--invert Invert selection (leave -n out) [off]
-r --remove-nonseq-chars Remove non sequence characters (like *) from sequences [off]
''')
# parser
p = ap.ArgumentParser()
p.add_argument("-in", "--input-file")
p.add_argument("-out", "--output-file")
p.add_argument("--invert", action="store_true")
p.add_argument("-n", "--names", metavar="NAMES")
p.add_argument("-r", "--remove-nonseq-chars", action="store_true")
args = p.parse_args()
# read input file
sys.stderr.write("[{0}]\tImporting list of names\n".format(at()))
FOFN = open(args.names, "r")
NAMES = []
for line in FOFN:
NAMES.append(line.rstrip().split()[0].strip(">"))
#
FOFN.close()
NAMES = list(set(NAMES))
sys.stderr.write("[{0}]\tStored {1} names\n".format(at(), len(NAMES)))
# parsing input fasta and writing to output
k = 0
sys.stderr.write(
"[{0}]\tParsing input FASTA and writing to output lines matching name list\n"
.format(at()))
else:
INPUT = sys.stdin
if args.output_file:
OUTPUT = open(args.output_file, "w")
else:
OUTPUT = sys.stdout
if args.error_file:
ERROR = open(args.error_file, "w")
else:
ERROR = sys.stderr
if args.verbose:
ERROR.write("[{0}] Reading input file, computing boundaries ... \n".format(
at()))
dic = {}
for line in INPUT:
lst = line.rstrip("\r\n\b").split("\t")
scaffold = lst[0]
position = int(lst[3])
#
try:
dic[scaffold]
except KeyError:
dic[scaffold] = [[position, position]]
#
k = 0
lastIndex = len(dic[scaffold]) - 1
while ((position > dic[scaffold][k][1] + 1) and (k < lastIndex)):
p.add_argument("-e", "--error-file")
args = p.parse_args()
if args.output_file:
OUTPUT = open(args.output_file, "w")
else:
OUTPUT = sys.stdout
if args.error_file:
ERROR = open(args.error_file, "w")
else:
ERROR = sys.stderr
# reading file A
if args.verbose:
ERROR.write("[{0}] Reading File A\n".format(at()))
FileA = {}
INPUT = open(args.gff_a, "r")
for line in INPUT:
lst = line.rstrip("\b\r\n").split("\t")
if lst[2] == args.feature:
scaffold = str(lst[0])
start = int(lst[3])
end = int(lst[4])
try:
if len(FileA[scaffold]) > 0:
for region in FileA[scaffold]:
if end == region[0] - 1:
idx = FileA[scaffold].index(region)
FileA[scaffold][idx] = [start, region[1]]
return y
# gtfdic function
def gtfdic(x):
t = x.split("; ")
y = {}
for z in t:
result = re.search('(.*) \"(.*)\"', z)
y[str(result.group(1))] = str(result.group(2))
return y
### CREATE NAMES LIST
sys.stderr.write("[{0}]\tStoring names ...\n".format(at()))
k = 0
INPUT = open(args.names, "r")
NAMES = []
for line in INPUT:
name = line.rstrip()
NAMES.append(name)
k += 1
INPUT.close()
sys.stderr.write("[{0}]\tStored {1} names\n".format(at(), k))
### SELECT GENES
else:
INPUT = sys.stdin
if args.output_file:
OUTPUT = open(args.output_file, "w")
else:
OUTPUT = sys.stdout
if args.error_file:
ERROR = open(args.error_file, "w")
else:
ERROR = sys.stderr
if args.verbose:
ERROR.write("[{0}] Reading input file, computing boundaries ... \n".format(at()))
dic = {}
for line in INPUT:
lst = line.rstrip("\r\n\b").split("\t")
scaffold = lst[0]
position = int(lst[3])
#
try:
dic[scaffold]
except KeyError:
dic[scaffold] = [[position,position]]
#
k=0
lastIndex = len(dic[scaffold])-1
while ((position > dic[scaffold][k][1]+1) and (k < lastIndex)):
#while True:
for vezes in range(5):
try:
qwertyuiop = 1+1
#r = session.get('https://www.inscricao.marinha.mil.br/marinha/index_concursos.jsp?id_concurso=384')
except Exception as e:
print('Conexão Rejeitada/Demorada')
else:
n_titulos = 0
n_titulos_novos = 0
#titulos_encontrados = [c.text for c in r.html.find('u')]
titulos_encontrados = teste[vezes].copy()
novos = []
inalterados = []
excluidos = []
hora_consulta = at(lt())
for c in range(len(titulos)):
for b in range(len(titulos_encontrados)):
if titulos[c] == titulos_encontrados[b]:
inalterados.append(c)
if not c in inalterados:
excluidos.append(c)
for c in range(len(titulos_encontrados)):
for b in range(len(titulos)):
if titulos[b] == titulos_encontrados[c]:
pass
if not c in inalterados and not c in excluidos:
novos.append(c)
args = p.parse_args()
if args.output_file:
OUTPUT = open(args.output_file, "w")
else:
OUTPUT = sys.stdout
if args.error_file:
ERROR = open(args.error_file, "w")
else:
ERROR = sys.stderr
# reading file A
if args.verbose:
ERROR.write("[{0}] Reading File A\n".format(at()))
FileA = {}
INPUT = open(args.gff_a, "r")
for line in INPUT:
lst = line.rstrip("\b\r\n").split("\t")
if lst[2] == args.feature:
scaffold = str(lst[0])
start = int(lst[3])
