def __iter__(self):
from pysam import Tabixfile, asTuple
f = Tabixfile(self.filename, mode='r')
try:
# header row
if self.header is not None:
yield self.header
else:
# assume last header line has fields
h = list(f.header)
if len(h) > 0:
header_line = text_type(h[-1], encoding='ascii')
yield tuple(header_line.split('\t'))
# data rows
for row in f.fetch(reference=self.reference,
start=self.start,
end=self.stop,
region=self.region,
parser=asTuple()):
yield tuple(row)
except:
raise
finally:
f.close()
def __init__(self, task_queue, results_queue, family, args):
multiprocessing.Process.__init__(self)
self.task_queue = task_queue
self.family = family
self.results_queue = results_queue
self.verbosity = args.verbose
self.phased = args.phased
self.cadd_file = args.cadd_file[0]
self.chr_prefix = args.chr_prefix
if self.cadd_file:
self.cadd_file = Tabixfile(self.cadd_file, parser=asTuple())
def __init__(self, *filenames, **kwargs): #data_format=None,printer=None):
"""Create a |BigBedGenomeHash|
Parameters
----------
filenames : str or list of str
Filename or list of filenames of `Tabix`_-compressed files
data_format : str
Format of tabix-compressed file(s). Choices are:
`'GTF2'`,`'GFF3'`,`'BED'`,`'PSL'` (Default: `GTF2`)
"""
from pysam import Tabixfile
if len(filenames) == 1 and isinstance(filenames[0], list):
filenames = filenames[0]
self.filenames = list(multiopen(filenames))
self.printer = kwargs.get("printer", NullWriter())
data_format = kwargs.get("data_format", "GTF2")
try:
self._reader_class = TabixGenomeHash._READERS[data_format]
except ValueError:
msg = "Supported file formats for TabixGenomeHash are: %s" % ", ".join(
sorted(TabixGenomeHash._READERS.keys()))
self.printer.write(msg)
raise ValueError(msg)
self.tabix_readers = [Tabixfile(X) for X in self.filenames]
def __init__(self, task_queue, results_queue, family, args):
multiprocessing.Process.__init__(self)
self.task_queue = task_queue
self.family = family
self.results_queue = results_queue
self.verbosity = args.verbose
self.phased = args.phased
self.cadd_file = args.cadd_file[0]
self.chr_prefix = args.chr_prefix
if self.cadd_file:
self.cadd_file = Tabixfile(self.cadd_file, parser = asTuple())
def __init__(self, chromosome, position, annotation_table_file):
annotation_table = Tabixfile(annotation_table_file)
self.line = annotation_table.fetch(reference=chromosome,
start=position - 1,
end=position).next()
self.chromosome, \
self.position, \
self.reference_base, \
self.genic, \
self.exonic, \
self.intronic, \
self.intergenic, \
self.utr5, \
self.utr3, \
self.fold0, \
self.fold4, \
self.fold2, \
self.fold3, \
self.CDS, \
self.mRNA, \
self.rRNA, \
self.tRNA, \
self.feature_names, \
self.feature_types, \
self.feature_ID, \
self.cds_position, \
self.strand, \
self.frame, \
self.codon, \
self.aa, \
self.degen, \
self.FPKM, \
self.rho, \
self.FAIRE, \
self.recombination, \
self.mutability, \
self.quebec_alleles = self.line.split('\t')
self.position = int(self.position)
annotation_table.close()
def __iter__(self):
try:
from pysam import Tabixfile, asTuple
except ImportError as e:
raise UnsatisfiedDependency(e, dep_message)
f = Tabixfile(self.filename, mode='r')
try:
# header row
if self.header is not None:
yield self.header
else:
# assume last header line has fields
h = list(f.header)
if len(h) > 0:
yield tuple(h[-1].split('\t'))
# data rows
for row in f.fetch(reference=self.reference, start=self.start, end=self.end, region=self.region, parser=asTuple()):
yield tuple(row)
except:
raise
finally:
f.close()
def __iter__(self):
from pysam import Tabixfile, asTuple
