", 18, "alt_5", "GGG", ["G"], None, None, {"ZOI": "yes"}), # ZOI downstream limit deletion
VCFRecord("artificial_chr1", 22, "alt_6", "T", ["TT"], None, None, {"ZOI": "yes"}),
VCFRecord("artificial_chr1", 9, "alt_7", "TT", ["TC"], None, None, {"ZOI": "no"}), # Substitution before end of upstream primer
VCFRecord("artificial_chr1", 10, "alt_8", "TG", ["TC"], None, None, {"ZOI": "yes"}), # Substitution in upstream limit of ZOI
VCFRecord("artificial_chr1", 15, "alt_9", "GG", ["GC"], None, None, {"ZOI": "yes"}), # Substitution in dosnstream limit of ZOI
VCFRecord("artificial_chr1", 20, "alt_10", "GT", ["GC"], None, None, {"ZOI": "no"}), # Substitution after start of downstream primer
VCFRecord("artificial_chr1", 21, "alt_11", "TT", ["TC"], None, None, {"ZOI": "no"}), # Substitution in downstream primer
VCFRecord("artificial_chr2", 1, "alt_12", "C", ["CTT"], None, None, {"ZOI": "no"}), # Insertion before end of upstream primer
VCFRecord("artificial_chr2", 2, "alt_13", "G", ["GCC"], None, None, {"ZOI": "yes"}), # Insertion in upstream limit of ZOI
VCFRecord("artificial_chr2", 3, "alt_14", "AT", ["CCGC"], None, None, {"ZOI": "yes"}), # Insertion in upstream limit of ZOI and without standardization
VCFRecord("artificial_chr2", 9, "alt_15", "G", ["GCC"], None, None, {"ZOI": "yes"}), # Insertion in downstream limit of ZOI
VCFRecord("artificial_chr2", 9, "alt_16", "G", ["NNN"], None, None, {"ZOI": "yes"}), # Insertion in downstream limit of ZOI and without standardization
VCFRecord("artificial_chr2", 10, "alt_17", "-", ["CC"], None, None, {"ZOI": "yes"}), # Insertion in downstream limit of ZOI
VCFRecord("artificial_chr2", 10, "alt_18", "A", ["ATT"], None, None, {"ZOI": "no"}), # Insertion after start of downstream primer
VCFRecord("artificial_chr2", 1, "alt_19", "CG", ["C"], None, None, {"ZOI": "no"}), # Deletion before end of upstream primer
VCFRecord("artificial_chr2", 2, "alt_20", "GA", ["G"], None, None, {"ZOI": "yes"}), # Deletion in upstream limit of ZOI
VCFRecord("artificial_chr2", 3, "alt_21", "AT", ["C"], None, None, {"ZOI": "yes"}), # Deletion in upstream limit of ZOI and without standardization
VCFRecord("artificial_chr2", 6, "alt_22", "NNCG", ["N"], None, None, {"ZOI": "yes"}), # Deletion in downstream limit of ZOI
VCFRecord("artificial_chr2", 8, "alt_23", "CG", ["C"], None, None, {"ZOI": "yes"}), # Deletion in downstream limit of ZOI
VCFRecord("artificial_chr2", 8, "alt_24", "CG", ["T"], None, None, {"ZOI": "yes"}), # Deletion in downstream limit of ZOI and without standardization
VCFRecord("artificial_chr2", 9, "alt_25", "GA", ["G"], None, None, {"ZOI": "no"}), # Insertion after start of downstream primer
VCFRecord("artificial_chr2", 10, "alt_26", "A", ["-"], None, None, {"ZOI": "no"}), # Insertion after start of downstream primer
VCFRecord("artificial_chr2", 10, "alt_27", "AT", ["A"], None, None, {"ZOI": "no"}), # Insertion after start of downstream primer
]
for idx, curr_var in enumerate(self.variants):
FH_var.write(curr_var)
help=
'Path to the definition of the amplicons (format: Illumina manifest).')
