def read_scanner_data(handle):
"""
Helper function to parse ScannerData object from file handle.
Args:
handle (file): File handle
Returns:
ScannerData
"""
name = read_string(handle)
pmt_green = read_int(handle)
pmt_red = read_int(handle)
scanner_version = read_string(handle)
imaging_user = read_string(handle)
return ScannerData(name, pmt_green, pmt_red, scanner_version, imaging_user)
def get_base_calls(self):
"""
Returns:
list(string): The genotype basecalls
The characters are A, C, G, T, or - for a no-call/null.
The calls are relative to the top strand.
"""
try:
ploidy_type = self.get_ploidy_type()
except:
ploidy_type = 1
if ploidy_type != 1:
genotypes = self.get_genotypes()
with open(self.filename, "rb") as gtc_handle:
gtc_handle.seek(self.toc_table[GenotypeCalls.__ID_BASE_CALLS])
num_entries = read_int(gtc_handle)
result = []
for idx in range(num_entries):
if ploidy_type == 1:
result.append(gtc_handle.read(2).decode())
else:
byte_string = gtc_handle.read(2).decode()
ab_genotype = code2genotype[genotypes[idx]]
if ab_genotype == "NC" or ab_genotype == "NULL":
result.append("-")
else:
top_genotype = "".join(
[byte_string[0] if allele == "A" else byte_string[1] for allele in ab_genotype])
result.append(top_genotype)
return result
def __get_generic_array(self, toc_entry, parse_function, item_size, offset, count):
"""
Internal helper function to access a data array in a generic
fashion.
Args:
toc_entry (int): Identifier for entry in table of contents
parse_function (function): A function used to parse the value
from a file handle
item_size (int): Size (in bytes) of individual entry
offset (int): Offset (in elements counts) to start reading
count (int): Number of entries to read (None is read all remaining entries)
Returns:
list(type): An array parsed from the file (type dependent on parse_function)
"""
with open(self.filename, "rb") as gtc_handle:
gtc_handle.seek(self.toc_table[toc_entry])
num_entries = read_int(gtc_handle) - offset
if count is not None:
num_entries = min(num_entries, count)
if offset > 0:
gtc_handle.seek(
self.toc_table[toc_entry] + 4 + offset * item_size)
result = []
for idx in range(num_entries):
result.append(parse_function(gtc_handle))
return result
def __init__(self, filename, ignore_version=False, check_write_complete=True):
"""
Constructor
Args:
filename (string): GTC filename
ignore_version (bool): boolean to ignore automated checks on
file version, not recommended (default: False)
Returns:
GenotypeCalls
"""
self.filename = filename
with open(self.filename, "rb") as gtc_handle:
identifier = gtc_handle.read(3).decode()
if identifier != "gtc":
raise Exception("GTC format error: bad format identifier")
self.version = read_byte(gtc_handle)
if self.version not in GenotypeCalls.supported_version and not ignore_version:
raise Exception("Unsupported GTC File version (" + str(self.version) + ")")
number_toc_entries = read_int(gtc_handle)
#
# Parse the table of contents and map the toc entry
# to the lookup
#
self.toc_table = {}
for toc_idx in range(number_toc_entries):
(id, offset) = struct.unpack("<hI", gtc_handle.read(6))
self.toc_table[id] = offset
if check_write_complete and not self.is_write_complete():
raise Exception("GTC file is incomplete")
def get_num_intensity_only(self):
"""
Returns:
int: The number of intensity only SNPs
"""
with open(self.filename, "rb") as gtc_handle:
gtc_handle.seek(self.toc_table[GenotypeCalls.__ID_GC50] + 12)
return read_int(gtc_handle)
def get_num_no_calls(self):
"""
Returns:
int: The number of no calls
"""
with open(self.filename, "rb") as gtc_handle:
gtc_handle.seek(self.toc_table[GenotypeCalls.__ID_GC50] + 8)
return read_int(gtc_handle)
def __parse_locus_version_6(self, handle):
"""
Helper function to parse version 6 locus entry
Args:
handle (file): File handle at start of locus entry record
Returns:
None
Raises:
Exception: Manifest format error
"""
self.ilmn_id = read_string(handle)
self.source_strand = SourceStrand.from_string(
self.ilmn_id.split("_")[-2])
self.name = read_string(handle)
for idx in range(3):
read_string(handle)
handle.read(4)
for idx in range(2):
read_string(handle)
self.snp = read_string(handle)
self.chrom = read_string(handle)
for idx in range(2):
