def _splitFile(self):
totalSize = os.path.getsize(self._inFile.name)
if totalSize <= self._splitSize:
# do not split file, the file isn't so big.
return None
fileNames = []
with open(self._inFile.name, 'r+b') as f:
size = 0
lines = []
for line in f:
if not is_number(line.rstrip().split('\t')[-1]):
print 'hej',line
size += len(line)
lines.append(line)
if size >= self._splitSize:
tmpFile = NamedTemporaryFile(delete=False)
fileNames.append(tmpFile)
tmpFile.write(''.join(lines))
tmpFile.close()
del lines[:]
size = 0
if size > 0:
tmpFile = NamedTemporaryFile(delete=False)
fileNames.append(tmpFile)
tmpFile.write(''.join(lines))
tmpFile.close()
for tmp_file in fileNames:
for line in open(tmp_file.name, 'rb'):
if not is_number(line.rstrip().split('\t')[-1]):
print line
return fileNames
def _splitFile(self):
totalSize = os.path.getsize(self._inFile.name)
if totalSize <= self._splitSize:
# do not split file, the file isn't so big.
return None
fileNames = []
with open(self._inFile.name, 'r+b') as f:
size = 0
lines = []
for line in f:
if not is_number(line.rstrip().split('\t')[-1]):
print('hej', line)
size += len(line)
lines.append(line)
if size >= self._splitSize:
tmpFile = NamedTemporaryFile(delete=False)
fileNames.append(tmpFile)
tmpFile.write(''.join(lines))
tmpFile.close()
del lines[:]
size = 0
if size > 0:
tmpFile = NamedTemporaryFile(delete=False)
fileNames.append(tmpFile)
tmpFile.write(''.join(lines))
tmpFile.close()
for tmp_file in fileNames:
for line in open(tmp_file.name, 'rb'):
if not is_number(line.rstrip().split('\t')[-1]):
print(line)
return fileNames
def test_negative():
"""Try if is_number behaves correct when not given a number."""
my_empty_string = ''
my_minus = '-'
my_string = 'g'
my_none = None
assert not is_number(my_none)
assert not is_number(my_empty_string)
assert not is_number(my_string)
assert not is_number(my_minus)
def test_negative(): """Try if is_number behaves correct when not given a number.""" my_empty_string = '' my_minus = '-' my_string = 'g' my_none = None assert not is_number(my_none) assert not is_number(my_empty_string) assert not is_number(my_string) assert not is_number(my_minus)
def check_predictions(mutation_taster = None, avsift = None, poly_phen = None):
"""Score the variant based on the scores from prediction databases."""
prediction_score = 0
if is_number.is_number(avsift):
if float(avsift) <= 0.05:
prediction_score += 1
if is_number.is_number(mutation_taster):
if float(mutation_taster) >= 0.05:
prediction_score += 1
if is_number.is_number(poly_phen):
if float(poly_phen) >= 0.85:
prediction_score += 1
return prediction_score
def check_predictions(mutation_taster=None, avsift=None, poly_phen=None):
"""Score the variant based on the scores from prediction databases."""
prediction_score = 0
if is_number.is_number(avsift):
if float(avsift) <= 0.05:
prediction_score += 1
if is_number.is_number(mutation_taster):
if float(mutation_taster) >= 0.05:
prediction_score += 1
if is_number.is_number(poly_phen):
if float(poly_phen) >= 0.85:
prediction_score += 1
return prediction_score
def ref_gene_parser(self, line, info, line_count):
"""Parse a file in the refGene format"""
line = line.split('\t')
if 'hr' in line[2]:
info['chrom'] = line[2][3:]
else:
info['chrom'] = line[2]
if is_number.is_number(line[4]) and is_number.is_number(line[5]):
info['start'] = int(line[4])
info['stop'] = int(line[5])
info['transcript_id'] = line[1] #???
info['gene_id'] = line[12]
info['feature_id'] = info['gene_id']
return info
def ref_gene_parser(self, line, info, line_count):
"""Parse a file in the refGene format"""
line = line.split('\t')
if 'hr' in line[2]:
info['chrom'] = line[2][3:]
else:
info['chrom'] = line[2]
if is_number.is_number(line[4]) and is_number.is_number(line[5]):
info['start'] = int(line[4])
info['stop'] = int(line[5])
info['transcript_id'] = line[1] #???
info['gene_id'] = line[12]
info['feature_id'] = info['gene_id']
return info
def ccds_parser(self, line, info, line_count):
"""Parse a ccds line"""
line = line.split('\t')
if 'hr' in line[0]:
info['chrom'] = line[0][3:]
else:
info['chrom'] = line[0]
info['transcript_id'] = line[1]
info['gene_id'] = line[2]
info['feature_id'] = info['gene_id']
if is_number.is_number(line[7]) and is_number.is_number(line[8]):
info['start'] = int(line[7])
info['stop'] = int(line[8])
return info
def ccds_parser(self, line, info, line_count):
"""Parse a ccds line"""
line = line.split('\t')
if 'hr' in line[0]:
info['chrom'] = line[0][3:]
else:
info['chrom'] = line[0]
info['transcript_id'] = line[1]
info['gene_id'] = line[2]
info['feature_id'] = info['gene_id']
if is_number.is_number(line[7]) and is_number.is_number(line[8]):
info['start'] = int(line[7])
info['stop'] = int(line[8])
return info
def main():
parser = argparse.ArgumentParser(description="Check files.")