group_output = parser.add_argument_group('Outputs') # Outputs
group_output.add_argument(
'-f',
'--fwd-barcodes',
default="fwd_barcodes.fasta",
help=
'******************************** (format: fasta). [Default: %(default)s]'
)
group_output.add_argument(
'-r',
'--rvs-barcodes',
default="rvs_barcodes.fasta",
help=
'******************************** (format: fasta). [Default: %(default)s]'
)
args = parser.parse_args()
# Process
amplicons = getAmplicons(args.input_manifest)
FH_fwd = FastaIO(args.fwd_barcodes, "w")
FH_rvs = FastaIO(args.rvs_barcodes, "w")
for ampl in amplicons:
record_fwd = Sequence(ampl.name, ampl.up_primer)
FH_fwd.write(record_fwd)
record_rvs = Sequence(ampl.name, revcom(ampl.down_primer))
FH_rvs.write(record_rvs)
FH_fwd.close()
FH_rvs.close()
def setUp(self):
tmp_folder = tempfile.gettempdir()
unique_id = str(uuid.uuid1())
# Temporary files
self.tmp_sequences = os.path.join(tmp_folder, unique_id + ".fasta")
self.tmp_faidx = os.path.join(tmp_folder, unique_id + ".fasta.fai")
self.tmp_regions = os.path.join(tmp_folder, unique_id + ".bed")
self.tmp_variants = os.path.join(tmp_folder, unique_id + ".vcf")
self.tmp_output = os.path.join(tmp_folder, unique_id + "_out.vcf")
# Exec command
self.cmd = [
"filterVCFTargets.py", "--mode", "remove", "--input-variants",
self.tmp_variants, "--input-targets", self.tmp_regions,
"--input-reference", self.tmp_sequences, "--output-variants",
self.tmp_output
]
# Create fasta
with FastaIO(self.tmp_sequences, "w") as FH_seq:
# Repeats: ****.... ...***
# Region: |----| |------------| |------|
FH_seq.write(
Sequence("artificial_chr1",
"CTCAGTCATGTATGTATGTGCTCACAAAGTAGTAGATCATGGCAC"))
# 123456789| | | | | | | | | | | | | | | | | |
# 10| 14| 18| 22| 26| 30| 34| 38| 42|
# 12 16 20 24 28 32 36 40 44
FH_seq.write(Sequence("artificial_chr2", "CGATNNNCGAT"))
# 123456789|
# 10
# Create faidx
with open(self.tmp_faidx, "w") as FH_fai:
FH_fai.write("""artificial_chr1 45 17 45 46
artificial_chr2 11 80 11 12""")
# Create targets
with BEDIO(self.tmp_regions, "w", write_nb_col=4) as FH_bed:
FH_bed.write(BEDRecord("artificial_chr1", 1, 6, "target_1"))
FH_bed.write(BEDRecord("artificial_chr1", 15, 28, "target_2"))
FH_bed.write(BEDRecord("artificial_chr1", 38, 45, "target_3"))
# Create VCF
with VCFIO(self.tmp_variants, "w") as FH_var:
FH_var.info = {
"target":
HeaderInfoAttr("target",
"The ID of the overlapped target.",
type="String",
number="1")
}
FH_var.writeHeader()
self.variants = [
# Substit single nt
VCFRecord("artificial_chr1", 14, "alt_00", "G", ["T"], None,
None, {"target": None
}), # Before target ; first nt before target
VCFRecord(
"artificial_chr1", 15, "alt_01", "G", ["T"], None, None,
{"target": "target_2"}), # On target ; first nt of target
VCFRecord("artificial_chr1", 21, "alt_02", "C", ["G"], None,
None, {"target": "target_2"}), # On target
VCFRecord("artificial_chr1", 28, "alt_03", "A", ["G"], None,
None, {"target": "target_2"}), # On target ; last nt
VCFRecord(
"artificial_chr1", 29, "alt_04", "G", ["C"], None, None,
{"target": None}), # After target ; first nt after target
