def _add_sv_coordinates(self, variant):
"""Add the neccesary sv coordinates for a variant
Args:
variant (puzzle.models.variant)
"""
variant.stop_chrom = variant.CHROM
variant.start = int(variant.POS)
# If we have a translocation:
if ':' in variant.ALT:
other_coordinates = variant.ALT.strip('ACGTN[]').split(':')
variant.stop_chrom = other_coordinates[0].lstrip('chrCHR')
other_position = other_coordinates[1]
# variant.stop = other_position
#Set 'infinity' to length if translocation
variant.sv_len = float('inf')
variant.sv_type = 'BND'
else:
variant.sv_len = variant.stop - variant.start
variant['cytoband_start'] = get_cytoband_coord(chrom=variant.CHROM,
pos=variant.start)
variant['cytoband_stop'] = get_cytoband_coord(chrom=variant.stop_chrom,
pos=variant.stop)
def _add_sv_coordinates(self, variant):
"""Add the neccesary sv coordinates for a variant
Args:
variant (puzzle.models.variant)
"""
variant.stop_chrom = variant.CHROM
variant.start = int(variant.POS)
# If we have a translocation:
if ":" in variant.ALT:
other_coordinates = variant.ALT.strip("ACGTN[]").split(":")
variant.stop_chrom = other_coordinates[0].lstrip("chrCHR")
other_position = other_coordinates[1]
# variant.stop = other_position
# Set 'infinity' to length if translocation
variant.sv_len = float("inf")
variant.sv_type = "BND"
else:
variant.sv_len = variant.stop - variant.start
variant["cytoband_start"] = get_cytoband_coord(chrom=variant.CHROM, pos=variant.start)
variant["cytoband_stop"] = get_cytoband_coord(chrom=variant.stop_chrom, pos=variant.stop)
def _add_sv_coordinates(self, variant):
"""Add the neccesary sv coordinates for a variant
Args:
variant (puzzle.models.variant)
"""
variant.stop_chrom = variant.CHROM
variant.start = int(variant.POS)
# If we have a translocation:
if ':' in variant.ALT:
other_coordinates = variant.ALT.strip('ACGTN[]').split(':')
variant.stop_chrom = other_coordinates[0].lstrip('chrCHR')
other_position = other_coordinates[1]
variant.stop = other_position
#Set 'infinity' to length if translocation
variant.sv_len = float('inf')
variant.sv_type = 'BND'
else:
variant.sv_len = variant.stop - variant.start
variant['cytoband_start'] = get_cytoband_coord(
chrom=variant.CHROM,
pos=variant.start
)
variant['cytoband_stop'] = get_cytoband_coord(
chrom=variant.stop_chrom,
pos=variant.stop
)
def test_get_cytoband_coord():
"""test get_cytoband_coord(chrom, pos) method"""
print("Test get_cytoband_coord with different input formats")
assert get_cytoband_coord('1', 3) == '1p36.33'
assert get_cytoband_coord('chr1', 3) == '1p36.33'
assert get_cytoband_coord('chr1', '3') == '1p36.33'
print("Test get_cytoband_coord with non existing chromosome")
assert get_cytoband_coord('chrMT', '3') is None
print("Test get_cytoband_coord with non existing position")
assert get_cytoband_coord('chrX', '155270600') is None
def test_get_cytoband_coord(self):
"""test get_cytoband_coord(chrom, pos) method"""
print "Test get_cytoband_coord with different input formats"
assert get_cytoband_coord('1', 3) == '1p36.33'
assert get_cytoband_coord('chr1', 3) == '1p36.33'
assert get_cytoband_coord('chr1', '3') == '1p36.33'
print "Test get_cytoband_coord with non existing chromosome"
assert get_cytoband_coord('chrMT', '3') == None
print "Test get_cytoband_coord with non existing position"
assert get_cytoband_coord('chrX', '155270600') == None
def _format_variant(self, gemini_variant, individual_objs, index=0):
"""Make a puzzle variant from a gemini variant
Args:
gemini_variant (GeminiQueryRow): The gemini variant
individual_objs (list(dict)): A list of Individuals
index(int): The index of the variant
Returns:
variant (dict): A Variant object
"""
variant_dict = {