end = int(lst[4])
try:
if len(FileA[scaffold]) > 0:
for region in FileA[scaffold]:
if end == region[0]-1:
idx = FileA[scaffold].index(region)
FileA[scaffold][idx] = [start,region[1]]
result = re.search('(.*)=(.*)', z)
y[str(result.group(1))] = str(result.group(2))
return y
# gtfdic function
def gtfdic(x):
t = x.split("; ")
y = {}
for z in t:
result = re.search('(.*) \"(.*)\"', z)
y[str(result.group(1))] = str(result.group(2))
return y
### CREATE NAMES LIST
sys.stderr.write("[{0}]\tStoring names ...\n".format(at()))
k=0
INPUT = open(args.names, "r")
NAMES = []
for line in INPUT:
name = line.rstrip()
NAMES.append(name)
k+=1
INPUT.close()
sys.stderr.write("[{0}]\tStored {1} names\n".format(at(), k))
### SELECT GENES
-r --remove-nonseq-chars Remove non sequence characters (like *) from sequences [off]
''')
# parser
p = ap.ArgumentParser()
p.add_argument("-in", "--input-file")
p.add_argument("-out", "--output-file")
p.add_argument("--invert", action="store_true")
p.add_argument("-n", "--names", metavar="NAMES")
p.add_argument("-r", "--remove-nonseq-chars", action="store_true")
args = p.parse_args()
# read input file
sys.stderr.write("[{0}]\tImporting list of names\n".format(at()))
FOFN = open(args.names, "r")
NAMES = []
for line in FOFN:
NAMES.append(line.rstrip().split()[0].strip(">"))
#
FOFN.close()
NAMES = list(set(NAMES))
sys.stderr.write("[{0}]\tStored {1} names\n".format(at(), len(NAMES)))
# parsing input fasta and writing to output
k=0
sys.stderr.write("[{0}]\tParsing input FASTA and writing to output lines matching name list\n".format(at()))
INPUT = open(args.input_file, "r")
fake_read = fake_read_name + "\n" + fake_read_seq + "\n"
return fake_read
revcomp = {"A":"T", "C":"G", "T":"A", "G":"C", "N":"N"}
def paired_end(record, start_1, end_1, start_2, end_2, k):
fake_pair_seq = [str(record.seq)[start_1:end_1], "".join([revcomp[i] for i in str(record.seq)[start_2:end_2]])[::-1]]
fake_pair_name = [">" + str(record.id) + "_" + str(k) + "/1", ">" + str(record.id) + "_" + str(k) + "/2"]
fake_pair = [fake_pair_name[0] + "\n" + fake_pair_seq[0] + "\n", fake_pair_name[1] + "\n" + fake_pair_seq[1] + "\n"]
return fake_pair
### detect number of cpu and define pool ###
if args.verbose:
if args.threads > 1:
ERROR.write("[{0}] Defined {1} threads\n".format(at(), args.threads))
elif args.threads == 1:
ERROR.write("[{0}] Defined {1} thread\n".format(at(), args.threads))
if args.verbose:
if args.type == "SE":
ERROR.write("[{0}] Generating reads of {1} length every {2} positions\n".format(at(), args.read_length, args.step_size))
elif args.type == "PE":
ERROR.write("[{0}] Generating paired-end reads of insert size {1} and length {2} every {3} positions\n".format(at(), args.insert_size, args.read_length, args.step_size))
ERROR.write("[{0}] Distance between mates: {1}\n".format(at(), args.insert_size-(2*args.read_length)))
### run processes
fake_pair_name = [
">" + str(record.id) + "_" + str(k) + "/1",
">" + str(record.id) + "_" + str(k) + "/2"
]
fake_pair = [
fake_pair_name[0] + "\n" + fake_pair_seq[0] + "\n",
fake_pair_name[1] + "\n" + fake_pair_seq[1] + "\n"
]
return fake_pair
### detect number of cpu and define pool ###
if args.verbose:
if args.threads > 1:
ERROR.write("[{0}] Defined {1} threads\n".format(at(), args.threads))
elif args.threads == 1:
ERROR.write("[{0}] Defined {1} thread\n".format(at(), args.threads))
if args.verbose:
if args.type == "SE":
ERROR.write(
"[{0}] Generating reads of {1} length every {2} positions\n".
format(at(), args.read_length, args.step_size))
elif args.type == "PE":
ERROR.write(
"[{0}] Generating paired-end reads of insert size {1} and length {2} every {3} positions\n"
.format(at(), args.insert_size, args.read_length, args.step_size))
ERROR.write("[{0}] Distance between mates: {1}\n".format(
at(), args.insert_size - (2 * args.read_length)))
# gtfdic function
# import re
def gtfdic(x):
t = x.split("; ")
y = {}
for z in t:
result = re.search('(.*) \"(.*)\"', z)
y[str(result.group(1))] = str(result.group(2))
return y
### reading scaffold lengths
if args.verbose:
sys.stderr.write("[{0}]\tReading scaffold lengths\n".format(at()))
Scaflen = {}
SCAFS = open(args.scaffold_lengths, "r")
for line in SCAFS:
lst = line.rstrip().split("\t")
Scaflen[lst[0]] = int(lst[1])
SCAFS.close()
if args.verbose:
sys.stderr.write("[{0}]\tStored information on {1} scaffolds\n".format(
at(), len(Scaflen.keys())))
### READ INPUT FILE