# Substit multi nt
VCFRecord("artificial_chr1", 7, "alt_05", "CATGTATG",
["GTACCCGC"], None, None,
{"target": None
}), # Before target ; first nt before target
VCFRecord("artificial_chr1", 11, "alt_06", "TATGTATG",
["GTACCCGC"], None, None,
{"target": "target_2"}), # Overlap target start
VCFRecord("artificial_chr1", 13, "alt_07",
"TGTATGTGCTCACAAAGTA", ["CCCGCCCCTACATTGCAGT"], None,
None, {"target": "target_2"}), # Include target
VCFRecord("artificial_chr1", 15, "alt_08", "TATGTGCTCACAAA",
["CGCCCCTACATTGC"], None, None,
{"target": "target_2"}), # Exact target
VCFRecord("artificial_chr1", 21, "alt_09", "CTCACAA",
["GTACCCG"], None, None,
{"target": "target_2"}), # Included by target
VCFRecord("artificial_chr1", 24, "alt_10", "ACAAAGTA",
["GTACCCG"], None, None,
{"target": "target_2"}), # Overlap target end
VCFRecord(
"artificial_chr1", 29, "alt_11", "GTAGTAGAT",
["GTACCCGA"], None, None,
{"target": None}), # After target ; first nt after target
# Ins single nt
VCFRecord("artificial_chr1", 14, "alt_12", "G", ["GA"], None,
None, {"target": None
}), # Before target ; first nt before target
VCFRecord("artificial_chr1", 15, "alt_12.2", "-", ["A"], None,
None, {"target": None
}), # Before target ; first nt before target
VCFRecord(
"artificial_chr1", 15, "alt_13", "A", ["TG"], None, None,
{"target": "target_2"}), # On target ; first nt of target
VCFRecord("artificial_chr1", 21, "alt_14", "C", ["CG"], None,
None, {"target": "target_2"}), # On target
VCFRecord("artificial_chr1", 27, "alt_15", "A", ["AT"], None,
None, {"target": "target_2"}), # On target ; last nt
VCFRecord("artificial_chr1", 28, "alt_15.2", "-", ["T"], None,
None, {"target": "target_2"}), # On target ; last nt
VCFRecord(
"artificial_chr1", 28, "alt_16", "A", ["AT"], None, None,
{"target": None}), # After target ; first nt afetr target
# Movable del multi nt
VCFRecord(
"artificial_chr1", 14, "alt_17", "G", ["GT"], None, None,
{"target": "target_2"}), # Movable to first nt of target
VCFRecord(
"artificial_chr1", 28, "alt_18", "A", ["AA"], None, None,
{"target": "target_2"}), # Movable to last nt of target
# Del single nt
VCFRecord("artificial_chr1", 14, "alt_19", "G", [""], None,
None, {"target": None
}), # Before target ; first nt before target
VCFRecord(
"artificial_chr1", 15, "alt_20", "T", [""], None, None,
{"target": "target_2"}), # On target ; first nt of target
VCFRecord("artificial_chr1", 21, "alt_21", "C", [""], None,
None, {"target": "target_2"}), # On target
VCFRecord("artificial_chr1", 28, "alt_22", "A", [""], None,
None, {"target": "target_2"}), # On target ; last nt
VCFRecord(
"artificial_chr1", 29, "alt_23", "G", [""], None, None,
{"target": None}), # After target ; first nt afetr target
# Del multi nt
VCFRecord("artificial_chr1", 11, "alt_24", "TATG", ["T"], None,
None, {"target": None
}), # Before target ; first nt before target
VCFRecord(
"artificial_chr1", 13, "alt_25", "TGTA", ["T"], None, None,
{"target": "target_2"}), # On target ; first nt of target
VCFRecord("artificial_chr1", 20, "alt_26", "GCTC", ["G"], None,
None, {"target": "target_2"}), # On target