'CHROM':gemini_variant['chrom'].lstrip('chrCHR'),
'POS':str(gemini_variant['start']),
'ID':gemini_variant['rs_ids'],
'REF':gemini_variant['ref'],
'ALT':gemini_variant['alt'],
'QUAL':gemini_variant['qual'],
'FILTER':gemini_variant['filter']
}
variant = Variant(**variant_dict)
variant['index'] = index
# Use the gemini id for fast search
variant.update_variant_id(gemini_variant['variant_id'])
# Update the individuals
individual_genotypes = self._get_genotypes(
gemini_variant=gemini_variant,
individual_objs=individual_objs
)
for individual in individual_genotypes:
# Add the genotype calls to the variant
variant.add_individual(individual)
for transcript in self._get_transcripts(gemini_variant):
variant.add_transcript(transcript)
#Add the most severe consequence
variant['most_severe_consequence'] = gemini_variant['impact_so']
for gene in self._get_genes(variant):
variant.add_gene(gene)
variant['start'] = int(variant_dict['POS'])
if self.variant_type == 'sv':
other_chrom = variant['CHROM']
# If we have a translocation:
if ':' in variant_dict['ALT']:
other_coordinates = variant_dict['ALT'].strip('ACGTN[]').split(':')
other_chrom = other_coordinates[0].lstrip('chrCHR')
other_position = other_coordinates[1]
variant['stop'] = other_position
#Set 'infinity' to length if translocation
variant['sv_len'] = float('inf')
variant['sv_type'] = 'BND'
else:
variant['stop'] = int(gemini_variant['end'])
variant['sv_len'] = variant['stop'] - variant['start']
variant['sv_type'] = gemini_variant['sub_type']
variant['stop_chrom'] = other_chrom
else:
variant['stop'] = int(variant_dict['POS']) + \
(len(variant_dict['REF']) - len(variant_dict['ALT']))
variant['cytoband_start'] = get_cytoband_coord(
chrom=variant['CHROM'],
pos=variant['start'])
if variant.get('stop_chrom'):
variant['cytoband_stop'] = get_cytoband_coord(
chrom=variant['stop_chrom'],
pos=variant['stop'])
#### Check the impact annotations ####
if gemini_variant['cadd_scaled']:
variant['cadd_score'] = gemini_variant['cadd_scaled']
# We use the prediction in text
polyphen = gemini_variant['polyphen_pred']
if polyphen:
variant.add_severity('Polyphen', polyphen)
# We use the prediction in text
sift = gemini_variant['sift_pred']
if sift:
variant.add_severity('SIFT', sift)
#### Check the frequencies ####
thousand_g = gemini_variant['aaf_1kg_all']
if thousand_g:
variant['thousand_g'] = float(thousand_g)
variant.add_frequency(name='1000GAF', value=float(thousand_g))
exac = gemini_variant['aaf_exac_all']
if exac:
variant.add_frequency(name='EXaC', value=float(exac))
esp = gemini_variant['aaf_esp_all']
if esp:
variant.add_frequency(name='ESP', value=float(esp))
max_freq = gemini_variant['max_aaf_all']
if max_freq:
variant.set_max_freq(max_freq)
return variant
def _formated_variants(self, raw_variants, case_obj):
"""Return variant objects
Args:
raw_variants (Iterable): An iterable with variant lines
case_obj (puzzle.nodels.Case): A case object
"""
vcf_file_path = case_obj.variant_source
logger.info("Parsing file {0}".format(vcf_file_path))
head = HeaderParser()
handle = get_vcf_handle(infile=vcf_file_path)
# Parse the header
for line in handle:
line = line.rstrip()
if line.startswith("#"):
if line.startswith("##"):
head.parse_meta_data(line)
else:
head.parse_header_line(line)
else:
break
handle.close()
header_line = head.header
# Get the individual ids for individuals in vcf file
vcf_individuals = set([ind_id for ind_id in head.individuals])
variant_columns = ["CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER"]
vep_header = head.vep_columns
snpeff_header = head.snpeff_columns
index = 0
for variant_line in raw_variants:
if not variant_line.startswith("#"):
index += 1
