def data_iterator(self,
keys=('tumor_bam', 'normal_bam', 'data_filename',
'project', 'dataset', 'sample', 'evidence_type')):
file = open(self.filename, 'rU')
reader = csv.DictReader(file, delimiter='\t')
logging.getLogger(__name__).info(
"Gathering variants from table of files:" + self.filename)
for file_data in reader:
if file_data.has_key('FILTER'):
if len(filter) > 0: continue
meta_data_dict = get_entries_from_dict(file_data,
keys=keys,
return_type=dict)
logging.getLogger(
__name__).info("Gathering variants from individual file:" +
meta_data_dict['data_filename'])
D = DatabaseParser(meta_data_dict['data_filename'])
self.current_file = meta_data_dict['data_filename']
n = 0
self.new_file = True
for variant_dict in D.get_variants():
yield merge_dicts(variant_dict, meta_data_dict)
if self.new_file == True: self.new_file = False
self.current_file = None
def data_iterator(self,keys=('tumor_bam','normal_bam',
'data_filename',
'project',
'dataset',
'sample',
'evidence_type')):
file = open(self.filename,'rU')
reader = csv.DictReader(file,delimiter='\t')
logging.getLogger(__name__).info("Gathering variants from table of files:"+ self.filename)
for file_data in reader:
if file_data.has_key('FILTER'):
if len(filter) > 0: continue
meta_data_dict = get_entries_from_dict(file_data,
keys=keys,
return_type=dict)
logging.getLogger(__name__).info("Gathering variants from individual file:"+ meta_data_dict['data_filename'])
D = DatabaseParser(meta_data_dict['data_filename'])
self.current_file = meta_data_dict['data_filename']
n=0
self.new_file = True
for variant_dict in D.get_variants():
yield merge_dicts(variant_dict, meta_data_dict)
if self.new_file == True: self.new_file = False
self.current_file = None
def survey(filename):
logging.getLogger(__name__).info("Beginning survey.")
query = "{'project' : { '$exists' : 'true' } }"
tally = defaultdict(int)
collector = connect_to_mongo()
# collect query information
n = 0
for record in collector.find(ast.literal_eval(query)):
sample_information = get_entries_from_dict(
record,
keys=['project', 'dataset', 'sample', 'evidence_type'],
return_type=dict)
feature = None
if is_snp(record):
feature = 'snp'
if is_indel(record):
feature = 'indel'
if feature is None:
print record
continue
if sample_information['evidence_type'] == 'TP':
n += 1
project = sample_information['project']
dataset = sample_information['dataset']
sample = sample_information['sample']
tally[(project, dataset, sample, feature)] += 1
tally[(project, dataset, '', feature)] += 1
tally[(project, '', '', feature)] += 1
tally[('', '', '', feature)] += 1
if not (n % 10000):
logging.getLogger(__name__).info("Variants seen: " + str(n))
fp = csv.DictWriter(
open(filename, 'w'),
fieldnames=['project', 'dataset', 'sample', 'feature', 'count'],
delimiter='\t')
fp.writeheader()
for item in tally:
fp.writerow({
'project': item[0],
'dataset': item[1],
'sample': item[2],
'feature': item[3],
'count': tally[item]
})
def survey(filename):
logging.getLogger(__name__).info("Beginning survey.")