VCFRecord("artificial_chr1", 27, "alt_27", "AAGT", ["A"], None,
None, {"target": "target_2"}), # On target ; last nt
VCFRecord(
"artificial_chr1", 28, "alt_28", "AGT", ["A"], None, None,
{"target": None}), # After target ; first nt afetr target
# Movable del multi nt
VCFRecord("artificial_chr1", 7, "alt_29", "CATGT", ["C"], None,
None,
{"target": "target_2"
}), # On repeat and movable to first nt of target
VCFRecord(
"artificial_chr1", 12, "alt_30", "ATG", ["A"], None, None,
{"target": "target_2"}), # Movable to first nt of target
VCFRecord(
"artificial_chr1", 28, "alt_31", "AGTA", ["A"], None, None,
{"target": "target_2"}), # Movable to last nt of target
VCFRecord("artificial_chr1", 30, "alt_32", "TAGT", ["T"], None,
None,
{"target": "target_2"
}), # On repeat and movable to last nt of target
]
for idx, curr_var in enumerate(self.variants):
FH_var.write(curr_var)
def setUp(self):
tmp_folder = tempfile.gettempdir()
unique_id = str(uuid.uuid1())
# Temporary files
self.tmp_sequences = os.path.join(tmp_folder, unique_id + ".fasta")
self.tmp_faidx = os.path.join(tmp_folder, unique_id + ".fasta.fai")
self.tmp_variants = os.path.join(tmp_folder, unique_id + ".vcf")
self.tmp_output = os.path.join(tmp_folder, unique_id + "_out.vcf")
# Exec command
self.cmd = [
"filterVCFHomopolym.py", "--mode", "remove", "--homopolym-length",
"4", "--input-variants", self.tmp_variants, "--input-reference",
self.tmp_sequences, "--output-variants", self.tmp_output
]
# Create fasta
with FastaIO(self.tmp_sequences, "w") as FH_seq:
# 12 16 20 24 28 32 36 40 44 48 52 56 60 64 68 72 76 80 84 88 92 96 100
# 2 4 6 8 10| 14| 18| 22| 26| 30| 34| 38| 42| 46| 50| 54| 58| 62| 66| 70| 74| 78| 82| 86| 90| 94| 98| 102
# | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
FH_seq.write(
Sequence(
"artificial_chr1",
"CGAATATGATCCAGCAATAAAAAGTTCCTACAGGAAAAAAGTAGAAAGAGAAACCTGTCTCTTGGATATTCTCGACACAGCAGGTCAAG"
))
FH_seq.write(
Sequence(
"artificial_chr2",
"CGAATATGATCCAGCAATAAAAAGCTCCTACAGGCAAAAGTAGGCAAAGAGAAACCTGTCTCTTGGATATTCTCGACACAGCAGGTCAA"
))
FH_seq.write(
Sequence(
"artificial_chr3",
"CGAATATGATCCAGCAATGAAAATTCCTACAGGTAAAACGTAGAAAGAGAAACCTGTCTCTTGGATATTCTCGACACAGCAGGTCAAG"
))
FH_seq.write(
Sequence(
"artificial_chr4",
"CGAATATGATCCAGCAATAAAAAGTTCCTACAGGAAAAAAGTAGAAAGAGAAACCTGTCAAAAGGATATTCTCGACAAAACAGCAGAAAGTCAAG"
))
FH_seq.write(
Sequence(
"artificial_chr5",
"CGAATATGATCCAGTAATAAAAAGTTCCTACAGGAAAAAAGTAGAAAGAGAAACCTGTCTCTTGGATATTCTCGACACAGCAGGTCAAG"
))
FH_seq.write(
Sequence(
"artificial_chr6",
"CGAATATGATCCAGCAATAAAAAGTTCCTACAGGAAAAAAGTAGAAAGCACAACCTGTCTCTTGGAAAATCTCGACACAGCAGGTAAAACAATGCAGTAAAT"
))
"""
Variant before_start before_end before_seq after_start after_end after_seq
alt_00 10 13 TCCA 15 18 CAAT
alt_01 20 23 AAAA 25 28 TTCC
alt_02 30 33 ACAG 35 38 AAAA
alt_03 40 43 AGTA 45 48 AAAG
alt_04 10 13 TCCA 16 19 AATA
alt_05 20 23 AAAA 26 29 TCCT
alt_06 30 33 ACAG 36 39 AAAA
alt_07 40 43 GTAG 46 49 AAAG
alt_08 11 14 CCAG 15 18 CAAT
alt_09 20 23 AAAA 24 27 TTCC
alt_10 31 34 AGGT 35 38 AAAA
alt_11 40 43 GTAG 44 47 AAAG
alt_12 11 14 CCAG 15 18 CAAT
alt_13 20 23 AAAA 24 27 GTTC
alt_14 31 34 CAGG 35 38 AAAA