# Create a variant dict:
variant_dict = get_variant_dict(variant_line=variant_line, header_line=header_line)
variant_dict["CHROM"] = variant_dict["CHROM"].lstrip("chrCHR")
# Crreate a info dict:
info_dict = get_info_dict(info_line=variant_dict["INFO"])
# Check if vep annotation:
vep_string = info_dict.get("CSQ")
# Check if snpeff annotation:
snpeff_string = info_dict.get("ANN")
if vep_string:
# Get the vep annotations
vep_info = get_vep_info(vep_string=vep_string, vep_header=vep_header)
elif snpeff_string:
# Get the vep annotations
snpeff_info = get_snpeff_info(snpeff_string=snpeff_string, snpeff_header=snpeff_header)
variant = Variant(**{column: variant_dict.get(column, ".") for column in variant_columns})
logger.debug("Creating a variant object of variant {0}".format(variant.get("variant_id")))
variant["index"] = index
logger.debug("Updating index to: {0}".format(index))
variant["start"] = int(variant_dict["POS"])
if self.variant_type == "sv":
other_chrom = variant["CHROM"]
# If we have a translocation:
if ":" in variant_dict["ALT"] and not "<" in variant_dict["ALT"]:
other_coordinates = variant_dict["ALT"].strip("ACGTN[]").split(":")
other_chrom = other_coordinates[0].lstrip("chrCHR")
other_position = other_coordinates[1]
variant["stop"] = other_position
# Set 'infinity' to length if translocation
variant["sv_len"] = float("inf")
else:
variant["stop"] = int(info_dict.get("END", variant_dict["POS"]))
variant["sv_len"] = variant["stop"] - variant["start"]
variant["stop_chrom"] = other_chrom
else:
variant["stop"] = int(variant_dict["POS"]) + (len(variant_dict["REF"]) - len(variant_dict["ALT"]))
variant["sv_type"] = info_dict.get("SVTYPE")
variant["cytoband_start"] = get_cytoband_coord(chrom=variant["CHROM"], pos=variant["start"])
if variant.get("stop_chrom"):
variant["cytoband_stop"] = get_cytoband_coord(chrom=variant["stop_chrom"], pos=variant["stop"])
# It would be easy to update these keys...
thousand_g = info_dict.get("1000GAF")
if thousand_g:
logger.debug("Updating thousand_g to: {0}".format(thousand_g))
variant["thousand_g"] = float(thousand_g)
variant.add_frequency("1000GAF", variant.get("thousand_g"))
# SV specific tag for number of occurances
occurances = info_dict.get("OCC")
if occurances:
logger.debug("Updating occurances to: {0}".format(occurances))
variant["occurances"] = float(occurances)
variant.add_frequency("OCC", occurances)
cadd_score = info_dict.get("CADD")
if cadd_score:
logger.debug("Updating cadd_score to: {0}".format(cadd_score))
variant["cadd_score"] = float(cadd_score)
rank_score_entry = info_dict.get("RankScore")
if rank_score_entry:
for family_annotation in rank_score_entry.split(","):
rank_score = family_annotation.split(":")[-1]
logger.debug("Updating rank_score to: {0}".format(rank_score))
variant["rank_score"] = float(rank_score)
genetic_models_entry = info_dict.get("GeneticModels")
if genetic_models_entry:
genetic_models = []
for family_annotation in genetic_models_entry.split(","):
for genetic_model in family_annotation.split(":")[-1].split("|"):
genetic_models.append(genetic_model)
logger.debug("Updating rank_score to: {0}".format(rank_score))
variant["genetic_models"] = genetic_models
# Add genotype calls:
for individual in case_obj.individuals:
sample_id = individual.ind_id
if sample_id in vcf_individuals:
raw_call = dict(zip(variant_dict["FORMAT"].split(":"), variant_dict[sample_id].split(":")))
variant.add_individual(
Genotype(
sample_id=sample_id,
genotype=raw_call.get("GT", "./."),
case_id=individual.case_name,
phenotype=individual.phenotype,
ref_depth=raw_call.get("AD", ",").split(",")[0],
alt_depth=raw_call.get("AD", ",").split(",")[1],
genotype_quality=raw_call.get("GQ", "."),
depth=raw_call.get("DP", "."),
