def testChromosomeConversionHG19(self):
"""Test that an hg19 build with chrom = 23 or 24 gets converted to X or Y
"""
self.assertEqual(MutUtils.convertChromosomeStringToMutationDataFormat("23", build="hg19"), "X", "chrom of 23 did not produce X: " + MutUtils.convertChromosomeStringToMutationDataFormat("23", build="hg19"))
self.assertEqual(MutUtils.convertChromosomeStringToMutationDataFormat("24", build="hg19"), "Y", "chrom of 24 did not produce Y: " + MutUtils.convertChromosomeStringToMutationDataFormat("24", build="hg19"))
self.assertEqual(MutUtils.convertChromosomeStringToMutationDataFormat("2", build="hg19"), "2", "chrom of 2 yielded different value: " + MutUtils.convertChromosomeStringToMutationDataFormat("2", build="hg19"))
self.assertEqual(MutUtils.convertChromosomeStringToMutationDataFormat("4", build="hg19"), "4", "chrom of 4 yielded different value: " + MutUtils.convertChromosomeStringToMutationDataFormat("4", build="hg19"))
def _determine_matching_alt_indices(self, mut, record, build):
"""
:param mut:
:param record:
:return:
"""
indices = []
if record.is_monomorphic:
chrom = MutUtils.convertChromosomeStringToMutationDataFormat(
record.CHROM)
startPos = record.POS
endPos = record.POS
ref_allele = record.REF
if self.match_mode == "exact":
if mut.chr == chrom and mut.ref_allele == ref_allele:
indices = [-1]
else:
if mut.chr == chrom and int(mut.start) <= startPos and int(
mut.end) >= endPos:
indices = [-1]
else:
# Iterate over all alternates in the record
for index in xrange(0, len(record.ALT)):
chrom = MutUtils.convertChromosomeStringToMutationDataFormat(
record.CHROM)
startPos = record.POS
endPos = record.POS
ref = str(record.REF)
alt = str(record.ALT[index])
ds_mut = MutUtils.initializeMutFromAttributes(
chrom, startPos, endPos, ref, alt, build)
if self.match_mode == "exact":
if mut.chr == ds_mut.chr and mut.ref_allele == ds_mut.ref_allele \
and mut.alt_allele == ds_mut.alt_allele and int(mut.start) == int(ds_mut.start) \
and int(mut.end) == int(ds_mut.end):
indices += [index]
else: # cases whether the match mode isn't exact
if mut.chr == ds_mut.chr and int(mut.start) == int(
ds_mut.start) and int(mut.end) == int(ds_mut.end):
indices += [index]
elif mut.chr == ds_mut.chr and int(mut.start) >= int(ds_mut.start) \
and int(mut.end) >= int(ds_mut.end) and int(mut.start) <= int(ds_mut.end):
indices += [index]
elif mut.chr == ds_mut.chr and int(mut.start) <= int(
ds_mut.start) and int(mut.end) >= int(ds_mut.end):
indices += [index]
elif mut.chr == ds_mut.chr and int(mut.start) <= int(ds_mut.start) \
and int(mut.end) <= int(ds_mut.end) and int(mut.end) >= int(ds_mut.start):
indices += [index]
# if len(indices) == 0:
# indices = [None]
return indices
def _determine_matching_alt_indices(self, mut, record, build):
"""
:param mut:
:param record:
:return:
"""
indices = []
if record.is_monomorphic:
chrom = MutUtils.convertChromosomeStringToMutationDataFormat(record.CHROM)
startPos = record.POS
endPos = record.POS
ref_allele = record.REF
if self.match_mode == "exact":
if mut.chr == chrom and mut.ref_allele == ref_allele:
indices = [-1]
else:
if mut.chr == chrom and int(mut.start) <= startPos and int(mut.end) >= endPos:
indices = [-1]
else:
# Iterate over all alternates in the record
for index in xrange(0, len(record.ALT)):
chrom = MutUtils.convertChromosomeStringToMutationDataFormat(record.CHROM)
startPos = record.POS
endPos = record.POS
ref = str(record.REF)
alt = str(record.ALT[index])