parser.add_argument('infile',
type=str,
nargs=1,
help='Specify the path to the file of interest.')
parser.add_argument('-out',
'--outfile',
type=str,
nargs=1,
default=[None],
help='Specify the path to the outfile.')
args = parser.parse_args()
infile = args.infile[0]
new_file = NamedTemporaryFile(delete=False)
with open(infile, 'rb') as f:
for line in f:
if not line.startswith('#'):
new_file.write(line)
for line in new_file.readlines():
if not is_number(line.rstrip().split('\t')[-1]):
print('du', line)
print('no errors')
fs = FileSort(new_file, args.outfile[0])
fs.sort()
def check_base_conservation(gerp_base_score=None):
"""Score the variant based on the base level conservation."""
base_conservation_score = 0
if is_number.is_number(gerp_base_score):
if float(gerp_base_score) >= 4:
base_conservation_score += 2
elif float(gerp_base_score) >= 2:
base_conservation_score += 1
return base_conservation_score
def check_phylop_score(phylop=None):
"""Score the variant based on the Phylop score."""
phylop_score = 0
if is_number.is_number(phylop):
if float(phylop) >= 0.9984188612:
phylop_score += 2
elif float(phylop) >= 0.95:
phylop_score += 1
return phylop_score
def check_base_conservation(gerp_base_score = None):
"""Score the variant based on the base level conservation."""
base_conservation_score = 0
if is_number.is_number(gerp_base_score):
if float(gerp_base_score) >= 4:
base_conservation_score += 2
elif float(gerp_base_score) >= 2:
base_conservation_score += 1
return base_conservation_score
def check_phylop_score(phylop = None):
"""Score the variant based on the Phylop score."""
phylop_score = 0
if is_number.is_number(phylop):
if float(phylop) >= 0.9984188612:
phylop_score += 2
elif float(phylop) >= 0.95:
phylop_score += 1
return phylop_score
def gtf_parser(self, line, info, line_count):
"""Parse a gtf line"""
line = line.split('\t')
if 'hr' in line[0]:
info['chrom'] = line[0][3:]
else:
info['chrom'] = line[0]
if is_number.is_number(line[3]) and is_number.is_number(line[4]):
info['start'] = int(line[3])
info['stop'] = int(line[4])
info_field = line[8].split(';')[:-1]
for information in info_field:
entry = information.split()
if entry[0] == 'transcript_id':
info['transcript_id'] = entry[1][1:-1]
if entry[0] == 'gene_id':
info['gene_id'] = entry[1][1:-1]
info['feature_id'] = info['gene_id']
return info
def gtf_parser(self, line, info, line_count):
"""Parse a gtf line"""
line = line.split('\t')
if 'hr' in line[0]:
info['chrom'] = line[0][3:]
else:
info['chrom'] = line[0]
if is_number.is_number(line[3]) and is_number.is_number(line[4]):
info['start'] = int(line[3])
info['stop'] = int(line[4])
info_field = line[8].split(';')[:-1]
for information in info_field:
entry = information.split()
if entry[0] == 'transcript_id':
info['transcript_id'] = entry[1][1:-1]
if entry[0] == 'gene_id':
info['gene_id'] = entry[1][1:-1]
info['feature_id'] = info['gene_id']
return info
def get_freq_score(frequency):
"""Returns a score depending on the frequency"""
if is_number.is_number(frequency):
if float(frequency) <= 0.005:
return 2
elif float(frequency) <= 0.02:
return 1
#If common variant:
else:
return -12
else: # If not existing in database
return 3
def get_freq_score(frequency):
"""Returns a score depending on the frequency"""
if is_number.is_number(frequency):
if float(frequency) <= 0.005:
return 2
elif float(frequency) <= 0.02:
return 1
#If common variant:
else:
return -12
else:# If not existing in database
return 3
def main():
parser = argparse.ArgumentParser(description="Check files.")
parser.add_argument('infile', type=str, nargs=1, help='Specify the path to the file of interest.')
parser.add_argument('-out', '--outfile', type=str, nargs=1, default=[None], help='Specify the path to the outfile.')
args = parser.parse_args()
infile = args.infile[0]
new_file = NamedTemporaryFile(delete=False)
with open(infile, 'rb') as f:
for line in f:
if not line.startswith('#'):
new_file.write(line)
for line in new_file.readlines():
if not is_number(line.rstrip().split('\t')[-1]):
print 'du', line
print 'no errors'
fs = FileSort(new_file, args.outfile[0])
fs.sort()
def test_integer():
"""Try if is_number behaves correct when given an integer."""
my_integer_string = '1'
my_integer = 1
assert is_number(my_integer_string)
assert is_number(my_integer)
def test_zero(): """Try how is_number behaves when given zero.""" my_zero = 0 my_zero_string = '0' assert is_number(my_zero) assert is_number(my_zero_string)
def test_float(): """Try is is_number behaves correct when given a float.""" my_float = 0.22 my_float_string = '0.22' assert is_number(my_float_string) assert is_number(my_float)
def test_integer(): """Try if is_number behaves correct when given an integer.""" my_integer_string = '1' my_integer = 1 assert is_number(my_integer_string) assert is_number(my_integer)
def test_float():
"""Try is is_number behaves correct when given a float."""
my_float = 0.22
my_float_string = '0.22'
assert is_number(my_float_string)
assert is_number(my_float)
def test_zero():
"""Try how is_number behaves when given zero."""
my_zero = 0
my_zero_string = '0'
assert is_number(my_zero)
assert is_number(my_zero_string)