supporting_evidence=raw_call.get("SU", "0"),
pe_support=raw_call.get("PE", "0"),
sr_support=raw_call.get("SR", "0"),
)
)
# Add transcript information:
gmaf = None
if vep_string:
for transcript_info in vep_info:
transcript = self._get_vep_transcripts(transcript_info)
gmaf_raw = transcript_info.get("GMAF")
if gmaf_raw:
gmaf = float(gmaf_raw.split(":")[-1])
variant.add_transcript(transcript)
if gmaf:
variant.add_frequency("GMAF", gmaf)
if not variant.thousand_g:
variant.thousand_g = gmaf
elif snpeff_string:
for transcript_info in snpeff_info:
transcript = self._get_snpeff_transcripts(transcript_info)
variant.add_transcript(transcript)
variant["most_severe_consequence"] = get_most_severe_consequence(variant["transcripts"])
for gene in self._get_genes(variant):
variant.add_gene(gene)
self._add_compounds(variant=variant, info_dict=info_dict)
yield variant
def _formated_variants(self, raw_variants, case_obj):
"""Return variant objects
Args:
raw_variants (Iterable): An iterable with variant lines
case_obj (puzzle.nodels.Case): A case object
"""
vcf_file_path = case_obj.variant_source
logger.info("Parsing file {0}".format(vcf_file_path))
head = HeaderParser()
handle = get_vcf_handle(infile=vcf_file_path)
# Parse the header
for line in handle:
line = line.rstrip()
if line.startswith('#'):
if line.startswith('##'):
head.parse_meta_data(line)
else:
head.parse_header_line(line)
else:
break
handle.close()
header_line = head.header
# Get the individual ids for individuals in vcf file
vcf_individuals = set([ind_id for ind_id in head.individuals])
variant_columns = ['CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER']
vep_header = head.vep_columns
snpeff_header = head.snpeff_columns
index = 0
for variant_line in raw_variants:
if not variant_line.startswith('#'):
index += 1
#Create a variant dict:
variant_dict = get_variant_dict(
variant_line = variant_line,
header_line = header_line
)
variant_dict['CHROM'] = variant_dict['CHROM'].lstrip('chrCHR')
#Crreate a info dict:
info_dict = get_info_dict(
info_line = variant_dict['INFO']
)
#Check if vep annotation:
vep_string = info_dict.get('CSQ')
#Check if snpeff annotation:
snpeff_string = info_dict.get('ANN')
if vep_string:
#Get the vep annotations
vep_info = get_vep_info(
vep_string = vep_string,
vep_header = vep_header
)
elif snpeff_string:
#Get the vep annotations
snpeff_info = get_snpeff_info(
snpeff_string = snpeff_string,
snpeff_header = snpeff_header
)
variant = Variant(
**{column: variant_dict.get(column, '.')
for column in variant_columns}
)
logger.debug("Creating a variant object of variant {0}".format(
variant.get('variant_id')))
variant['index'] = index
logger.debug("Updating index to: {0}".format(
index))
variant['start'] = int(variant_dict['POS'])
if self.variant_type == 'sv':
other_chrom = variant['CHROM']
# If we have a translocation:
if ':' in variant_dict['ALT']:
other_coordinates = variant_dict['ALT'].strip('ACGTN[]').split(':')
other_chrom = other_coordinates[0].lstrip('chrCHR')
other_position = other_coordinates[1]
variant['stop'] = other_position
#Set 'infinity' to length if translocation
variant['sv_len'] = float('inf')
else:
variant['stop'] = int(info_dict.get('END', variant_dict['POS']))
variant['sv_len'] = variant['stop'] - variant['start']
variant['stop_chrom'] = other_chrom
else:
variant['stop'] = int(variant_dict['POS']) + \
(len(variant_dict['REF']) - len(variant_dict['ALT']))
variant['sv_type'] = info_dict.get('SVTYPE')
variant['cytoband_start'] = get_cytoband_coord(
chrom=variant['CHROM'],
pos=variant['start'])
if variant.get('stop_chrom'):
variant['cytoband_stop'] = get_cytoband_coord(
chrom=variant['stop_chrom'],
pos=variant['stop'])