alt_15 41 44 GTAG 45 48 AAAG
alt_16 50 53 GAAA 57 60 GTCA
alt_17 60 63 AAAA 67 70 TATT
alt_18 70 73 TCTC 77 80 AAAA
alt_19 80 83 ACAG 87 90 AAAG
alt_20 11 14 CCAG 16 19 AATA
alt_21 20 23 AAAA 25 28 TTCC
alt_22 31 34 CAGG 36 39 AAAA
alt_23 40 43 AGTA 45 48 AAAG
alt_24 11 14 CCAG 17 20 ATAA
alt_25 19 22 AAAA 26 29 TCCT
alt_26 29 32 TACA 35 38 AAAA
alt_27 38 41 AAAG 45 48 AAAG
alt_28 50 53 ACAA 61 64 CTTG
alt_29 66 69 AAAA 76 79 CACA
alt_30 76 79 CACA 86 89 AAAA
alt_31 88 91 AACA 99 102 AAAT
"""
# Create faidx
with open(self.tmp_faidx, "w") as FH_fai:
FH_fai.write("""artificial_chr1 89 17 89 90
artificial_chr2 89 124 89 90
artificial_chr3 88 231 88 89
artificial_chr4 95 337 95 96
artificial_chr5 89 450 89 90
artificial_chr6 102 557 102 103""")
# Create VCF
with VCFIO(self.tmp_variants, "w") as FH_var:
FH_var.info = {
"is_filtered":
HeaderInfoAttr(
"is_filtered",
"1 if the variant is adjacent to an homopolymer.",
type="Integer",
number="1")
}
FH_var.writeHeader()
self.variants = [
# Substit single nt
VCFRecord("artificial_chr1", 14, "alt_00", "G", ["T"], None,
None,
{"is_filtered": 0}), # Without adjacent homopolymers
VCFRecord(
"artificial_chr1", 24, "alt_01", "G", ["T"], None, None,
{"is_filtered": 1}), # Adjacent homopolymers upstream
VCFRecord(
"artificial_chr1", 34, "alt_02", "G", ["T"], None, None,
{"is_filtered": 1}), # Adjacent homopolymers downstream
VCFRecord(
"artificial_chr1", 44, "alt_03", "G", ["T"], None, None,
{"is_filtered": 0}), # Adjacent too short homopolymers
# Substit multi nt
VCFRecord("artificial_chr2", 14, "alt_04", "GC", ["TA"], None,
None,
{"is_filtered": 0}), # Without adjacent homopolymers
VCFRecord(
"artificial_chr2", 24, "alt_05", "GC", ["TA"], None, None,
{"is_filtered": 1}), # Adjacent homopolymers upstream
VCFRecord(
"artificial_chr2", 34, "alt_06", "GC", ["TA"], None, None,
{"is_filtered": 1}), # Adjacent homopolymers downstream
VCFRecord(
"artificial_chr2", 44, "alt_07", "GC", ["TA"], None, None,
{"is_filtered": 0}), # Adjacent too short homopolymers
# Ins single nt
VCFRecord("artificial_chr3", 14, "alt_08", "G", ["GT"], None,
None,
{"is_filtered": 0}), # Without adjacent homopolymers
VCFRecord(
"artificial_chr3", 23, "alt_09", "A", ["AT"], None, None,
{"is_filtered": 1}), # Adjacent homopolymers upstream
VCFRecord(
"artificial_chr3", 34, "alt_10", "T", ["TA"], None, None,
{"is_filtered": 1}), # Adjacent homopolymers downstream
VCFRecord(
"artificial_chr3", 43, "alt_11", "G", ["GT"], None, None,
{"is_filtered": 0}), # Adjacent too short homopolymers
# Ins multi nt
VCFRecord("artificial_chr4", 14, "alt_12", "G", ["GTA"], None,
None,
{"is_filtered": 0}), # Without adjacent homopolymers
VCFRecord(
"artificial_chr4", 23, "alt_13", "A", ["ATA"], None, None,
{"is_filtered": 1}), # Adjacent homopolymers upstream
VCFRecord(
"artificial_chr4", 34, "alt_14", "G", ["GTA"], None, None,
{"is_filtered": 1}), # Adjacent homopolymers downstream
VCFRecord(
"artificial_chr4", 44, "alt_15", "G", ["GTC"], None, None,
{"is_filtered": 0}), # Adjacent too short homopolymer
VCFRecord("artificial_chr4", 54, "alt_16", "CCT", ["ATCCAGA"],