ds_mut = MutUtils.initializeMutFromAttributes(chrom, startPos, endPos, ref, alt, build)
if self.match_mode == "exact":
if mut.chr == ds_mut.chr and mut.ref_allele == ds_mut.ref_allele \
and mut.alt_allele == ds_mut.alt_allele and int(mut.start) == int(ds_mut.start) \
and int(mut.end) == int(ds_mut.end):
indices += [index]
else: # cases whether the match mode isn't exact
if mut.chr == ds_mut.chr and int(mut.start) == int(ds_mut.start) and int(mut.end) == int(ds_mut.end):
indices += [index]
elif mut.chr == ds_mut.chr and int(mut.start) >= int(ds_mut.start) \
and int(mut.end) >= int(ds_mut.end) and int(mut.start) <= int(ds_mut.end):
indices += [index]
elif mut.chr == ds_mut.chr and int(mut.start) <= int(ds_mut.start) and int(mut.end) >= int(ds_mut.end):
indices += [index]
elif mut.chr == ds_mut.chr and int(mut.start) <= int(ds_mut.start) \
and int(mut.end) <= int(ds_mut.end) and int(mut.end) >= int(ds_mut.start):
indices += [index]
# if len(indices) == 0:
# indices = [None]
return indices
def testChromosomeConversionHG19(self):
"""Test that an hg19 build with chrom = 23 or 24 gets converted to X or Y
"""
self.assertEqual(
MutUtils.convertChromosomeStringToMutationDataFormat("23",
build="hg19"),
"X", "chrom of 23 did not produce X: " +
MutUtils.convertChromosomeStringToMutationDataFormat("23",
build="hg19"))
self.assertEqual(
MutUtils.convertChromosomeStringToMutationDataFormat("24",
build="hg19"),
"Y", "chrom of 24 did not produce Y: " +
MutUtils.convertChromosomeStringToMutationDataFormat("24",
build="hg19"))
self.assertEqual(
MutUtils.convertChromosomeStringToMutationDataFormat("2",
build="hg19"),
"2", "chrom of 2 yielded different value: " +
MutUtils.convertChromosomeStringToMutationDataFormat("2",
build="hg19"))
self.assertEqual(
MutUtils.convertChromosomeStringToMutationDataFormat("4",
build="hg19"),
"4", "chrom of 4 yielded different value: " +
MutUtils.convertChromosomeStringToMutationDataFormat("4",
build="hg19"))
def createMutations(self):
""" No inputs.
Returns a generator of mutations built from the specified maflite file. """
aliasKeys = self._reverseAlternativeDict.keys()
allColumns = self._specified_fields
for line in self._tsvReader:
# We only need to assign fields that are mutation attributes and have a different name in the maflite file.
mut = self._mutation_data_factory.create(build=self._build)
for col in allColumns:
# Three scenarios:
# 1) col is name of mutation data field -- simple createAnnotation
# 2) col name is an alias for a mutation data field -- do lookup then createAnnotation
# 3) col name is not an alias for a mutation data field -- simple createAnnotation
if col in aliasKeys:
realKey = self._reverseAlternativeDict[col]
self.logger.debug(realKey + " found from " + col)
val = line[col]
if realKey == "chr":
val = MutUtils.convertChromosomeStringToMutationDataFormat(
line[col])
mut.createAnnotation(realKey, val, 'INPUT')
else:
# Scenario 1 and 3
# Make sure to convert chromosome values.
val = line[col]
if col == "chr":
val = MutUtils.convertChromosomeStringToMutationDataFormat(
line[col])
mut.createAnnotation(col, val, 'INPUT')
mut.ref_allele, mut.alt_allele = mut.ref_allele.strip(
), mut.alt_allele.strip(
) #remove any trailing whitespace if present
# if the alt allele == ref_allele, check that this is not a case where there is an alt_allele2 that is different.
if mut.alt_allele == mut.ref_allele:
mut.alt_allele = self._find_alt_allele_in_other_field(
line, mut.ref_allele)