f = Tabixfile(self.filename, mode='r')
try:
# header row
if self.header is not None:
yield self.header
else:
# assume last header line has fields
h = list(f.header)
if len(h) > 0:
header_line = text_type(h[-1], encoding='ascii')
yield tuple(header_line.split('\t'))
# data rows
for row in f.fetch(reference=self.reference, start=self.start,
end=self.stop, region=self.region,
parser=asTuple()):
yield tuple(row)
except:
raise
finally:
f.close()
def __iter__(self):
try:
from pysam import Tabixfile, asTuple
except ImportError as e:
raise UnsatisfiedDependency(e, dep_message)
f = Tabixfile(self.filename, mode="r")
try:
# header row
if self.header is not None:
yield self.header
else:
# assume last header line has fields
h = list(f.header)
if len(h) > 0:
yield tuple(h[-1].split("\t"))
# data rows
for row in f.fetch(
reference=self.reference, start=self.start, end=self.end, region=self.region, parser=asTuple()
):
yield tuple(row)
except:
raise
finally:
f.close()
class VariantConsumer(multiprocessing.Process):
"""Yeilds all unordered pairs from a list of objects as tuples, like (obj_1, obj_2)"""
def __init__(self, task_queue, results_queue, family, args):
multiprocessing.Process.__init__(self)
self.task_queue = task_queue
self.family = family
self.results_queue = results_queue
self.verbosity = args.verbose
self.phased = args.phased
self.cadd_file = args.cadd_file[0]
self.chr_prefix = args.chr_prefix
if self.cadd_file:
self.cadd_file = Tabixfile(self.cadd_file, parser=asTuple())
def fix_variants(self, variant_batch):
"""Merge the variants into one dictionary, make shure that the compounds are treated right."""
fixed_variants = {}
for feature in variant_batch:
for variant_id in variant_batch[feature]:
if variant_id in fixed_variants:
# We need to add compound information from different features
if len(variant_batch[feature][variant_id]
['Compounds']) > 0:
fixed_variants[variant_id]['Compounds'] = (dict(
list(variant_batch[feature][variant_id]
['Compounds'].items()) +
list(fixed_variants[variant_id]
['Compounds'].items())))
else:
fixed_variants[variant_id] = variant_batch[feature][
variant_id]
return fixed_variants
def get_cadd_score(self, variant):
"""Get the cadd score and add it to the variant."""
cadd_score = '-'
alternatives = variant['ALT'].split(',')
# CADD vales are only for snps:
if max([len(alt)
for alt in alternatives]) == 1 and len(variant['REF']) == 1:
if self.cadd_file:
cadd_key = int(variant['POS'])
try:
for tpl in self.cadd_file.fetch(str(variant['CHROM']),
cadd_key - 1, cadd_key):
if alternatives[0] == str(tpl[3]):
try:
return str(tpl[5], encoding='utf-8')
except TypeError:
return str(unicode(tpl[5], encoding='utf-8'))
except (IndexError, KeyError) as e:
if self.verbosity:
print(e, variant['CHROM'], variant['POS'])
return cadd_score
def make_print_version(self, variant_dict):
"""Get the variants ready for printing"""
for variant_id in variant_dict:
if self.cadd_file:
variant_dict[variant_id]['CADD'] = self.get_cadd_score(
variant_dict[variant_id])
model_list = []
compounds_list = []
#Remove the 'Genotypes' post since we will not need them for now
variant_dict[variant_id].pop('Genotypes', 0)
feature_list = variant_dict[variant_id]['Annotation']
if len(variant_dict[variant_id]['Compounds']) > 0:
#We do not want reference to itself as a compound:
variant_dict[variant_id]['Compounds'].pop(variant_id, 0)
compounds_list = list(
variant_dict[variant_id]['Compounds'].keys())
else:
compounds_list = ['-']
for model in variant_dict[variant_id]['Inheritance_model']:
if variant_dict[variant_id]['Inheritance_model'][model]:
