def get_stats(blastfile, strict=False):
from jcvi.utils.range import range_union, range_span
from .pyblast import BlastLine
logging.debug("Report stats on `%s`" % blastfile)
fp = open(blastfile)
ref_ivs = []
qry_ivs = []
identicals = 0
ngaps = 0
alignlens = []
for row in fp:
c = BlastLine(row)
qstart, qstop = c.qstart, c.qstop
if qstart > qstop:
qstart, qstop = qstop, qstart
qry_ivs.append((c.query, qstart, qstop))
sstart, sstop = c.sstart, c.sstop
if sstart > sstop:
sstart, sstop = sstop, sstart
ref_ivs.append((c.subject, sstart, sstop))
alen = c.hitlen
ngaps += c.ngaps
identicals += c.hitlen - c.nmismatch - c.ngaps
alignlens.append(alen)
qrycovered = range_union(qry_ivs)
refcovered = range_union(ref_ivs)
if strict:
# We discount gaps in counting covered bases, since we
# did not track individually gaps in qry and ref, we assume
# the gaps are opened evenly in the two sequences
qrycovered -= ngaps / 2
refcovered -= ngaps / 2
qryspan = range_span(qry_ivs)
refspan = range_span(ref_ivs)
_, AL50, _ = calculate_A50(alignlens)
filename = op.basename(blastfile)
alignstats = AlignStats(
filename, qrycovered, refcovered, qryspan, refspan, identicals, AL50
)
return alignstats
def get_stats(blastfile, strict=False):
from jcvi.utils.range import range_union, range_span
from .pyblast import BlastLine
logging.debug("Report stats on `%s`" % blastfile)
fp = open(blastfile)
ref_ivs = []
qry_ivs = []
identicals = 0
ngaps = 0
alignlens = []
for row in fp:
c = BlastLine(row)
qstart, qstop = c.qstart, c.qstop
if qstart > qstop:
qstart, qstop = qstop, qstart
qry_ivs.append((c.query, qstart, qstop))
sstart, sstop = c.sstart, c.sstop
if sstart > sstop:
sstart, sstop = sstop, sstart
ref_ivs.append((c.subject, sstart, sstop))
alen = c.hitlen
ngaps += c.ngaps
identicals += c.hitlen - c.nmismatch - c.ngaps
alignlens.append(alen)
qrycovered = range_union(qry_ivs)
refcovered = range_union(ref_ivs)
if strict:
# We discount gaps in counting covered bases, since we
# did not track individually gaps in qry and ref, we assume
# the gaps are opened evenly in the two sequences
qrycovered -= ngaps / 2
refcovered -= ngaps / 2
qryspan = range_span(qry_ivs)
refspan = range_span(ref_ivs)
_, AL50, _ = calculate_A50(alignlens)
filename = op.basename(blastfile)
alignstats = AlignStats(filename, qrycovered, refcovered,
qryspan, refspan, identicals, AL50)
return alignstats
def test_range_span(ranges, expected):
from jcvi.utils.range import range_span
assert range_span(ranges) == expected