# FIXME: Support more than one alias in the reverse dictionary. Then this line can be removed.
if mut.start is not "" and mut.end is "":
mut.end = mut.start
if mut.end is not "" and mut.start is "":
mut.start = mut.end
yield mut
def retrieveExons(self, gene, padding=10, isCodingOnly=False):
"""Return a list of (chr, start, end) tuples for each exon"""
result = set()
geneTuple = self.gene_id_idx.get(gene, None)
if geneTuple is None:
return result
ctr = 0
contig = MutUtils.convertChromosomeStringToMutationDataFormat(geneTuple[0])
for b in self.Transcripts.get(contig, []):
for i in self.Transcripts[contig][b]:
if i["gene"] == gene:
if isCodingOnly and gaf_annotation.is_non_coding_transcript(i, self):
ctr += 1
continue
if isCodingOnly:
genomic_coords = self.getCodingTranscriptCoords(i)
else:
genomic_coords = i["genomic_coords"]
for coord in genomic_coords:
start = min(coord[0], coord[1])
end = max(coord[0], coord[1])
result.add((gene, i["chr"], str(start - padding), str(end + padding)))
return result
def retrieveExons(self, gene, padding=10, isCodingOnly=False):
"""Return a list of (chr, start, end) tuples for each exon"""
result = set()
geneTuple = self.gene_id_idx.get(gene, None)
if geneTuple is None:
return result
ctr = 0
contig = MutUtils.convertChromosomeStringToMutationDataFormat(
geneTuple[0])
for b in self.Transcripts.get(contig, []):
for i in self.Transcripts[contig][b]:
if i['gene'] == gene:
if isCodingOnly and gaf_annotation.is_non_coding_transcript(
i, self):
ctr += 1
continue
if isCodingOnly:
genomic_coords = self.getCodingTranscriptCoords(i)
else:
genomic_coords = i['genomic_coords']
for coord in genomic_coords:
start = min(coord[0], coord[1])
end = max(coord[0], coord[1])
result.add((gene, i['chr'], str(start - padding),
str(end + padding)))
return result
def _createMutation(self, record, alt_index, build):
chrom = MutUtils.convertChromosomeStringToMutationDataFormat(
record.CHROM)
startPos = int(record.POS)
endPos = int(record.POS)
ref = record.REF.strip()
ref = "" if ref == "." else ref
alt = ref
if not record.is_monomorphic:
alt = str(record.ALT[alt_index]).strip()
mut = MutUtils.initializeMutFromAttributes(chrom, startPos, endPos,
ref, alt, build,
self._mutation_data_factory)
ID = "" if record.ID is None else record.ID
mut.createAnnotation("id", ID, "INPUT", tags=[TagConstants.ID])
mut.createAnnotation("qual",
str(record.QUAL),
"INPUT",
tags=[TagConstants.QUAL])
mut.createAnnotation("alt_allele_seen", str(True), "INPUT")
if self.collapse_filter_fields:
mut = self._add_filter_data_2_mutation_single_field(mut, record)
else:
mut = self._addFilterData2Mutation(mut, record)
mut = self._addInfoData2Mutation(mut, record, alt_index)
return mut
def createMutations(self):
""" No inputs.
Returns a generator of mutations built from the specified maflite file. """
aliasKeys = self._reverseAlternativeDict.keys()
allColumns = self._specified_fields
for line in self._tsvReader:
# We only need to assign fields that are mutation attributes and have a different name in the maflite file.
mut = self._mutation_data_factory.create(build=self._build)
for col in allColumns:
# Three scenarios:
# 1) col is name of mutation data field -- simple createAnnotation
# 2) col name is an alias for a mutation data field -- do lookup then createAnnotation
# 3) col name is not an alias for a mutation data field -- simple createAnnotation
if col in aliasKeys:
realKey = self._reverseAlternativeDict[col]
self.logger.debug(realKey + " found from " + col)
val = line[col]
if realKey == "chr":
val = MutUtils.convertChromosomeStringToMutationDataFormat(line[col])
mut.createAnnotation(realKey, val, 'INPUT')
else:
# Scenario 1 and 3
# Make sure to convert chromosome values.
val = line[col]
if col == "chr":
val = MutUtils.convertChromosomeStringToMutationDataFormat(line[col])
mut.createAnnotation(col, val, 'INPUT')
mut.ref_allele, mut.alt_allele = mut.ref_allele.strip(), mut.alt_allele.strip() #remove any trailing whitespace if present
# if the alt allele == ref_allele, check that this is not a case where there is an alt_allele2 that is different.
if mut.alt_allele == mut.ref_allele:
mut.alt_allele = self._find_alt_allele_in_other_field(line, mut.ref_allele)
# FIXME: Support more than one alias in the reverse dictionary. Then this line can be removed.
if mut.start is not "" and mut.end is "":
mut.end = mut.start
if mut.end is not "" and mut.start is "":
mut.start = mut.end
yield mut
def _createMutation(self, record, alt_index, build):
chrom = MutUtils.convertChromosomeStringToMutationDataFormat(record.CHROM)
startPos = int(record.POS)
endPos = int(record.POS)
ref = record.REF
ref = "" if ref == "." else ref
alt = ref
if not record.is_monomorphic:
alt = str(record.ALT[alt_index])
mut = MutUtils.initializeMutFromAttributes(chrom, startPos, endPos, ref, alt, build)
ID = "" if record.ID is None else record.ID
mut.createAnnotation("id", ID, "INPUT", tags=[TagConstants.ID])
mut.createAnnotation("qual", str(record.QUAL), "INPUT", tags=[TagConstants.QUAL])
mut.createAnnotation("alt_allele_seen", str(True), "INPUT")
mut = self._addFilterData2Mutation(mut, record)
mut = self._addInfoData2Mutation(mut, record, alt_index)
return mut
def _convertGFFRecordToTranscript(self, gff_record, seq_dict, seq_dict_keys, tx_to_protein_mapping):
"""
:param gff_record:
:param seq_dict:
:return: None if the record is a gene record or otherwise does not represent a transcript, CDS, *_codon, or exon
"""
types_of_interest = ["exon", "CDS", "start_codon", "stop_codon"]
if gff_record['type'] not in types_of_interest:
return None
quals = gff_record['quals']
transcript_id = quals['transcript_id'][0]
try:
tx = self._transcript_index[transcript_id]
except KeyError:
# Create the initial record for this transcript.
contig = MutUtils.convertChromosomeStringToMutationDataFormat(gff_record['rec_id'])
tx = Transcript(transcript_id, gene=quals['gene_name'][0], gene_id=quals['gene_id'][0], contig=contig)
self._transcript_index[transcript_id] = tx
# Set the gene_type based on gene_type or gene_biotype
key = "gene_biotype"
if key not in quals.keys():
key = "gene_type"
self._transcript_index[transcript_id].set_gene_type(quals.get(key, [""])[0])
if gff_record['strand'] == 1:
self._transcript_index[transcript_id].set_strand("+")
else:
self._transcript_index[transcript_id].set_strand("-")
qual_keys = quals.keys()
for attribute in GenomeBuildFactory.QUALS_TO_CHECK:
if attribute in qual_keys:
self._transcript_index[transcript_id].add_other_attribute(attribute, "|".join(quals[attribute]))
seq = seq_dict.get(transcript_id, None)
if seq is not None:
genome_seq_as_str = str(seq.seq)
else:
genome_seq_as_str = ""
self._transcript_index[transcript_id].set_seq(genome_seq_as_str)
tx_id_for_protein_lookup = transcript_id
if '.' in transcript_id:
tx_id_for_protein_lookup = tx_id_for_protein_lookup[:tx_id_for_protein_lookup.index('.')]
self._transcript_index[transcript_id].set_protein_id(tx_to_protein_mapping.get(tx_id_for_protein_lookup, ""))
tx = self._transcript_index[transcript_id]
gff_type = gff_record['type']
if gff_type == 'exon':
tx.add_exon(gff_record['location'][0], gff_record['location'][1], quals['exon_number'][0])
elif gff_type == 'CDS':
tx.add_cds(gff_record['location'][0], gff_record['location'][1])
elif gff_type == 'start_codon':
tx.set_start_codon(gff_record['location'][0], gff_record['location'][1])
elif gff_type == 'stop_codon':
tx.set_stop_codon(gff_record['location'][0], gff_record['location'][1])
def _convertGFFRecordToTranscript(self, gff_record, seq_dict,
seq_dict_keys, tx_to_protein_mapping):
"""
:param gff_record:
:param seq_dict:
:return: None if the record is a gene record or otherwise does not represent a transcript, CDS, *_codon, or exon
"""
types_of_interest = ["exon", "CDS", "start_codon", "stop_codon"]
if gff_record['type'] not in types_of_interest:
return None
quals = gff_record['quals']
transcript_id = quals['transcript_id'][0]
try:
tx = self._transcript_index[transcript_id]
except KeyError:
# Create the initial record for this transcript.
contig = MutUtils.convertChromosomeStringToMutationDataFormat(
gff_record['rec_id'])
tx = Transcript(transcript_id,
gene=quals['gene_name'][0],
gene_id=quals['gene_id'][0],
contig=contig)
self._transcript_index[transcript_id] = tx
# Set the gene_type based on gene_type or gene_biotype
key = "gene_biotype"
if key not in quals.keys():
key = "gene_type"
self._transcript_index[transcript_id].set_gene_type(
quals.get(key, [""])[0])
if gff_record['strand'] == 1:
self._transcript_index[transcript_id].set_strand("+")
else:
self._transcript_index[transcript_id].set_strand("-")
qual_keys = quals.keys()
for attribute in GenomeBuildFactory.QUALS_TO_CHECK:
if attribute in qual_keys:
self._transcript_index[transcript_id].add_other_attribute(
attribute, "|".join(quals[attribute]))
seq = seq_dict.get(transcript_id, None)
if seq is not None:
genome_seq_as_str = str(seq.seq)
else:
genome_seq_as_str = ""
self._transcript_index[transcript_id].set_seq(genome_seq_as_str)
tx_id_for_protein_lookup = transcript_id
if '.' in transcript_id:
tx_id_for_protein_lookup = tx_id_for_protein_lookup[:
tx_id_for_protein_lookup
.index('.'
)]
self._transcript_index[transcript_id].set_protein_id(
tx_to_protein_mapping.get(tx_id_for_protein_lookup, ""))
tx = self._transcript_index[transcript_id]
gff_type = gff_record['type']
if gff_type == 'exon':
tx.add_exon(gff_record['location'][0], gff_record['location'][1],
quals['exon_number'][0])
elif gff_type == 'CDS':
tx.add_cds(gff_record['location'][0], gff_record['location'][1])
elif gff_type == 'start_codon':
tx.set_start_codon(gff_record['location'][0],
gff_record['location'][1])
elif gff_type == 'stop_codon':
tx.set_stop_codon(gff_record['location'][0],
gff_record['location'][1])