model_list.append(model)
if len(model_list) == 0:
model_list = ['NA']
model_score = '-'
genotype_scores = []
for individual in self.family.individuals:
gt_call = variant_dict[variant_id][individual].split(':')
gt_info = variant_dict[variant_id]['FORMAT'].split(':')
if len(gt_call) == 1:
gt_call = {'GT': gt_call[0]}
else:
gt_call = dict(zip(gt_info, gt_call))
if 'GQ' in gt_call:
# Add the error probabilities to genotype scores
genotype_scores.append(10**-(float(gt_call['GQ']) / 10))
if len(genotype_scores) > 0:
model_score = (str(
round(-10 * log10(1 - reduce(
operator.mul, [1 - score
for score in genotype_scores])))))
variant_dict[variant_id].pop('Compounds', 0)
variant_dict[variant_id].pop('Inheritance_model', 0)
variant_dict[variant_id].pop('Annotation', 0)
vcf_info = variant_dict[variant_id]['INFO'].split(';')
if self.chr_prefix:
variant_dict[variant_id][
'CHROM'] = 'chr' + variant_dict[variant_id]['CHROM']
# if we should include the annotation:
vcf_info.append('ANN=' + ':'.join(feature_list))
# if we should include compounds:
vcf_info.append('Comp=' + ':'.join(compounds_list))
# if we should include genetic models:
vcf_info.append('GM=' + ':'.join(model_list))
if model_list == ['NA']:
model_score = '-'
vcf_info.append('MS=' + model_score)
if self.cadd_file:
vcf_info.append('CADD=%s' %
str(variant_dict[variant_id].pop('CADD', '-')))
variant_dict[variant_id]['INFO'] = ';'.join(vcf_info)
return
def run(self):
"""Run the consuming"""
proc_name = self.name
if self.verbosity:
print('%s: Starting!' % proc_name)
while True:
# A batch is a dictionary on the form {gene:{variant_id:variant_dict}}
next_batch = self.task_queue.get()
# if self.verbosity:
# if self.results_queue.full():
# print('Batch results queue Full! %s' % proc_name)
# if self.task_queue.full():
# print('Variant queue full! %s' % proc_name)
if next_batch is None:
self.task_queue.task_done()
if self.verbosity:
print('%s: Exiting' % proc_name)
break
genetic_models.check_genetic_models(next_batch, self.family,
self.verbosity, self.phased,
proc_name)
# Make shure we only have one copy of each variant:
fixed_variants = self.fix_variants(next_batch)
# Now we want to make versions of the variants that are ready for printing.
self.make_print_version(fixed_variants)
self.results_queue.put(fixed_variants)
self.task_queue.task_done()
return
class VariantConsumer(multiprocessing.Process):
"""Yeilds all unordered pairs from a list of objects as tuples, like (obj_1, obj_2)"""
def __init__(self, task_queue, results_queue, family, args):
multiprocessing.Process.__init__(self)
self.task_queue = task_queue
self.family = family
self.results_queue = results_queue
self.verbosity = args.verbose
self.phased = args.phased
self.cadd_file = args.cadd_file[0]
self.chr_prefix = args.chr_prefix
if self.cadd_file:
self.cadd_file = Tabixfile(self.cadd_file, parser = asTuple())
def fix_variants(self, variant_batch):
"""Merge the variants into one dictionary, make shure that the compounds are treated right."""
fixed_variants = {}
for feature in variant_batch:
for variant_id in variant_batch[feature]:
if variant_id in fixed_variants:
# We need to add compound information from different features
if len(variant_batch[feature][variant_id]['Compounds']) > 0:
fixed_variants[variant_id]['Compounds'] = (
dict(list(variant_batch[feature][variant_id]['Compounds'].items()) +
list(fixed_variants[variant_id]['Compounds'].items())))
else:
fixed_variants[variant_id] = variant_batch[feature][variant_id]
return fixed_variants
def get_cadd_score(self, variant):
"""Get the cadd score and add it to the variant."""