None, None,
{"is_filtered": 0}), # Without adjacent homopolymers
VCFRecord(
"artificial_chr4", 64, "alt_17", "GGA", ["CTCCAGT"], None,
None,
{"is_filtered": 1}), # Adjacent homopolymers upstream
VCFRecord(
"artificial_chr4", 74, "alt_18", "GAC", ["ATCCAGT"], None,
None,
{"is_filtered": 1}), # Adjacent homopolymers downstream
VCFRecord(
"artificial_chr4", 84, "alt_19", "CAG", ["ATCCAGT"], None,
None,
{"is_filtered": 0}), # Adjacent too short homopolymer
# Del single nt
VCFRecord("artificial_chr5", 14, "alt_20", "GT", ["G"], None,
None,
{"is_filtered": 0}), # Without adjacent homopolymers
VCFRecord(
"artificial_chr5", 23, "alt_21", "AG", ["A"], None, None,
{"is_filtered": 1}), # Adjacent homopolymers upstream
VCFRecord(
"artificial_chr5", 34, "alt_22", "GA", ["G"], None, None,
{"is_filtered": 1}), # Adjacent homopolymers downstream
VCFRecord(
"artificial_chr5", 43, "alt_23", "AG", ["A"], None, None,
{"is_filtered": 0}), # Adjacent too short homopolymers
# # Del multi nt
VCFRecord("artificial_chr6", 14, "alt_24", "GCA", ["G"], None,
None,
{"is_filtered": 0}), # Without adjacent homopolymers
VCFRecord(
"artificial_chr6", 23, "alt_25", "AGT", ["C"], None, None,
{"is_filtered": 1}), # Adjacent homopolymers upstream
VCFRecord(
"artificial_chr6", 32, "alt_26", "AGG", ["A"], None, None,
{"is_filtered": 1}), # Adjacent homopolymers downstream
VCFRecord(
"artificial_chr6", 42, "alt_27", "TAG", ["C"], None, None,
{"is_filtered": 0}), # Adjacent too short homopolymer
VCFRecord("artificial_chr6", 54, "alt_28", "CCTGTCT", ["GAA"],
None, None,
{"is_filtered": 0}), # Without adjacent homopolymers
VCFRecord(
"artificial_chr6", 70, "alt_29", "TCTCGA", ["CCC"], None,
None,
{"is_filtered": 1}), # Adjacent homopolymers upstream
VCFRecord(
"artificial_chr6", 80, "alt_30", "GCAGGT", ["CCC"], None,
None,
{"is_filtered": 1}), # Adjacent homopolymers downstream
VCFRecord(
"artificial_chr6", 92, "alt_31", "ATGCAGT", ["CCC"], None,
None,
{"is_filtered": 0}), # Adjacent too short homopolymer
]
for idx, curr_var in enumerate(self.variants):
FH_var.write(curr_var)
args = parser.parse_args()
# Logger initialisation
logging.basicConfig(
level=logging.DEBUG,
format=
'%(asctime)s -- [%(filename)s][pid:%(process)d][%(levelname)s] -- %(message)s'
)
log = logging.getLogger(os.path.basename(__file__))
log.info(" ".join(sys.argv))
log.info("Random seed used: {}".format(args.random_seed))
# Get number of duplications by reads
log.info("Get duplication count for each read")
random.seed(args.random_seed)
nb_reads = FastaIO.nbSeq(args.input_R1)
if nb_reads < 10000:
log.error(
"The number of reads in {} is unsufficient to simulate duplication (found: {} ; expected: {})."
.format(args.input_R1, nb_reads, 10000))
nb_occurences = getNbOccur(args.duplication_profile, nb_reads)
# Witre reads
log.info("Write reads")
with FastaIO(args.output_R1, "w") as FH_out_R1:
with FastaIO(args.output_R2, "w") as FH_out_R2:
with FastaIO(args.input_R1) as FH_in_R1:
with FastaIO(args.input_R2) as FH_in_R2:
for curr_nb_occur, R1, R2 in zip(nb_occurences, FH_in_R1,
FH_in_R2):
