def test_variant(self):
"""testing get mature sequence"""
from mirtop.mirna import fasta, mapper
from mirtop.mirna.realign import get_mature_sequence, \
align_from_variants
precursors = fasta.read_precursor("data/examples/annotate/hairpin.fa",
"hsa")
matures = mapper.read_gtf_to_precursor(
"data/examples/annotate/hsa.gff3")
res = get_mature_sequence("GAAAATTTTTTTTTTTAAAAG", [5, 15])
if res != "AAAATTTTTTTTTTTAAAA":
raise ValueError("Results for GAAAATTTTTTTTTTTAAAAG was %s" % res)
mature = get_mature_sequence(precursors["hsa-let-7a-1"],
matures["hsa-let-7a-1"]["hsa-let-7a-5p"])
if mature != "GGGATGAGGTAGTAGGTTGTATAGTTTTAG":
raise ValueError("Results for hsa-let-7a-5p is %s" % mature)
res = align_from_variants("AGGTAGTAGGTTGTATAGTT", mature,
"iso_5p:-2")
if res:
raise ValueError("Wrong alignment for test 1 %s" % res)
res = align_from_variants("GATGAGGTAGTAGGTTGTATAGTT", mature,
"iso_5p:+2")
if res:
raise ValueError("Wrong alignment for test 2 %s" % res)
res = align_from_variants("AGGTAGTAGGTTGTATAGTTTT", mature,
"iso_5p:-2,iso_add:2")
if res:
raise ValueError("Wrong alignment for test 3 %s" % res)
res = align_from_variants("AGGTAGTAGGTTGTATAGTTTT", mature,
"iso_5p:-2,iso_3p:2")
if res:
raise ValueError("Wrong alignment for test 4 %s" % res)
res = align_from_variants("AGGTAGTAGGTTGTATAG", mature,
"iso_5p:-2,iso_3p:-2")
if res:
raise ValueError("Wrong alignment for test 5 %s" % res)
res = align_from_variants("AGGTAGTAGGTTGTATAGAA", mature,
"iso_5p:-2,iso_3p:-2,iso_add:2")
if res:
raise ValueError("Wrong alignment for test 6 %s" % res)
res = align_from_variants("AGGTAGTAGGATGTATAGTT", mature,
"iso_5p:-2,iso_snp_central")
if not res:
if res[0][0] != 10:
raise ValueError("Wrong alignment for test 7 %s" % res)
res = align_from_variants("AGGTAGTAGGATGTATAGAA", mature,
"iso_5p:-2,iso_3p:-2,iso_add:2")
if res:
raise ValueError("Wrong alignment for test 8 %s" % res)
def test_variant(self):
"""testing get mature sequence"""
from mirtop.mirna import fasta, mapper
from mirtop.mirna.realign import get_mature_sequence, \
align_from_variants
precursors = fasta.read_precursor("data/examples/annotate/hairpin.fa",
"hsa")
matures = mapper.read_gtf_to_precursor(
"data/examples/annotate/hsa.gff3")
res = get_mature_sequence("GAAAATTTTTTTTTTTAAAAG", [5, 15])
if res != "AAAATTTTTTTTTTTAAAA":
raise ValueError("Results for GAAAATTTTTTTTTTTAAAAG was %s" % res)
mature = get_mature_sequence(precursors["hsa-let-7a-1"],
matures["hsa-let-7a-1"]["hsa-let-7a-5p"])
if mature != "GGGATGAGGTAGTAGGTTGTATAGTTTTAG":
raise ValueError("Results for hsa-let-7a-5p is %s" % mature)
res = align_from_variants("AGGTAGTAGGTTGTATAGTT", mature, "iso_5p:-2")
if res:
raise ValueError("Wrong alignment for test 1 %s" % res)
res = align_from_variants("GATGAGGTAGTAGGTTGTATAGTT", mature,
"iso_5p:+2")
if res:
raise ValueError("Wrong alignment for test 2 %s" % res)
res = align_from_variants("AGGTAGTAGGTTGTATAGTTTT", mature,
"iso_5p:-2,iso_add:2")
if res:
raise ValueError("Wrong alignment for test 3 %s" % res)
res = align_from_variants("AGGTAGTAGGTTGTATAGTTTT", mature,
"iso_5p:-2,iso_3p:2")
if res:
raise ValueError("Wrong alignment for test 4 %s" % res)
res = align_from_variants("AGGTAGTAGGTTGTATAG", mature,
"iso_5p:-2,iso_3p:-2")
if res:
raise ValueError("Wrong alignment for test 5 %s" % res)
res = align_from_variants("AGGTAGTAGGTTGTATAGAA", mature,
"iso_5p:-2,iso_3p:-2,iso_add:2")
if res:
raise ValueError("Wrong alignment for test 6 %s" % res)
res = align_from_variants("AGGTAGTAGGATGTATAGTT", mature,
"iso_5p:-2,iso_snp_central")
if not res:
if res[0][0] != 10:
raise ValueError("Wrong alignment for test 7 %s" % res)
res = align_from_variants("AGGTAGTAGGATGTATAGAA", mature,
"iso_5p:-2,iso_3p:-2,iso_add:2")
if res:
raise ValueError("Wrong alignment for test 8 %s" % res)
def variant_with_nt(line, precursors, matures):
"""
Return nucleotides changes for each variant type
using Variant attribute, precursor sequences and
mature position.