read_string(handle)
self.map_info = int(read_string(handle))
for idx in range(2):
read_string(handle)
self.address_a = read_int(handle)
self.address_b = read_int(handle)
for idx in range(7):
read_string(handle)
handle.read(3)
self.assay_type = read_byte(handle)
if self.assay_type not in [0, 1, 2]:
raise Exception(
"Format error in reading assay type from locus entry")
if self.address_b == 0:
if self.assay_type != 0:
raise Exception(
"Manifest format error: Assay type is inconsistent with address B"
)
else:
if self.assay_type == 0:
raise Exception(
"Manifest format error: Assay type is inconsistent with address B"
)
def __parse_file(self, handle):
"""
Helper function to initialize this object from a file handle
Args:
handle (file handle): File handle at start of locus entry record
Returns:
None
"""
version = read_int(handle)
if version == 6:
self.__parse_locus_version_6(handle)
elif version == 7:
self.__parse_locus_version_7(handle)
elif version == 8:
self.__parse_locus_version_8(handle)
else:
raise Exception(
"Manifest format error: unknown version for locus entry (" +
str(version) + ")")
def __get_generic_array_numpy(self, toc_entry, numpy_type, offset=0, count=None):
"""
Internal helper function to access a data array in a generic
fashion.
Args:
toc_entry (int): Identifier for entry in table of contents
numpy_type (numpy.dtype): Data type to read into array
offset (int): Offset (in element counts) to start reading
count (int): Number of entries to read (None will read remaining entries)
Returns:
list(type): An array parsed from the file (type dependent on parse_function)
"""
numpy_type = dtype(numpy_type)
with open(self.filename, "rb") as gtc_handle:
gtc_handle.seek(self.toc_table[toc_entry])
num_entries = read_int(gtc_handle) - offset
if count is not None:
num_entries = min(num_entries, count)
if offset > 0:
gtc_handle.seek(
self.toc_table[toc_entry] + 4 + offset * numpy_type.itemsize)
return frombuffer(gtc_handle.read(num_entries * numpy_type.itemsize), dtype=numpy_type)
def read_cluster_file(handle):
"""
Read a cluster file
Args:
file: EGT cluster file handle
Returns:
ClusterFile
Raises:
Exception: Incompatible cluster file format
"""
version = read_int(handle)
if version != 3:
raise Exception("Cluster file version " + str(version) +
" not supported")
gencall_version = read_string(handle)
cluster_version = read_string(handle)
call_version = read_string(handle)
normalization_version = read_string(handle)
date_created = read_string(handle)
is_wgt = read_byte(handle) == 1
if not is_wgt:
raise Exception("Only WGT cluster file version supported")
manifest_name = read_string(handle)
result = ClusterFile(gencall_version, cluster_version, call_version,
normalization_version, date_created,
manifest_name)
data_block_version = read_int(handle)
if data_block_version not in [8, 9]:
raise Exception("Data block version in cluster file " +
str(data_block_version) + " not supported")
# opa
_ = read_string(handle)
num_records = read_int(handle)
cluster_records = ClusterFile.read_array(
handle, num_records, lambda handle: ClusterRecord.read_record(
handle, data_block_version))
cluster_scores = ClusterFile.read_array(handle, num_records,
ClusterScore.read_record)
# genotypes
_ = ClusterFile.read_array(handle, num_records, read_string)
loci_names = ClusterFile.read_array(handle, num_records, read_string)
addresses = ClusterFile.read_array(handle, num_records, read_int)
# cluster counts
cluster_counts = []
for idx in range(num_records):
# 3 corresponds to number genotypes (AA, AB, BB)
cluster_counts.append(ClusterFile.read_array(handle, 3, read_int))
for (cluster_record, count_record) in zip(cluster_records,
cluster_counts):
assert cluster_record.aa_cluster_stats.N == count_record[0]
assert cluster_record.ab_cluster_stats.N == count_record[1]
assert cluster_record.bb_cluster_stats.N == count_record[2]
for (locus_name, address, cluster_record,
cluster_score) in zip(loci_names, addresses, cluster_records,
cluster_scores):
cluster_record.address = address
cluster_record.cluster_score = cluster_score
result.add_record(locus_name, cluster_record)
return result
def __parse_file(self, manifest_file):
"""
Helper function to initialize this object from a file.
