def get_matched_segments(self, seqrecord_name):
"It returns the matched segments for the given query (SeqRecord) name."
try:
blast = self._blasts[seqrecord_name]
except KeyError:
# There was no match in the blast
return None
match_parts = [mp for m in blast["matches"] for mp in m["match_parts"]]
segments = covered_segments_from_match_parts(match_parts, in_query=False)
return segments
def get_matched_segments(self, seqrecord_name):
'It returns the matched segments for the given query (SeqRecord) name.'
try:
blast = self._blasts[seqrecord_name]
except KeyError:
# There was no match in the blast
return None
match_parts = [mp for m in blast['matches'] for mp in m['match_parts']]
segments = covered_segments_from_match_parts(match_parts,
in_query=False)
return segments
def get_matched_segments(self, seqrecord_name):
"it return the matched segments for the given seqrecord"
ignore_elongation_shorter = DEFAULT_IGNORE_ELONGATION_SHORTER
try:
match_parts = self._match_parts[seqrecord_name]
except KeyError:
# There was no match in the blast
return None
# Any of the match_parts has been elongated?
elongated_match = False
for m_p in match_parts:
if ELONGATED in m_p and m_p[ELONGATED] > ignore_elongation_shorter:
elongated_match = True
segments = covered_segments_from_match_parts(match_parts, in_query=False)
return segments, elongated_match
def get_matched_segments_for_read(self, read_name):
"It returns the matched segments for any oligo"
setting_key = "DEFAULT_IGNORE_ELONGATION_SHORTER"
ignore_elongation_shorter = get_setting(setting_key)
try:
match_parts = self._match_parts[read_name]
except KeyError:
# There was no match in the blast
return None
# Any of the match_parts has been elongated?
elongated_match = False
for m_p in match_parts:
if ELONGATED in m_p and m_p[ELONGATED] > ignore_elongation_shorter:
elongated_match = True
segments = covered_segments_from_match_parts(match_parts, in_query=False)
return segments, elongated_match
def get_matched_segments_for_read(self, read_name):
'It returns the matched segments for any oligo'
setting_key = 'DEFAULT_IGNORE_ELONGATION_SHORTER'
ignore_elongation_shorter = get_setting(setting_key)
try:
match_parts = self._match_parts[read_name]
except KeyError:
# There was no match in the blast
return None
# Any of the match_parts has been elongated?
elongated_match = False
for m_p in match_parts:
if ELONGATED in m_p and m_p[ELONGATED] > ignore_elongation_shorter:
elongated_match = True
segments = covered_segments_from_match_parts(match_parts,
in_query=False)
return segments, elongated_match
def test_match_parts_merging(self):
'''Merging match parts'''
# --- ---
# ---
match_part1 = {'query_start': 80, 'query_end': 100,
'subject_start': 180, 'subject_end': 200}
match_part2 = {'query_start': 90, 'query_end': 110,
'subject_start': 190, 'subject_end': 210}
match_part3 = {'query_start': 190, 'query_end': 200,
'subject_start': 290, 'subject_end': 300}
mparts = [match_part1, match_part2, match_part3]
covered_segs = covered_segments_from_match_parts(mparts)
assert covered_segs == [(80, 110), (190, 200)]
match_part2 = {'query_start': 90, 'query_end': 110,
'subject_start': 190, 'subject_end': 210}
match_part3 = {'query_start': 190, 'query_end': 200,
'subject_start': 290, 'subject_end': 300}
covered_segs = covered_segments_from_match_parts([match_part2,
match_part3])
assert covered_segs == [(90, 110), (190, 200)]
# q 0---10
# s 0---10
# q 5---15
# s 15--25
match_part1 = {'query_start': 0, 'query_end': 10,
'subject_start': 0, 'subject_end': 10}
match_part2 = {'query_start': 5, 'query_end': 15,
'subject_start': 15, 'subject_end': 25}
mparts = [match_part1, match_part2]
covered_segs = covered_segments_from_match_parts(mparts)
assert covered_segs == [(0, 15)]
covered_segs = covered_segments_from_match_parts(mparts,
in_query=False)
assert covered_segs == [(0, 10), (15, 25)]
match_part1 = {'query_start': 1, 'query_end': 10,
'subject_start': 1, 'subject_end': 10}
match_part2 = {'query_start': 11, 'query_end': 20,
'subject_start': 11, 'subject_end': 20}
match_part3 = {'query_start': 30, 'query_end': 40,
'subject_start': 30, 'subject_end': 40}
mparts = [match_part1, match_part2, match_part3]
covered_segs = covered_segments_from_match_parts(mparts)
assert covered_segs == [(1, 20), (30, 40)]
match_part1 = {'query_start': 1, 'query_end': 10,
'subject_start': 1, 'subject_end': 10}
match_part2 = {'query_start': 10, 'query_end': 20,
'subject_start': 10, 'subject_end': 20}
mparts = [match_part1, match_part2]
covered_segs = covered_segments_from_match_parts(mparts)
assert covered_segs == [(1, 20)]
match_part1 = {'query_start': 80, 'query_end': 85,
'subject_start': 180, 'subject_end': 185}
match_part2 = {'query_start': 90, 'query_end': 110,
'subject_start': 190, 'subject_end': 210}
match_part3 = {'query_start': 190, 'query_end': 200,
'subject_start': 290, 'subject_end': 300}
mparts = [match_part1, match_part2, match_part3]
covered_segs = covered_segments_from_match_parts(mparts,
merge_segments_closer=10)
assert covered_segs == [(80, 110), (190, 200)]
covered_segs = covered_segments_from_match_parts(mparts)
assert covered_segs == [(80, 85), (90, 110), (190, 200)]
mpart1 = {'query_start': 0, 'query_end': 41,
'subject_end': 140, 'subject_start': 99}
mpart2 = {'query_start': 0, 'query_end': 41,
'subject_start': 140, 'subject_end': 99}
mpart3 = {'query_start': 0, 'query_end': 41,
'subject_start': 0, 'subject_end': 41}
mparts = [mpart1, mpart2, mpart3]
covered_segs = covered_segments_from_match_parts(mparts,
in_query=False)
assert covered_segs == [(0, 41), (99, 140)]