"""
cols = read_gff_line(line)
attr = cols["attrb"]
read = read_id(attr["UID"])
logger.debug("GFF::BODY::precursors %s" % precursors[attr["Parent"]])
logger.debug("GFF:BODY::mature %s" % matures[attr["Parent"]][attr["Name"]])
t5 = variant_to_5p(precursors[attr["Parent"]],
matures[attr["Parent"]][attr["Name"]],
attr["Variant"])
t3 = variant_to_3p(precursors[attr["Parent"]],
matures[attr["Parent"]][attr["Name"]],
attr["Variant"])
add = variant_to_add(read,
attr["Variant"])
mature_sequence = get_mature_sequence(
precursors[attr["Parent"]],
matures[attr["Parent"]][attr["Name"]])
logger.debug("GFF::BODY::mature_sequence %s" % mature_sequence)
mm = align_from_variants(read,
mature_sequence,
attr["Variant"])
if mm == "Invalid":
return mm
if len(mm) > 0:
mm = "".join(["".join(map(str, m)) for m in mm])
else:
mm = "0"
return "iso_5p:%s,iso_3p:%s,iso_add:%s,iso_snp:%s" % (t5, t3, add, mm)
def _align_to_mature(seq, hairpin, mature):
"""Get alignment between seq and mature"""
mirna = get_mature_sequence(hairpin, mature)
hit = align(seq, mirna)
start = hit[0][:8].count("-") - 4 + int(mature[0])
logger.debug("PROST::align:sequence to mature %s" % hit[0])
logger.debug("PROST::align:start: %s -> %s" % (mature[0], start))
return start
def _read_file(fn, precursors, matures, out_dir):
samples = read_samples(fn)
for sample in samples:
with open(os.path.join(out_dir, "%s.mirna" % sample), 'w') as outh:
print("\t".join([
"seq", "name", "freq", "mir", "start", "end", "mism", "add",
"t5", "t3", "s5", "s3", "DB", "precursor", "ambiguity"
]),
file=outh)
with open(fn) as inh:
for line in inh:
if line.startswith("#"):
continue
gff = feature(line)
cols = gff.columns
attr = gff.attributes
read = read_id(attr["UID"])
t5 = variant_to_5p(precursors[attr["Parent"]],
matures[attr["Parent"]][attr["Name"]],
attr["Variant"])
t3 = variant_to_3p(precursors[attr["Parent"]],
matures[attr["Parent"]][attr["Name"]],
attr["Variant"])
add = variant_to_add(read, attr["Variant"])
mature_sequence = get_mature_sequence(
precursors[attr["Parent"]],
matures[attr["Parent"]][attr["Name"]])
mm = align_from_variants(read, mature_sequence, attr["Variant"])
if len(mm) > 1:
continue
elif len(mm) == 1:
mm = "".join(list(map(str, mm[0])))
else:
mm = "0"
hit = attr["Hits"] if "Hits" in attr else "1"
logger.debug("exporter::isomir::decode %s" %
[attr["Variant"], t5, t3, add, mm])
# Error if attr["Read"] doesn't exist
# print(cols)
line = [
read, attr["Read"], "0", attr["Name"], cols['source'],
cols['type'], mm, add, t5, t3, "NA", "NA", "miRNA",
attr["Parent"], hit
]
for sample, counts in zip(samples, attr["Expression"].split(",")):
with open(os.path.join(out_dir, "%s.mirna" % sample),
'a') as outh:
line[2] = counts
print("\t".join(line), file=outh)
def _read_file(fn, precursors, matures, out_dir):
samples = read_samples(fn)
for sample in samples:
with open(os.path.join(out_dir, "%s.mirna" % sample), 'w') as outh:
print("\t".join(
["seq", "name", "freq", "mir", "start", "end",
"mism", "add", "t5", "t3", "s5", "s3", "DB",
"precursor", "ambiguity"]), file=outh)
with open(fn) as inh:
for line in inh:
if line.startswith("#"):
continue
cols = line.strip().split("\t")
attr = read_attributes(line)
read = read_id(attr["UID"])
