def parse(self, edge_ids=None):
# type: (Optional[Dict[int, List[str]]]) -> Generator[Tuple[int, int, int, int, EdgeInfo]]
for s in self.dot.readlines():
if s.find("->") == -1:
continue
v_from = basic.parseNumber(s)
v_to = basic.parseNumber(s, s.find("->"))
eid = basic.parseNegativeNumber(s, s.find("id"))
len = basic.parseNegativeNumber(s, s.find("\\l"))
cov = basic.parseNumber(s, s.find("k "))
unique = (s.find("black") != -1)
src = (s.find("dir = both") != -1)
if edge_ids is None or eid in edge_ids:
if edge_ids is not None:
if "sink" in edge_ids[eid]:
v_to = "sink"
if "source" in edge_ids[eid]:
v_from = "source"
yield eid, v_from, v_to, cov, EdgeInfo(s, unique, cov, len,
src)
def FillSeq(self, f, numeric=True):
for s in SeqIO.parse_fasta(open(f, "r")):
if numeric:
s.id = str(basic.parseNumber(s.id))
if s.id in self.e:
self.e[s.id].seq = s.seq
self.e[s.id].len = len(s.seq)
if "-" + s.id in self.e:
self.e["-" + s.id].seq = basic.RC(s.seq)
self.e["-" + s.id].len = len(s.seq)
return self
def __init__(self, dir, clean=False):
# type: (str, bool) -> None
self.dir = dir
if clean:
basic.recreate(self.dir)
else:
basic.ensure_dir_existance(self.dir)
self.cnt = 0
for name in os.listdir(self.dir):
num = basic.parseNumber(name)
if num is not None and num >= self.cnt:
self.cnt = num + 1
def FillSeq(self, f, numeric=True):
for s in SeqIO.parse_fasta(open(f, "r")):
if numeric:
s.id = str(basic.parseNumber(s.id))
if s.id in self.e:
self.e[s.id].seq = s.seq
self.e[s.id].len = len(s.seq)
if basic.Reverse(s.id) in self.e:
self.e[basic.Reverse(s.id)].seq = basic.RC(s.seq)
self.e[basic.Reverse(s.id)].len = len(s.seq)
for edge in self.e.values():
assert (edge.seq is not None)
return self
def ReadDot(self, f):
for s in open(f, "r").readlines():
tmp = s
if s[0] != "\"":
continue
s = s.strip().split()
if len(s) < 2 or s[1] != "->":
vid = s[0][1:-1]
self.AddVertex(vid, tmp)
continue
v_from = s[0][1:-1]
v_to = s[2][1:-1]
label = tmp
cov = basic.parseNumber(tmp, tmp.find("k "))
l = int(float(tmp[tmp.find("\\l") + 2:tmp.find("k ")]) * 1000)
id = tmp[tmp.find("id ") + 3:tmp.find("\\l")]
edge = self.AddEdge(id, v_from, v_to, l, label, cov)
return self
import sys
sys.path.append("py")
from common import basic
ll = []
start = False
for s in open(sys.argv[1], "r").readlines():
if s.startswith("New depth 24218"):
start = True
if not start:
continue
if s.startswith("Tail"):
continue
if s.startswith("New tails"):
break
if s.find("Fail") != -1:
ll = []
elif s.find("success") != -1:
call = basic.parseNumber(s)
for tmp in map(eval, ll):
if tmp[call] < tmp[1 - call]:
print min(tmp), max(tmp), 0
else:
print min(tmp), max(tmp), 1
ll = []
elif s.find("[") != -1:
ll.append(s.strip())
import os
import shutil
import sys
from common import basic
in_dir = sys.argv[1]
out_dir = sys.argv[2]
basic.ensure_dir_existance(out_dir)
for f in os.listdir(in_dir):
fig_dir = os.path.join(in_dir, f, "pictures")
cur = 0
nums = map(basic.parseNumber, os.listdir(fig_dir))
last = max(*nums)
f_name = None
for f in os.listdir(fig_dir):
if basic.parseNumber(f) == last:
f_name = f
break
shutil.copy(os.path.join(fig_dir, f_name),
os.path.join(out_dir, f + ".dot"))