def test_to_string():
f = "tests/data/tabd.blast"
for line in open(f):
a = BlastLine(line)
b = BlastLine(a.to_blast_line())
# works better than string comparison because of floats.
for attr in some_attrs:
assert getattr(a, attr) == getattr(b, attr), (a, b, attr)
def test_query_subject_props():
f = "tests/data/tabd.blast"
line = BlastLine(open(f).readline())
line.query = "asdf"
line.subject = "dddd"
assert line.query == "asdf"
assert line.subject == "dddd"
assert "asdf" in line.to_blast_line()
assert "dddd" in line.to_blast_line()
def test_to_string():
f = "tests/data/tabd.blast"
for line in open(f):
a = BlastLine(line)
b = BlastLine(a.to_blast_line())
# works better than string comparison because of floats.
for attr in some_attrs:
assert getattr(a, attr) == getattr(b, attr), (a, b, attr)
def test_query_subject_props():
f = "tests/data/tabd.blast"
line = BlastLine(open(f).readline())
line.query = "asdf"
line.subject = "dddd"
assert line.query == "asdf"
assert line.subject == "dddd"
assert "asdf" in line.to_blast_line()
assert "dddd" in line.to_blast_line()
QSEQ = '2'
SSEQ = '4'
print >>sys.stderr, ortho[(QSEQ, SSEQ)]
for line in open(fblast):
b = BlastLine(line)
q = gff[b.query]
s = gff[b.subject]
if not (q.seqid == QSEQ and s.seqid == SSEQ): continue
b.qstart += q.start
b.qstop += q.start
b.sstart += s.start
b.sstop += s.start
print b.to_blast_line()
xs.append(b.qstart)
ys.append(b.sstart)
import matplotlib.pyplot as plt
from matplotlib.patches import Rectangle
f = plt.figure()
ax = f.add_subplot(1, 1, 1)
for xmin, xmax, ymin, ymax in ortho[('2', '4')]:
r = Rectangle((xmin, ymin), width=xmax-xmin, height=ymax-ymin, ec='r', fc='none')
ax.add_patch(r)
QSEQ = '2'
SSEQ = '4'
print >> sys.stderr, ortho[(QSEQ, SSEQ)]
for line in open(fblast):
b = BlastLine(line)
q = gff[b.query]
s = gff[b.subject]
if not (q.seqid == QSEQ and s.seqid == SSEQ): continue
b.qstart += q.start
b.qstop += q.start
b.sstart += s.start
b.sstop += s.start
print b.to_blast_line()
xs.append(b.qstart)
ys.append(b.sstart)
import matplotlib.pyplot as plt
from matplotlib.patches import Rectangle
f = plt.figure()
ax = f.add_subplot(1, 1, 1)
for xmin, xmax, ymin, ymax in ortho[('2', '4')]:
r = Rectangle((xmin, ymin),
width=xmax - xmin,
height=ymax - ymin,
ec='r',