t5 = variant_to_5p(precursors[attr["Parent"]],
matures[attr["Parent"]][attr["Name"]],
attr["Variant"])
t3 = variant_to_3p(precursors[attr["Parent"]],
matures[attr["Parent"]][attr["Name"]],
attr["Variant"])
add = variant_to_add(read,
attr["Variant"])
mature_sequence = get_mature_sequence(
precursors[attr["Parent"]],
matures[attr["Parent"]][attr["Name"]])
mm = align_from_variants(read,
mature_sequence,
attr["Variant"])
if len(mm) > 1:
continue
elif len(mm) == 1:
mm = "".join(map(str, mm[0]))
else:
mm = "0"
hit = attr["Hits"] if "Hits" in attr else "1"
logger.debug("exporter::isomir::decode %s" % [attr["Variant"],
t5, t3, add, mm])
# Error if attr["Read"] doesn't exist
line = [read, attr["Read"], "0", attr["Name"], cols[1], cols[2],
mm, add, t5, t3, "NA", "NA", "miRNA", attr["Parent"], hit]
for sample, counts in zip(samples, attr["Expression"].split(",")):
with open(os.path.join(out_dir, "%s.mirna" % sample),
'a') as outh:
line[2] = counts
print("\t".join(line), file=outh)
def variant_with_nt(line, precursors, matures):
"""
Return nucleotides changes for each variant type
using Variant attribute, precursor sequences and
mature position.
"""
gff = feature(line)
attr = gff.attributes
read = read_id(attr["UID"])
attr["Parent"] = attr["Parent"].split(",")[0]
if attr["Parent"] not in matures:
logger.warning("Parent miRNA not found in database %s" % attr["Parent"])
return ""
if attr["Name"] not in matures[attr["Parent"]]:
logger.warning("miRNA not found in database %s" % attr["Name"])
return ""
logger.debug("GFF::BODY::precursors %s" % precursors[attr["Parent"]])
logger.debug("GFF:BODY::mature %s" % matures[attr["Parent"]][attr["Name"]])
t5 = variant_to_5p(precursors[attr["Parent"]],
matures[attr["Parent"]][attr["Name"]],
attr["Variant"])
t3 = variant_to_3p(precursors[attr["Parent"]],
matures[attr["Parent"]][attr["Name"]],
attr["Variant"])
add = variant_to_add(read,
attr["Variant"])
mature_sequence = get_mature_sequence(
precursors[attr["Parent"]],
matures[attr["Parent"]][attr["Name"]],
nt=8)
logger.debug("GFF::BODY::mature_sequence %s" % mature_sequence)
mm = align_from_variants(read,
mature_sequence,
attr["Variant"])
if mm == "Invalid":
return mm
if len(mm) > 0:
mm = "".join(["".join([str(v) for v in m]) for m in mm])
else:
mm = "0"
return "iso_5p:%s,iso_3p:%s,iso_add3p:%s,iso_snv:%s" % (t5, t3, add, mm)
def test_spikeins(self):
"""Test spikeins reading and annotation"""
from mirtop.libs import spikeins
from mirtop.mirna.realign import get_mature_sequence
load = spikeins.read_spikeins("data/examples/spikeins/spikeins.fa")
print(load)
load1 = load['spikein-1']
mature_from_data = get_mature_sequence(load1['precursor'],
load1['position'],
exact=True)
if mature_from_data != load1['mature']:
raise ValueError("Sequences doesn't match \n%s\n%s" %
(mature_from_data, load1['mature']))
file_fasta = "data/examples/spikeins/spikeins_pre.fasta"
file_gff = "data/examples/spikeins/spikeins_pre.gff"
spikeins.write_precursors(load, file_fasta)
spikeins.write_gff(load, file_gff)
from mirtop.mirna import mapper, fasta
map_mir = mapper.read_gtf_to_mirna(file_gff)
print(map_mir)
fasta_precursor = fasta.read_precursor(file_fasta, None)
print(fasta_precursor)