# It would be easy to update these keys...
thousand_g = info_dict.get('1000GAF')
if thousand_g:
logger.debug("Updating thousand_g to: {0}".format(
thousand_g))
variant['thousand_g'] = float(thousand_g)
variant.add_frequency('1000GAF', variant.get('thousand_g'))
#SV specific tag for number of occurances
occurances = info_dict.get('OCC')
if occurances:
logger.debug("Updating occurances to: {0}".format(
occurances))
variant['occurances'] = float(occurances)
variant.add_frequency('OCC', occurances)
cadd_score = info_dict.get('CADD')
if cadd_score:
logger.debug("Updating cadd_score to: {0}".format(
cadd_score))
variant['cadd_score'] = float(cadd_score)
rank_score_entry = info_dict.get('RankScore')
if rank_score_entry:
for family_annotation in rank_score_entry.split(','):
rank_score = family_annotation.split(':')[-1]
logger.debug("Updating rank_score to: {0}".format(
rank_score))
variant['rank_score'] = float(rank_score)
genetic_models_entry = info_dict.get('GeneticModels')
if genetic_models_entry:
genetic_models = []
for family_annotation in genetic_models_entry.split(','):
for genetic_model in family_annotation.split(':')[-1].split('|'):
genetic_models.append(genetic_model)
logger.debug("Updating rank_score to: {0}".format(
rank_score))
variant['genetic_models'] = genetic_models
#Add genotype calls:
for individual in case_obj.individuals:
sample_id = individual.ind_id
if sample_id in vcf_individuals:
raw_call = dict(zip(
variant_dict['FORMAT'].split(':'),
variant_dict[sample_id].split(':'))
)
variant.add_individual(Genotype(
sample_id = sample_id,
genotype = raw_call.get('GT', './.'),
case_id = individual.case_name,
phenotype = individual.phenotype,
ref_depth = raw_call.get('AD', ',').split(',')[0],
alt_depth = raw_call.get('AD', ',').split(',')[1],
genotype_quality = raw_call.get('GQ', '.'),
depth = raw_call.get('DP', '.'),
supporting_evidence = raw_call.get('SU', '0'),
pe_support = raw_call.get('PE', '0'),
sr_support = raw_call.get('SR', '0'),
))
# Add transcript information:
if vep_string:
for transcript in self._get_vep_transcripts(variant, vep_info):
variant.add_transcript(transcript)
elif snpeff_string:
for transcript in self._get_snpeff_transcripts(variant, snpeff_info):
variant.add_transcript(transcript)
variant['most_severe_consequence'] = get_most_severe_consequence(
variant['transcripts']
)
for gene in self._get_genes(variant):
variant.add_gene(gene)
self._add_compounds(variant=variant, info_dict=info_dict)
yield variant
def _format_variant(self, variant_line, index, case_obj, head):
"""Return variant objects
Args:
raw_variants (Iterable): An iterable with variant lines
case_obj (puzzle.nodels.Case): A case object
"""
header_line = head.header
# Get the individual ids for individuals in vcf file
vcf_individuals = set([ind_id for ind_id in head.individuals])
variant_columns = ['CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER']
vep_header = head.vep_columns
snpeff_header = head.snpeff_columns
#Create a variant dict:
variant_dict = get_variant_dict(
variant_line = variant_line,
header_line = header_line
)
variant_dict['CHROM'] = variant_dict['CHROM'].lstrip('chrCHR')
#Crreate a info dict:
info_dict = get_info_dict(
info_line = variant_dict['INFO']
)
#Check if vep annotation:
vep_string = info_dict.get('CSQ')
#Check if snpeff annotation:
snpeff_string = info_dict.get('ANN')
if vep_string:
#Get the vep annotations
vep_info = get_vep_info(
vep_string = vep_string,
vep_header = vep_header
)
elif snpeff_string:
#Get the vep annotations
snpeff_info = get_snpeff_info(
snpeff_string = snpeff_string,
snpeff_header = snpeff_header
)
variant = Variant(
**{column: variant_dict.get(column, '.')
for column in variant_columns}
)
logger.debug("Creating a variant object of variant {0}".format(
variant.get('variant_id')))
variant['index'] = index
logger.debug("Updating index to: {0}".format(
index))
variant['start'] = int(variant_dict['POS'])
if self.variant_type == 'sv':
other_chrom = variant['CHROM']
# If we have a translocation:
if ':' in variant_dict['ALT'] and not '<' in variant_dict['ALT']:
other_coordinates = variant_dict['ALT'].strip('ACGTN[]').split(':')
other_chrom = other_coordinates[0].lstrip('chrCHR')
other_position = other_coordinates[1]
variant['stop'] = other_position
#Set 'infinity' to length if translocation
variant['sv_len'] = float('inf')
else:
variant['stop'] = int(info_dict.get('END', variant_dict['POS']))
variant['sv_len'] = variant['stop'] - variant['start']
variant['stop_chrom'] = other_chrom
else:
variant['stop'] = int(variant_dict['POS']) + \
(len(variant_dict['REF']) - len(variant_dict['ALT']))
variant['sv_type'] = info_dict.get('SVTYPE')
variant['cytoband_start'] = get_cytoband_coord(
chrom=variant['CHROM'],
pos=variant['start'])
if variant.get('stop_chrom'):
variant['cytoband_stop'] = get_cytoband_coord(
chrom=variant['stop_chrom'],
pos=variant['stop'])