description = "dupCount={}".format(curr_nb_occur)
def setUp(self):
tmp_folder = tempfile.gettempdir()
unique_id = str(uuid.uuid1())
# Temporary files
self.tmp_sequences = os.path.join(tmp_folder, unique_id + ".fasta")
self.tmp_faidx = os.path.join(tmp_folder, unique_id + ".fasta.fai")
self.tmp_variants = os.path.join(tmp_folder, unique_id + ".vcf")
self.tmp_output = os.path.join(tmp_folder, unique_id + "_out.vcf")
# Exec command
self.cmd = [
"standardizeVCF.py",
"--trace-unstandard",
"--input-reference", self.tmp_sequences,
"--input-variants", self.tmp_variants,
"--output-variants", self.tmp_output
]
# Create fasta
with FastaIO(self.tmp_sequences, "w") as FH_seq:
# Repeats: ****.... ...***
# Region: |----| |------------| |------|
FH_seq.write(Sequence("artificial_chr1", "CTCAGTCATGTATGTATGTGCTCACAAAGTAGTAGATCATGGCAC"))
# 123456789| | | | | | | | | | | | | | | | | |
# 10| 14| 18| 22| 26| 30| 34| 38| 42|
# 12 16 20 24 28 32 36 40 44
FH_seq.write(Sequence("artificial_chr2", "CGATNNNCGAT"))
# 123456789|
# 10
# Create faidx
with open(self.tmp_faidx, "w") as FH_fai:
FH_fai.write("""artificial_chr1 45 17 45 46
artificial_chr2 11 80 11 12""")
# Create VCF
with VCFIO(self.tmp_variants, "w") as FH_var:
FH_var.info = {
"expected": HeaderInfoAttr("expected", "Standardized version of {chrom}:{pos}={ref}/{alt}.", type="String", number="."),
"ANN": HeaderInfoAttr("ANN", "Annotation of variants Format: Allele|Annotation_id|Alt_allele_idx", type="String", number="."),
"expectedANN": HeaderInfoAttr("expectedANN", "Standardized version of annotations Format: Allele|Annotation_id|Alt_allele_idx", type="String", number=".")
}
FH_var.writeHeader()
self.variants = [
# Substit single nt
VCFRecord("artificial_chr1", 14, "sub_01", "G", ["T"], None, None, {
"expected": ["artificial_chr1:14=G/T"],
"ANN": ["T|ann_1|0", "T|ann_2|0", "A|ann_3|"],
"expectedANN": ["T|ann_1|0", "T|ann_2|0"]
}),
VCFRecord("artificial_chr1", 19, "sub_02", "T", ["A", "C"], None, None, {
"expected": ["artificial_chr1:19=T/A", "artificial_chr1:19=T/C"],
"ANN": ["A|ann_1|0", "A|ann_2|0", "T|ann_3|"],
"expectedANN": ["A|ann_1|0", "A|ann_2|0"]
}),
# Substit multi nt
VCFRecord("artificial_chr1", 7, "sub_03", "CATGTATG", ["GTACCCGC"], None, None, {
"expected": ["artificial_chr1:7=CATGTATG/GTACCCGC"],
"ANN": ["GTACCCGC|ann_1|0", "GTACCCGC|ann_2|0", "GTGT|ann_3|"],
"expectedANN": ["GTACCCGC|ann_1|0", "GTACCCGC|ann_2|0"]
}),
VCFRecord("artificial_chr1", 11, "sub_04", "TATGTATG", ["GTACCCGC", "GTACCCAA"], None, None, {
"expected": ["artificial_chr1:11=TATGTATG/GTACCCGC", "artificial_chr1:11=TATGTATG/GTACCCAA"],
"ANN": ["GTACCCGC|ann_1|0", "GTACCCGC|ann_2|0", "GTACCCAA|ann_3|1"],
"expectedANN": ["GTACCCGC|ann_1|0", "GTACCCGC|ann_2|0", "GTACCCAA|ann_3|1"]
}),
# Insertion single nt
VCFRecord("artificial_chr1", 14, "ins_01", "G", ["GA"], None, None, {
"expected": ["artificial_chr1:14=G/GA"],
"ANN": ["GA|ann_1|0", "GA|ann_2|0", "GT|ann_3|"],
"expectedANN": ["GA|ann_1|0", "GA|ann_2|0"]
}),
VCFRecord("artificial_chr1", 20, "ins_02", "-", ["A"], None, None, {
"expected": ["artificial_chr1:19=T/TA"],