cadd_score = '-'
alternatives = variant['ALT'].split(',')
# CADD vales are only for snps:
if max([len(alt) for alt in alternatives]) == 1 and len(variant['REF']) == 1:
if self.cadd_file:
cadd_key = int(variant['POS'])
try:
for tpl in self.cadd_file.fetch(str(variant['CHROM']), cadd_key-1, cadd_key):
if alternatives[0] == str(tpl[3]):
try:
return str(tpl[5], encoding='utf-8')
except TypeError:
return str(unicode(tpl[5], encoding='utf-8'))
except (IndexError, KeyError) as e:
if self.verbosity:
print(e, variant['CHROM'], variant['POS'])
return cadd_score
def make_print_version(self, variant_dict):
"""Get the variants ready for printing"""
for variant_id in variant_dict:
if self.cadd_file:
variant_dict[variant_id]['CADD'] = self.get_cadd_score(variant_dict[variant_id])
model_list = []
compounds_list = []
#Remove the 'Genotypes' post since we will not need them for now
variant_dict[variant_id].pop('Genotypes', 0)
feature_list = variant_dict[variant_id]['Annotation']
if len(variant_dict[variant_id]['Compounds']) > 0:
#We do not want reference to itself as a compound:
variant_dict[variant_id]['Compounds'].pop(variant_id, 0)
compounds_list = list(variant_dict[variant_id]['Compounds'].keys())
else:
compounds_list = ['-']
for model in variant_dict[variant_id]['Inheritance_model']:
if variant_dict[variant_id]['Inheritance_model'][model]:
model_list.append(model)
if len(model_list) == 0:
model_list = ['NA']
model_score = '-'
genotype_scores = []
for individual in self.family.individuals:
gt_call = variant_dict[variant_id][individual].split(':')
gt_info = variant_dict[variant_id]['FORMAT'].split(':')
if len(gt_call) == 1:
gt_call = {'GT':gt_call[0]}
else:
gt_call = dict(zip(gt_info, gt_call))
if 'GQ' in gt_call:
# Add the error probabilities to genotype scores
genotype_scores.append(10**-(float(gt_call['GQ'])/10))
if len(genotype_scores) > 0:
model_score = (str(round(-10*log10(1-reduce(operator.mul, [1-score for score in genotype_scores])))))
variant_dict[variant_id].pop('Compounds',0)
variant_dict[variant_id].pop('Inheritance_model',0)
variant_dict[variant_id].pop('Annotation',0)
vcf_info = variant_dict[variant_id]['INFO'].split(';')
if self.chr_prefix:
variant_dict[variant_id]['CHROM'] = 'chr'+variant_dict[variant_id]['CHROM']
# if we should include the annotation:
vcf_info.append('ANN=' + ':'.join(feature_list))
# if we should include compounds:
vcf_info.append('Comp=' + ':'.join(compounds_list))
# if we should include genetic models:
vcf_info.append('GM=' + ':'.join(model_list))
if model_list == ['NA']:
model_score = '-'
vcf_info.append('MS=' + model_score)
if self.cadd_file:
vcf_info.append('CADD=%s' % str(variant_dict[variant_id].pop('CADD', '-')))
variant_dict[variant_id]['INFO'] = ';'.join(vcf_info)
return
def run(self):
"""Run the consuming"""
proc_name = self.name
if self.verbosity:
print('%s: Starting!' % proc_name)
while True:
# A batch is a dictionary on the form {gene:{variant_id:variant_dict}}
next_batch = self.task_queue.get()
# if self.verbosity:
# if self.results_queue.full():
# print('Batch results queue Full! %s' % proc_name)
# if self.task_queue.full():
# print('Variant queue full! %s' % proc_name)
if next_batch is None:
self.task_queue.task_done()
if self.verbosity:
print('%s: Exiting' % proc_name)
break
genetic_models.check_genetic_models(next_batch, self.family, self.verbosity, self.phased, proc_name)
# Make shure we only have one copy of each variant:
fixed_variants = self.fix_variants(next_batch)
# Now we want to make versions of the variants that are ready for printing.
self.make_print_version(fixed_variants)
self.results_queue.put(fixed_variants)
self.task_queue.task_done()
return
genofins = []
for line in genofinfile:
genofins.append(line.strip().split()[1])
genofinfile.close()
genoinds = [genofins.index(x) + 6 for x in officialfindivs]
y = {}
currbimbam = open(currfiles + '.bimbam','w')
#t0 = time.time()
for snp in masterdic.keys():
#for snp in masterdic.keys()[0:1000]:
chrm = masterdic[snp][0]
if chrm == 'chrm':
continue
tabixer = Tabixfile('/mnt/lustre/home/cusanovich/500HT/Imputed1415/ByChr/hutt.all.imputed.' + chrm + '.txt.gz')
tempgenos = [x.split('\t') for x in tabixer.fetch(chrm,int(masterdic[snp][1])-1,int(masterdic[snp][2]))][0]
genos = [tempgenos[x] for x in range(0,6) + genoinds]
tabixer.close()
y[snp] = [genos[3], 'A', 'G'] + genos[6:]
print >> currbimbam, ", ".join(y)
#t1 = time.time()
#print t1-t0
currbimbam.close()
#genomat = matrix_reader(genodir + 'hutt.imputed.dhssnps.bimbam',sep=",")
print "Running GEMMA..."