# It would be easy to update these keys...
thousand_g = info_dict.get('1000GAF')
if thousand_g:
logger.debug("Updating thousand_g to: {0}".format(
thousand_g))
variant['thousand_g'] = float(thousand_g)
variant.add_frequency('1000GAF', variant.get('thousand_g'))
#SV specific tag for number of occurances
occurances = info_dict.get('OCC')
if occurances:
logger.debug("Updating occurances to: {0}".format(
occurances))
variant['occurances'] = float(occurances)
variant.add_frequency('OCC', occurances)
cadd_score = info_dict.get('CADD')
if cadd_score:
logger.debug("Updating cadd_score to: {0}".format(
cadd_score))
variant['cadd_score'] = float(cadd_score)
rank_score_entry = info_dict.get('RankScore')
if rank_score_entry:
for family_annotation in rank_score_entry.split(','):
rank_score = family_annotation.split(':')[-1]
logger.debug("Updating rank_score to: {0}".format(
rank_score))
variant['rank_score'] = float(rank_score)
genetic_models_entry = info_dict.get('GeneticModels')
if genetic_models_entry:
genetic_models = []
for family_annotation in genetic_models_entry.split(','):
for genetic_model in family_annotation.split(':')[-1].split('|'):
genetic_models.append(genetic_model)
logger.debug("Updating rank_score to: {0}".format(
rank_score))
variant['genetic_models'] = genetic_models
#Add genotype calls:
for individual in case_obj.individuals:
sample_id = individual.ind_id
if sample_id in vcf_individuals:
raw_call = dict(zip(
variant_dict['FORMAT'].split(':'),
variant_dict[sample_id].split(':'))
)
genotype = Genotype(**raw_call)
variant.add_individual(puzzle_genotype(
sample_id = sample_id,
genotype = genotype.genotype,
case_id = individual.case_name,
phenotype = individual.phenotype,
ref_depth = genotype.ref_depth,
alt_depth = genotype.alt_depth,
genotype_quality = genotype.genotype_quality,
depth = genotype.depth_of_coverage,
supporting_evidence = genotype.supporting_evidence,
pe_support = genotype.pe_support,
sr_support = genotype.sr_support,
))
# Add transcript information:
gmaf = None
if vep_string:
for transcript_info in vep_info:
transcript = self._get_vep_transcripts(transcript_info)
gmaf_raw = transcript_info.get('GMAF')
if gmaf_raw:
gmaf = float(gmaf_raw.split(':')[-1])
variant.add_transcript(transcript)
if gmaf:
variant.add_frequency('GMAF', gmaf)
if not variant.thousand_g:
variant.thousand_g = gmaf
elif snpeff_string:
for transcript_info in snpeff_info:
transcript = self._get_snpeff_transcripts(transcript_info)
variant.add_transcript(transcript)
most_severe_consequence = get_most_severe_consequence(
variant['transcripts']
)
if most_severe_consequence:
variant['most_severe_consequence'] = most_severe_consequence
variant['impact_severity'] = IMPACT_SEVERITIES.get(most_severe_consequence)
for gene in self._get_genes(variant):
variant.add_gene(gene)
self._add_compounds(variant=variant, info_dict=info_dict)
return variant
def test_get_cytoband_coord_chr():
chrom = 'chr1'
pos = 3
assert get_cytoband_coord(chrom, pos) == '1p36.33'
def test_get_cytoband_coord_non_existing_pos():
chrom = 'chrX'
pos = '155270600'
assert get_cytoband_coord(chrom, pos) == None
def test_get_cytoband_coord_non_existing_chr():
chrom = 'chrMT'
pos = '3'
assert get_cytoband_coord(chrom, pos) == None
def test_get_cytoband_coord_str_pos():
chrom = 'chr1'
pos = '3'
assert get_cytoband_coord(chrom, pos) == '1p36.33'