"ANN": ["A|ann_1|0", "A|ann_2|0", "T|ann_3|"],
"expectedANN": ["TA|ann_1|0", "TA|ann_2|0"]
}),
VCFRecord("artificial_chr1", 14, "ins_03", "G", ["GA", "GC"], None, None, {
"expected": ["artificial_chr1:14=G/GA", "artificial_chr1:14=G/GC"],
"ANN": ["GA|ann_1|0", "GA|ann_2|0", "GC|ann_3|1", "GT|ann_4|"],
"expectedANN": ["GA|ann_1|0", "GA|ann_2|0", "GC|ann_3|1"]
}),
VCFRecord("artificial_chr1", 20, "ins_04", "-", ["A", "C"], None, None, {
"expected": ["artificial_chr1:19=T/TA", "artificial_chr1:19=T/TC"],
"ANN": ["A|ann_1|0", "A|ann_2|0", "C|ann_3|1", "T|ann_4|"],
"expectedANN": ["TA|ann_1|0", "TA|ann_2|0", "TC|ann_3|1"]
}),
# Insertion multi nt
VCFRecord("artificial_chr1", 14, "ins_05", "G", ["GATGC"], None, None, {
"expected": ["artificial_chr1:14=G/GATGC"],
"ANN": ["GATGC|ann_1|0", "GATGC|ann_2|0", "GAAAC|ann_3|"],
"expectedANN": ["GATGC|ann_1|0", "GATGC|ann_2|0"]
}),
VCFRecord("artificial_chr1", 20, "ins_06", "-", ["AAATC"], None, None, {
"expected": ["artificial_chr1:19=T/TAAATC"],
"ANN": ["AAATC|ann_1|0", "AAATC|ann_2|0", "GAAAC|ann_3|"],
"expectedANN": ["TAAATC|ann_1|0", "TAAATC|ann_2|0"]
}),
# Movable insertion multi nt
VCFRecord("artificial_chr1", 14, "ins_07", "G", ["GTG"], None, None, {
"expected": ["artificial_chr1:12=A/ATG"],
"ANN": ["GTG|ann_1|0", "GTG|ann_2|0", "GAAAC|ann_3|"],
"expectedANN": ["ATG|ann_1|0", "ATG|ann_2|0"]
}),
VCFRecord("artificial_chr1", 27, "ins_08", "A", ["AAAA"], None, None, {
"expected": ["artificial_chr1:25=C/CAAA"],
"ANN": ["AAAA|ann_1|0", "AAAA|ann_2|0", "CAAA|ann_3|"],
"expectedANN": ["CAAA|ann_1|0", "CAAA|ann_2|0"]
}),
# Deletion single nt
VCFRecord("artificial_chr1", 14, "del_01", "G", [""], None, None, {
"expected": ["artificial_chr1:13=TG/T"],
"ANN": ["-|ann_1|0", "-|ann_2|0", "T|ann_3|"],
"expectedANN": ["T|ann_1|0", "T|ann_2|0"]
}),
VCFRecord("artificial_chr1", 14, "del_02", "G", ["-"], None, None, {
"expected": ["artificial_chr1:13=TG/T"],
"ANN": ["-|ann_1|0", "-|ann_2|0", "T|ann_3|"],
"expectedANN": ["T|ann_1|0", "T|ann_2|0"]
}),
VCFRecord("artificial_chr1", 13, "del_03", "TG", ["T"], None, None, {
"expected": ["artificial_chr1:13=TG/T"],
"ANN": ["T|ann_1|0", "T|ann_2|0", "A|ann_3|"],
"expectedANN": ["T|ann_1|0", "T|ann_2|0"]
}),
VCFRecord("artificial_chr1", 13, "del_04", "TG", ["T", "-"], None, None, {
"expected": ["artificial_chr1:13=TG/T", "artificial_chr1:12=ATG/A"],
"ANN": ["T|ann_1|0", "T|ann_2|0", "-|ann_3|1"],
"expectedANN": ["T|ann_1|0", "T|ann_2|0", "A|ann_3|1"]
}),
# Movable deletion multi nt
VCFRecord("artificial_chr1", 11, "del_05", "TATG", ["T", "TA", "-"], None, None, {
"expected": ["artificial_chr1:11=TATG/T", "artificial_chr1:12=ATG/A", "artificial_chr1:7=CATGT/C"],
"ANN": ["T|ann_1|0", "T|ann_2|0", "TA|ann_3|1", "-|ann_4|2"],
"expectedANN": ["T|ann_1|0", "T|ann_2|0", "A|ann_3|1", "C|ann_4|2"]
}),
]
for idx, curr_var in enumerate(self.variants):
FH_var.write(curr_var)
def testWrite(self):
with FastaIO(self.tmp_out, "w") as FH_out:
for curr_rec in self.expected_rec:
FH_out.write(curr_rec)
self.assertTrue(FastaIO.isValid(self.tmp_out))
self.assertTrue(filecmp.cmp(self.tmp_out, self.tmp_mono_line))