def test_two_splitters():
"""
Test how split_strings splits a string with two splitters
"""
string = "1:a,2:b"
splitters = [',', ':']
assert set(split_strings(string, splitters)) == set(['1', 'a', '2', 'b'])
def test_complex():
"""
Test how split_strings splits a complex string
"""
string = "a:1,b:2|3"
splitters = [',',':','|']
assert set(split_strings(string, splitters)) == set(['1','a','2','b','3'])
def test_two_splitters():
"""
Test how split_strings splits a string with two splitters
"""
string = "1:a,2:b"
splitters = [',',':']
assert set(split_strings(string, splitters)) == set(['1','a','2','b'])
def test_complex():
"""
Test how split_strings splits a complex string
"""
string = "a:1,b:2|3"
splitters = [',', ':', '|']
assert set(split_strings(string,
splitters)) == set(['1', 'a', '2', 'b', '3'])
def get_entry(self, variant_line=None, variant_dict=None, raw_entry=None,
vcf_header=None, csq_format=None, dict_key=None, individual_id=None):
"""Return the splitted entry from variant information
Args:
variant_line (str): A vcf formated variant line
vcf_header (list): A list with the vcf header line
csq_format (list): A list with the csq headers
family_id (str): The family id that should be searched. If no id
the first family found will be used
Returns:
entry (list): A list with the splitted entry
"""
if not raw_entry:
raw_entry = self.get_raw_entry(
variant_line=variant_line,
variant_dict=variant_dict,
vcf_header=vcf_header,
individual_id=individual_id,
dict_key=dict_key
)
entry = []
if raw_entry:
if self.field in ['CHROM', 'POS', 'REF', 'QUAL']:
# We know these fields allways has one entry
entry = [raw_entry]
elif self.field in ['ID', 'FILTER']:
# We know ID is allways splitted on ';'
entry = raw_entry.split(';')
elif self.field == 'ALT':
# We know ALT is allways splitted on ','
entry = raw_entry.split(',')
elif self.field == 'FORMAT':
entry = raw_entry.split(':')
elif self.field == 'INFO':
# We are going to treat csq fields separately
if self.info_key == 'CSQ':
if not csq_format:
raise IOError("If CSQ the csq format must be provided")
if not self.csq_key:
raise IOError("If CSQ a csq key must be provided")
for i, head in enumerate(csq_format):
if head == self.csq_key:
# This is the csq entry we are looking for
csq_column = i
# CSQ entries are allways splitted on ','
for csq_entry in raw_entry.split(','):
entry += split_strings(csq_entry.split('|')[csq_column], self.separators)
else:
if self.dict_entry:
separators = self.separators[2:]
else:
separators = self.separators
entry = split_strings(raw_entry, separators)
elif self.field == 'sample_id':
if not self.separators:
entry = split_strings(raw_entry, '/')
#If variant calls are phased we need to split on '|'
if len(entry) == 1:
entry = split_strings(raw_entry, '|')
else:
entry = split_strings(raw_entry, self.separators)
return entry
def test_simple_string():
"""Test how split_strings splits a simple string"""
string = "1,2"
splitters = [',']
assert set(split_strings(string, splitters)) == set(['1', '2'])
def test_simple_string_no_splitters():
"""Test how split_strings splits a simple string"""
string = "1,2"
splitters = []
assert set(split_strings(string, splitters)) == set(['1,2'])
def test_simple_string_no_splitters():
"""Test how split_strings splits a simple string"""
string = "1,2"
splitters = []
assert set(split_strings(string, splitters)) == set(['1,2'])
def test_simple_string():
"""Test how split_strings splits a simple string"""
string = "1,2"
splitters = [',']
assert set(split_strings(string, splitters)) == set(['1','2'])
