def testRnaRevCom(self):
# Without quality
test_record = Sequence("id1", "AuMGCUN").rnaRevCom()
expected_revcom = Sequence("id1", "NAGCKaU")
self.assertTrue(cmpSequences(test_record, expected_revcom))
# With quality
test_record = Sequence("id1", "AuMGCUN", "", "18AAEGH").rnaRevCom()
expected_revcom = Sequence("id1", "NAGCKaU", "", "HGEAA81")
self.assertTrue(cmpSequences(test_record, expected_revcom))
def setUp(self):
tmp_folder = tempfile.gettempdir()
unique_id = str(uuid.uuid1())
# Temporary files
self.tmp_multi_line = os.path.join(tmp_folder,
unique_id + "_multi.fasta")
self.tmp_multi_line_gz = os.path.join(tmp_folder,
unique_id + "_multi.fasta.gz")
self.tmp_mono_line = os.path.join(tmp_folder,
unique_id + "_mono.fasta")
self.tmp_out = os.path.join(tmp_folder, unique_id + "_out.fasta")
# Expected records
self.expected_rec = [
Sequence(
"seq1",
"ATAGATAGCATCCCCCCNATACATAGATAGCATCCCCCCNATACATAGATAGCATCCCCCCNATAC",
"test description"),
Sequence("seq2", ""),
Sequence("seq3", "ATGAAAAAAAAAAAAANTGATGAAAAAAAAAAAAANTG",
"test description 2"),
Sequence("seq4", "", "trimmed")
]
# Create multi line
content = """>seq1 test description
ATAGATAGCATCCCCCCNATAC
ATAGATAGCATCCCCCCNATAC
ATAGATAGCATCCCCCCNATAC
>seq2
>seq3 test description 2
ATGAAAAAAAAAAAAANTG
ATGAAAAAAAAAAAAANTG
>seq4 trimmed
"""
with open(self.tmp_multi_line, "w") as FH_out:
FH_out.write(content)
# Create mono line
content = """>seq1 test description
ATAGATAGCATCCCCCCNATACATAGATAGCATCCCCCCNATACATAGATAGCATCCCCCCNATAC
>seq2
>seq3 test description 2
ATGAAAAAAAAAAAAANTGATGAAAAAAAAAAAAANTG
>seq4 trimmed
"""
with open(self.tmp_mono_line, "w") as FH_out:
FH_out.write(content)
with gzip.open(self.tmp_multi_line_gz, "wt") as FH_out:
FH_out.write(content)
def nextSeq(self):
"""
Return the next sequence.
:return: The next sequence or None if it is the end of file.
:rtype: anacore.sequence.Sequence
"""
seq_record = None
try:
prev_file_pos = self.file_handle.tell()
header = self.file_handle.readline().strip()
new_file_pos = self.file_handle.tell()
if prev_file_pos != new_file_pos:
# Header
fields = header[1:].split(None, 1)
seq_id = fields[0]
seq_desc = fields[1] if len(fields) == 2 else None
self.current_line_nb += 1
# Sequence
seq_str = self.file_handle.readline().strip()
self.current_line_nb += 1
# Separator
self.file_handle.readline()
self.current_line_nb += 1
# Quality
seq_qual = self.file_handle.readline().strip()
self.current_line_nb += 1
# Record
seq_record = Sequence(seq_id, seq_str, seq_desc, seq_qual)
except Exception:
raise IOError('The line {} in "{}" cannot be parsed by {}.'.format(
self.current_line_nb, self.filepath, self.__class__.__name__))
return seq_record
def setUp(self):
tmp_folder = tempfile.gettempdir()
unique_id = str(uuid.uuid1())
# Temporary files
self.tmp_seq = os.path.join(tmp_folder, unique_id + "_ref.fastq")
self.tmp_seq_gz = os.path.join(tmp_folder, unique_id + "_ref.fastq.gz")
self.tmp_out = os.path.join(tmp_folder, unique_id + "_out.fastq")
# Expected
self.expected_rec = [
Sequence("seq1", "ATAGATAGCATCCCCCCNATAC", "test description",
"@?>=<;:9876543210##-,+"),
Sequence("seq2", "", None, ""),
Sequence("seq3", "ATGAAAAAAAAAAAAANTG", "test description 2",
"@?>=<;:987654321#/."),
Sequence("seq4", "", "trimmed", "")
]
# Create file
content = """@seq1 test description
ATAGATAGCATCCCCCCNATAC
+
@?>=<;:9876543210##-,+
@seq2
+
@seq3 test description 2
ATGAAAAAAAAAAAAANTG
+
@?>=<;:987654321#/.
@seq4 trimmed
+
"""
with open(self.tmp_seq, "w") as FH_out:
FH_out.write(content)
with gzip.open(self.tmp_seq_gz, "wt") as FH_out:
FH_out.write(content)
def setUp(self):
tmp_folder = tempfile.gettempdir()
unique_id = str(uuid.uuid1())
# Temporary files
self.tmp_fasta_idx = os.path.join(tmp_folder, unique_id + ".fasta.fai")
self.tmp_fasta = os.path.join(tmp_folder, unique_id + ".fasta")
# Expected
self.expected_rec = {
"one":
Sequence(
"one",
"ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT"
),
"two":
Sequence("two", "ATGCATGCATGCATGCATGCATGCATGC",
"another chromosome")
}
# Create sequence file
content_fasta = """>one
ATGCATGCATGCATGCATGCATGCATGCAT
GCATGCATGCATGCATGCATGCATGCATGC
ATGCAT
>two another chromosome
ATGCATGCATGCAT
GCATGCATGCATGC"""
with open(self.tmp_fasta, "w") as FH_out:
FH_out.write(content_fasta)
# Create index
content_fasta_idx = """one 66 5 30 31
two 28 98 14 15"""
with open(self.tmp_fasta_idx, "w") as FH_out:
FH_out.write(content_fasta_idx)
def get(self, id):
"""
Return the sequence from file.
:param id: The sequence ID.
:type id: str
:return: The sequence selected from the file.
:rtype: anacore.sequence.Sequence
"""
if self.cached is not None:
if self.cached.id == id:
return self.cached
# The sequence is not already cached
seq = self.getSub(id, 1, None)
selected = Sequence(id, seq)
if self.use_cache:
self.cached = selected
return selected
def nextSeq(self):
"""
Return the next sequence.
:return: The next sequence.
:rtype: anacore.sequence.Sequence
"""
seq_record = None
if not self._end_of_file:
line = ""
try:
# First line in file
if self.current_line_nb == 1:
self._next_id = self.file_handle.readline().strip()
self.current_line_nb += 1
# Sequence
seq_str = ""
while not line.startswith('>'):
seq_str += line.strip()
line = self.file_handle.readline()
if not line:
line = None
self._end_of_file = True
break
self.current_line_nb += 1
fields = self._next_id[1:].split(None, 1)
seq_id = fields[0]
seq_desc = fields[1].strip() if len(fields) == 2 else None
seq_record = Sequence(seq_id, seq_str, seq_desc)
self._next_id = line # next seq_id
except Exception:
raise IOError(
'The line {} in "{}" cannot be parsed by {}.\ncontent: {}'.
format(self.current_line_nb, self.filepath,
self.__class__.__name__, line))
return seq_record