def main():
if len(sys.argv) != 3:
drdcommon.error("Wrong # of args", usage)
pattern = sys.argv[1]
re_id = sys.argv[2] # Regular expression to extract id
l = lambda:defaultdict(l)
h = l()
l_ids = []
for fn in drdcommon.files_in_dir(".", pattern):
try:
sid = re.search(re_id, fn).group(1)
l_ids.append(sid)
except:
raise(Exception('Problems extracting id using regular expression.'))
load_data(sid, fn, h)
# print header
sys.stdout.write("chrm coor type num_over_zero ")
for _id in l_ids:
sys.stdout.write("%s " % _id)
print ""
for t, one in h.items():
for chrm, two in one.items():
for coor, three in two.items():
sys.stdout.write("%s %s %s %s " % (str(chrm), str(coor), t, len(three)))
for sid in l_ids:
if sid in three:
sys.stdout.write(str(three[sid]) + " ")
else:
sys.stdout.write("0 ")
print ""
def main():
if len(sys.argv) != 3:
drdcommon.error("Wrong # of args", usage)
pattern = sys.argv[1]
re_id = sys.argv[2] # Regular expression to extract id
l = lambda: defaultdict(l)
h = l()
l_ids = []
for fn in drdcommon.files_in_dir(".", pattern):
try:
sid = re.search(re_id, fn).group(1)
l_ids.append(sid)
except:
raise (
Exception('Problems extracting id using regular expression.'))
load_data(sid, fn, h)
# print header
sys.stdout.write("chrm coor type num_over_zero ")
for _id in l_ids:
sys.stdout.write("%s " % _id)
print ""
for t, one in h.items():
for chrm, two in one.items():
for coor, three in two.items():
sys.stdout.write("%s %s %s %s " %
(str(chrm), str(coor), t, len(three)))
for sid in l_ids:
if sid in three:
sys.stdout.write(str(three[sid]) + " ")
else:
sys.stdout.write("0 ")
print ""
def do_work(pattern):
data = []
for f in drdcommon.files_in_dir('.', pattern):
fd = open(f)
for l in fd.readline():
print l
fd.close()
def do_work(pattern):
data = []
for f in drdcommon.files_in_dir('.', pattern):
fd = open(f)
for l in fd.readline():
print l
fd.close()
def main():
if len(sys.argv) != 4:
drdcommon.error("Wrong # of args", usage)
pattern = sys.argv[1]
re_id = sys.argv[2] # Regular expression to extract id
f_dir = sys.argv[3]
l_ids = []
l = lambda:defaultdict(l)
h = l() # hold all data in mem
files_to_iterate = drdcommon.files_in_dir(f_dir, pattern)
sys.stderr.write("# of files to process: " + str(len(files_to_iterate)) + "\n")
for fn in files_to_iterate:
try:
sid = re.search(re_id, fn).group(1)
l_ids.append(sid)
except:
raise(Exception('Problems extracting id using regular expression.'))
load_data(sid, fn, h)
# print header
out("chrm start ")
for _id in l_ids:
out("%s " % _id)
out("\n")
for chrm, one in h.items():
for start, two in one.items():
out("%s %s " % (str(chrm), str(start)))
for sid, nr in two.items():
out(str(nr[1]) + " ")
out("\n")
def load_hits(self):
drdcommon.log("Loading hits")
for f in drdcommon.files_in_dir('.', self.pattern):
sample_id = self.extract_id(f)
drdcommon.log("fn: %s | id: %s" % (f, sample_id))
for line in drdcommon.xopen(f):
s = line.split()
assert len(s) == 2
n_hits, p_id = s[0], s[1].rstrip()
self.d_hits[p_id][sample_id] = n_hits
def load_hits(self):
drdcommon.log("Loading hits")
for f in drdcommon.files_in_dir('.', self.pattern):
sample_id = self.extract_id(f)
drdcommon.log("fn: %s | id: %s" % (f, sample_id))
for line in drdcommon.xopen(f):
s = line.split()
assert len(s) == 2
n_hits, p_id = s[0], s[1].rstrip()
self.d_hits[p_id][sample_id] = n_hits
def load_data(pattern):
data = []
for f in drdcommon.files_in_dir('.', pattern):
sys.stderr.write(f + "\n")
l_cov_vals = []
for l in open(f):
l_cov_vals.append(int(l.split()[0]))
data.append(l_cov_vals)
if len(data) == 1:
data = data[0]
sys.stderr.write(str(len(data)) + "\n")
return data
if len(sys.argv) != 3:
sys.stderr.write("tool <file_pattern> <pattern_to_extract_id> > out.bed" +
"\n")
sys.exit(1)
out = sys.stdout.write
err = sys.stderr.write
file_pattern, re_id = sys.argv[1], re.compile(sys.argv[2])
err("re for id: %s\n" % (re_id))
# Load data for all genes all samples
data = {}
ids = []
for f in drdcommon.files_in_dir(".", file_pattern):
# extract sample id
match = re_id.search(f)
if match:
_id = match.group(1)
else:
raise (Exception("Problems extracting id for: " + f))
err("Working on id: %s\n" % (_id))
ids.append(_id)
first_line = True
for l in drdcommon.xopen(f):
if first_line:
first_line = False
continue
import re
if len(sys.argv) != 3:
sys.stderr.write("tool <file_pattern> <pattern_to_extract_id> > out.bed" + "\n")
sys.exit(1)
out = sys.stdout.write
err = sys.stderr.write
file_pattern, re_id = sys.argv[1], re.compile(sys.argv[2])
err("re for id: %s\n" % (re_id))
# Load data for all genes all samples
data = {}
ids = []
for f in drdcommon.files_in_dir(".", file_pattern):
# extract sample id
match = re_id.search(f)
if match:
_id = match.group(1)
else:
raise(Exception("Problems extracting id for: " + f))
err("Working on id: %s\n" % (_id) )
ids.append(_id)
first_line = True
for l in drdcommon.xopen(f):
if first_line:
first_line = False
continue
def load_ids_order(self):
for f in drdcommon.files_in_dir('.', self.pattern):
self.ids.append(self.extract_id(f))
drdcommon.log("# of samples loaded: %s" % len(self.ids))
def load_ids_order(self):
for f in drdcommon.files_in_dir('.', self.pattern):
self.ids.append(self.extract_id(f))
drdcommon.log("# of samples loaded: %s" % len(self.ids))