Args:
manifest_file (string): Location of BPM (bead pool manifest) file
Returns:
None
Raises:
Exception: Unsupported or unknown BPM version
Exception: Manifest format error
"""
with open(manifest_file, "rb") as manifest_handle:
header = manifest_handle.read(3).decode()
if len(header) != 3 or header != "BPM":
raise Exception("Invalid BPM format")
version = read_byte(manifest_handle)
if version != 1:
raise Exception("Unknown BPM version (" + str(ord(version)) +
")")
version = read_int(manifest_handle)
version_flag = 0x1000
if version & version_flag == version_flag:
version = version ^ version_flag
if version > 5 or version < 3:
raise Exception("Unsupported BPM version (" + str(version) +
")")
self.manifest_name = read_string(manifest_handle)
if version > 1:
self.control_config = read_string(manifest_handle)
self.num_loci = read_int(manifest_handle)
manifest_handle.seek(4 * self.num_loci, 1)
name_lookup = {}
for idx in range(self.num_loci):
self.names.append(read_string(manifest_handle))
name_lookup[self.names[-1]] = idx
for idx in range(self.num_loci):
normalization_id = read_byte(manifest_handle)
if normalization_id >= 100:
raise Exception(
"Manifest format error: read invalid normalization ID")
self.normalization_ids.append(normalization_id)
self.assay_types = [0] * self.num_loci
self.addresses = [0] * self.num_loci
self.snps = [""] * self.num_loci
self.chroms = [""] * self.num_loci
self.map_infos = [0] * self.num_loci
self.ref_strands = [RefStrand.Unknown] * self.num_loci
self.source_strands = [SourceStrand.Unknown] * self.num_loci
for idx in range(self.num_loci):
locus_entry = LocusEntry(manifest_handle)
self.assay_types[name_lookup[
locus_entry.name]] = locus_entry.assay_type
self.addresses[name_lookup[
locus_entry.name]] = locus_entry.address_a
self.snps[name_lookup[locus_entry.name]] = locus_entry.snp
self.chroms[name_lookup[locus_entry.name]] = locus_entry.chrom
self.map_infos[name_lookup[
locus_entry.name]] = locus_entry.map_info
self.ref_strands[name_lookup[
locus_entry.name]] = locus_entry.ref_strand
self.source_strands[name_lookup[
locus_entry.name]] = locus_entry.source_strand
if len(self.normalization_ids) != len(self.assay_types):
raise Exception(
"Manifest format error: read invalid number of assay entries"
)
all_norm_ids = set()
for locus_idx in range(self.num_loci):
self.normalization_ids[locus_idx] += 100 * \
self.assay_types[locus_idx]
all_norm_ids.add(self.normalization_ids[locus_idx])
sorted_norm_ids = sorted(all_norm_ids)
lookup_dictionary = {}
for idx in range(len(sorted_norm_ids)):
lookup_dictionary[sorted_norm_ids[idx]] = idx
self.normalization_lookups = [
lookup_dictionary[normalization_id]
for normalization_id in self.normalization_ids
]
