base += "20150501-original/Restored GW screen/"
plates = "idr-metadata/idr0010-doil-dnadamage/screenA/plates/"
dirs = glob(base + "/*")
def iglob(pattern):
def either(c):
return '[%s%s]' % (c.lower(), c.upper()) if c.isalpha() else c
return glob(''.join(map(either, pattern)))
for dir in dirs:
try:
dapi, = [x for x in iglob(dir + "/*dapi*") if "spot" not in x]
try:
bp, = [x for x in iglob(dir + "/*bp*") if "spot" not in x]
except Exception: # Try BB
bp, = [x for x in iglob(dir + "/*bb*") if "spot" not in x]
except Exception:
raise Exception(dir)
plate = basename(dir)
bp = bp.replace("bp", "bxxx")
rv = fp.find_pattern_2seq(dapi, bp)
rv = rv.replace("bxxx", "bp")
print plate, " ".join(rv.split("/")[-1].split(" ")[1:])
with open("%s/%s" % (plates, plate), "w") as screen_file:
screen_file.write("%s/%s.pattern\n" % (plates, plate))
with open("%s/%s.pattern" % (plates, plate), "w") as pattern_file:
pattern_file.write(rv)
plates = "idr-metadata/idr0010-doil-dnadamage/screenA/plates/"
dirs = glob(base + "/*")
def iglob(pattern):
def either(c):
return '[%s%s]' % (c.lower(), c.upper()) if c.isalpha() else c
return glob(''.join(map(either, pattern)))
for dir in dirs:
try:
dapi, = [x for x in iglob(dir + "/*dapi*") if "spot" not in x]
try:
bp, = [x for x in iglob(dir + "/*bp*") if "spot" not in x]
except Exception: # Try BB
bp, = [x for x in iglob(dir + "/*bb*") if "spot" not in x]
except Exception:
raise Exception(dir)
plate = basename(dir)
bp = bp.replace("bp", "bxxx")
rv = fp.find_pattern_2seq(dapi, bp)
rv = rv.replace("bxxx", "bp")
print(plate, " ".join(rv.split("/")[-1].split(" ")[1:]))
with open("%s/%s" % (plates, plate), "w") as screen_file:
screen_file.write("%s/%s.pattern\n" % (plates, plate))
with open("%s/%s.pattern" % (plates, plate), "w") as pattern_file:
pattern_file.write(rv)
def runTest(self):
for (s1, s2), exp_p in self.data:
p = fp.find_pattern_2seq(s1, s2)
self.assertEqual(p, exp_p)
self.assertEqual(set(fp.FilePattern(p).filenames()), set((s1, s2)))