gemmer = (hmdir + 'Programs/gemma0.94 -g ' + currfiles + '.bimbam -p ' + currfiles + '.pheno -k ' + currfiles + '.square.txt -c ' + currfiles + '.covariates -lmm 4 -maf 0.05 -o curr_' + pheno)
t0 = time.time()
ifier(gemmer)
fmt='%s')
if not regressPCs:
phener = ('cut -f' + str(int(exprcoldic[gene]) + 1) + ' -d" " ' +
hmdir + '500HT/Exprs/qqnorm.500ht' + gccor + covcor +
'.ordered.' + chrm + '.bimbam > ' + currfiles + '.pheno')
ifier(phener)
currgenos = []
####Pull genotypes for the SNPs in cis, if genotypes not already in dictionary: go to geno file and pull in appropriate data
for snp in masterdic[gene]:
try:
currgenos.append(", ".join(genodic[snp]))
except KeyError:
#tabixer = pysam.Tabixfile('/mnt/lustre/home/cusanovich/500HT/Imputed1415/ByChr/hutt.imputed.' + chrm + '.txt.gz')
#tabixer = pysam.Tabixfile('/mnt/lustre/home/cusanovich/500HT/' + mapper + '/ByChr/hutt.' + mapper + '.' + distance + '.' + chrm + '.txt.gz')
tabixer = Tabixfile(
'/mnt/lustre/home/cusanovich/500HT/Imputed1415/ByChr/hutt' +
mapper + '.' + chrm + '.txt.gz')
genos = [
x.split('\t') for x in tabixer.fetch(chrm, int(snpdic[snp][1]),
int(snpdic[snp][2]))
][0]
tabixer.close()
y = [genos[3], 'A', 'G'] + genos[6:len(genos)]
genodic[snp] = y
currgenos.append(", ".join(genodic[snp]))
currbimbam = open(currfiles + '.bimbam', 'w')
print >> currbimbam, "\n".join(currgenos)
currbimbam.close()
#print "Running GEMMA..."
if regressPCs:
gemmer = (hmdir + 'Programs/gemma0.94 -g ' + currfiles +
if regressPCs:
numpy.savetxt(currfiles + '.pheno',Yfit[exprcoldic[gene],],delimiter='\n',fmt='%s')
if not regressPCs:
phener = ('cut -f' + str(int(exprcoldic[gene]) + 1) + ' -d" " ' +
hmdir + '500HT/Exprs/qqnorm.500ht' + gccor + covcor +
'.ordered.' + chrm + '.bimbam > ' + currfiles + '.pheno')
ifier(phener)
currgenos = []
####Pull genotypes for the SNPs in cis, if genotypes not already in dictionary: go to geno file and pull in appropriate data
for snp in masterdic[gene]:
try:
currgenos.append(", ".join(genodic[snp]))
except KeyError:
#tabixer = pysam.Tabixfile('/mnt/lustre/home/cusanovich/500HT/Imputed1415/ByChr/hutt.imputed.' + chrm + '.txt.gz')
#tabixer = pysam.Tabixfile('/mnt/lustre/home/cusanovich/500HT/' + mapper + '/ByChr/hutt.' + mapper + '.' + distance + '.' + chrm + '.txt.gz')
tabixer = Tabixfile('/mnt/lustre/home/cusanovich/500HT/Imputed1415/ByChr/hutt' + mapper + '.' + chrm + '.txt.gz')
genos = [x.split('\t') for x in tabixer.fetch(chrm,int(snpdic[snp][1]),int(snpdic[snp][2]))][0]
tabixer.close()
y = [genos[3], 'A', 'G'] + genos[6:len(genos)]
genodic[snp] = y
currgenos.append(", ".join(genodic[snp]))
currbimbam = open(currfiles + '.bimbam','w')
print >> currbimbam, "\n".join(currgenos)
currbimbam.close()
#print "Running GEMMA..."
if regressPCs:
gemmer = (hmdir + 'Programs/gemma0.94 -g ' + currfiles + '.bimbam -p ' + currfiles + '.pheno -k ' + currfiles + '.square.txt -lmm 4 -maf 0.05 -o curr_' + chrm + '_pc' + str(pcs) + '_' + correction)
ifier(gemmer)
if not regressPCs:
gemmer = (hmdir + 'Programs/gemma0.94 -g ' + currfiles + '.bimbam -p ' + currfiles + '.pheno -k ' + currfiles + '.square.txt -c ' + currfiles + '.pcs.txt -lmm 4 -maf 0.05 -o curr_' + chrm + '_pc' + str(pcs) + '_' + correction)
ifier(gemmer)
