def test_e2e_ovl_8_20_7(self, e2e_ovl_8_20_7: FixtureForFindOvl):
# Should find overlap of 7 bp length
seq1: str = e2e_ovl_8_20_7[0]
seq2: str = e2e_ovl_8_20_7[1]
mink: int = e2e_ovl_8_20_7[2]
maxk: int = e2e_ovl_8_20_7[3]
assert fov.find_overlap_e2e(seq1, seq2, mink, maxk) == 0
def test_e2e_ovl_7_6(self, e2e_ovl_7_6: FixtureForFindOvl):
# Should not find any overlap
seq1: str = e2e_ovl_7_6[0]
seq2: str = e2e_ovl_7_6[1]
mink: int = e2e_ovl_7_6[2]
maxk: int = e2e_ovl_7_6[3]
assert fov.find_overlap_e2e(seq1, seq2, mink, maxk) == 0
def detect_adjacent_contigs(contig_collection: ContigCollection, mink: int,
maxk: int) -> OverlapCollection:
# Function detects adjacent contigs by comparing their termini.
#
# :param contig_collection: instance of ContigCollection returned by
# `src.contigs.get_contig_collection` function;
# :param mink: minimum length of and overlap to be detected;
# :param maxk: maximum length of and overlap to be detected;
# Count contigs and save this length in order nom to re-cont it later.
num_contigs: int = len(contig_collection)
# Initialize `OverlapCollection` instance
overlap_collection: OverlapCollection = OverlapCollection()
# Iterate over contigs and compare it's termini to other termini
ovl_len: int
i: ContigIndex
for i in range(num_contigs):
# Omit contigs shorter that 'mink'
if contig_collection[i].length <= mink:
print('\r{}/{}'.format(i + 1, num_contigs), end='')
continue
# end if
# === Compare start of the current contig to end of the current contig ===
ovl_len = find_overlap_e2s(contig_collection[i].end,
contig_collection[i].start, mink, maxk)
if not ovl_len in (0, contig_collection[i].length):
overlap_collection.add_overlap(i, Overlap(i, END, i, START,
ovl_len))
overlap_collection.add_overlap(i, Overlap(i, START, i, END,
ovl_len))
# end if
# === Compare start of the current conitg to rc-end of the current contig ===
ovl_len = find_overlap_s2s(contig_collection[i].start,
contig_collection[i].rcend, mink, maxk)
if ovl_len != 0:
overlap_collection.add_overlap(
i, Overlap(i, START, i, RCEND, ovl_len))
overlap_collection.add_overlap(
i, Overlap(i, RCEND, i, START, ovl_len))
# end if
# |=== Compare i-th contig to contigs from i+1 to N ===|
# We do it in order not to compare pairs of contigs more than one time
j: ContigIndex
for j in range(i + 1, num_contigs):
# === Compare i-th start to j-th end ===
ovl_len = find_overlap_e2s(contig_collection[j].end,
contig_collection[i].start, mink, maxk)
if ovl_len != 0:
overlap_collection.add_overlap(
i, Overlap(i, START, j, END, ovl_len))
overlap_collection.add_overlap(
j, Overlap(j, END, i, START, ovl_len))
# end if
# === Compare i-th end to j-th start ===
ovl_len = find_overlap_e2s(contig_collection[i].end,
contig_collection[j].start, mink, maxk)
if ovl_len != 0:
overlap_collection.add_overlap(
i, Overlap(i, END, j, START, ovl_len))
overlap_collection.add_overlap(
j, Overlap(j, START, i, END, ovl_len))
# end if
# === Compare i-th start to reverse-complement j-th start ===
ovl_len = find_overlap_e2s(contig_collection[j].rcstart,
contig_collection[i].start, mink, maxk)
if ovl_len != 0:
overlap_collection.add_overlap(
i, Overlap(i, START, j, RCSTART, ovl_len))
overlap_collection.add_overlap(
j, Overlap(j, START, i, RCSTART, ovl_len))
# end if
# === Compare i-th end to reverse-complement j-th end ===
ovl_len = find_overlap_e2s(contig_collection[i].end,
contig_collection[j].rcend, mink, maxk)
if ovl_len != 0:
overlap_collection.add_overlap(
i, Overlap(i, END, j, RCEND, ovl_len))
overlap_collection.add_overlap(
j, Overlap(j, END, i, RCEND, ovl_len))
# end if
# === Compare i-th start to j-th start ===
ovl_len = find_overlap_s2s(contig_collection[i].start,
contig_collection[j].start, mink, maxk)
if ovl_len != 0:
overlap_collection.add_overlap(
i, Overlap(i, START, j, START, ovl_len))
overlap_collection.add_overlap(
j, Overlap(j, START, i, START, ovl_len))
# end if
# === Compare i-th end to j-th end ===
ovl_len = find_overlap_e2e(contig_collection[i].end,
contig_collection[j].end, mink, maxk)
if ovl_len != 0:
overlap_collection.add_overlap(
i, Overlap(i, END, j, END, ovl_len))
overlap_collection.add_overlap(
j, Overlap(j, END, i, END, ovl_len))
# end if
# === Compare i-th start to reverse-complement j-th end ===
ovl_len = find_overlap_s2s(contig_collection[i].start,
contig_collection[j].rcend, mink, maxk)
if ovl_len != 0:
overlap_collection.add_overlap(
i, Overlap(i, START, j, RCEND, ovl_len))
overlap_collection.add_overlap(
j, Overlap(j, RCEND, i, START, ovl_len))
# end if
# === Compare i-th end to reverse-complement j-th start ===
ovl_len = find_overlap_e2e(contig_collection[i].end,
contig_collection[j].rcstart, mink,
maxk)
if ovl_len != 0:
overlap_collection.add_overlap(
i, Overlap(i, END, j, RCSTART, ovl_len))
overlap_collection.add_overlap(
j, Overlap(j, RCSTART, i, END, ovl_len))
# end if
# end for
print('\r{}/{}'.format(i + 1, num_contigs), end='')
# end for
print()
return overlap_collection