query = "{'project' : { '$exists' : 'true' } }"
tally = defaultdict(int)
collector = connect_to_mongo()
# collect query information
n = 0
for record in collector.find(ast.literal_eval(query)):
sample_information = get_entries_from_dict(record, keys=['project',
'dataset',
'sample',
'evidence_type'],return_type=dict)
feature = None
if is_snp(record):
feature = 'snp'
if is_indel(record):
feature = 'indel'
if feature is None:
print record
continue
if sample_information['evidence_type'] == 'TP':
n+=1
project = sample_information['project']
dataset = sample_information['dataset']
sample = sample_information['sample']
tally[(project,dataset,sample,feature)]+=1
tally[(project,dataset,'',feature)]+=1
tally[(project,'','',feature)]+=1
tally[('','','',feature)]+=1
if not (n % 10000): logging.getLogger(__name__).info("Variants seen: "+str(n))
fp = csv.DictWriter(open(filename,'w'), fieldnames=['project','dataset','sample','feature','count'],delimiter='\t')
fp.writeheader()
for item in tally:
fp.writerow({'project':item[0],'dataset':item[1],'sample':item[2],'feature':item[3],'count': tally[item] })
def variant_extract(query, output_filename, max_number_of_records):
query = query_processor(query)
output = []
collection = connect_to_mongo()
for record in collection.find(ast.literal_eval(query)):
sample_information = get_entries_from_dict(record,
keys=[
'chromosome', 'start',
'ref', 'alt', 'project',
'dataset', 'sample',
'evidence_type'
],
return_type=dict)
for sample in sample_information:
sample_information[sample] = str(sample_information[sample])
output.append(sample_information)
output = pd.DataFrame(output)
if max_number_of_records is not None:
if len(output) > max_number_of_records:
output = output[:max_number_of_records]
if output_filename == "<stdout>":
print "project, dataset, sample, evidence_type, chromosome, start, ref, alt"
for k, row in output.iterrows():
row = [
row['project'], row['dataset'], row['sample'],
row['evidence_type'], row['chrosome'], row['start'],
row['ref'], row['alt']
]
row = ",".join(row)
print row
else:
output.to_csv(output_filename,
index=False,
columns=[
"project", "dataset", "sample", "evidence_type",
"chromosome", "start", "ref", "alt"
],
sep='\t')
def variant_extract(query, output_filename, max_number_of_records):
query = query_processor(query)
output = []
collection = connect_to_mongo()
for record in collection.find(ast.literal_eval(query)):
sample_information = get_entries_from_dict(record, keys=['chromosome',
'start',
'ref',
'alt',
'project',
'dataset',
'sample',
'evidence_type'],return_type=dict)
for sample in sample_information:
sample_information[sample] = str(sample_information[sample])
output.append(sample_information)
output = pd.DataFrame(output)
if max_number_of_records is not None:
if len(output) > max_number_of_records: output = output[:max_number_of_records]
if output_filename == "<stdout>":
print "project, dataset, sample, evidence_type, chromosome, start, ref, alt"
for k, row in output.iterrows():
row = [row['project'],row['dataset'],row['sample'],row['evidence_type'],row['chrosome'],row['start'],row['ref'],row['alt']]
row =",".join(row)
print row
else:
output.to_csv(output_filename,index=False,columns=["project",
"dataset",
"sample",
"evidence_type",
"chromosome",
"start",
"ref",
"alt"], sep='\t')
def VariantUploader(tsv, submit_to_filesystem=False):
gather = DataGatherer(tsv)
variants = connect_to_mongo()
if submit_to_filesystem:
filesystem = SomaticFileSystem('/dsde/working/somaticDB/master/data')
S = SubmissionFile(tsv)
S.change_file_dir()
S.to_csv(
os.path.join('/dsde/working/somaticDB/master/records',
os.path.basename(tsv)))
else:
filesystem = None
bulk_count = 0
bulk = variants.initialize_unordered_bulk_op()
start_time = time.time()
n = 0
for variant_dict in gather.data_iterator():
n += 1
bulk_count += 1
additional_data_dict = {}
mongo_submission = merge_dicts(variant_dict, additional_data_dict)
# if the user is uploading a mutect1 maf ... rename fields
if mongo_submission.has_key('contig'):
mongo_submission['chromosome'] = mongo_submission.pop('contig')
if mongo_submission.has_key('position'):
mongo_submission['start'] = mongo_submission.pop('position')
if mongo_submission.has_key('ref_allele'):
mongo_submission['ref'] = mongo_submission.pop('ref_allele')
if mongo_submission.has_key('alt_allele'):
mongo_submission['alt'] = mongo_submission.pop('alt_allele')
unique_data = get_entries_from_dict(mongo_submission,
keys=[
'chromosome', 'start', 'ref',
'alt', 'project', 'dataset',
'evidence_type'
],
return_type=dict)
if filesystem:
project = mongo_submission['project']
dataset = mongo_submission['dataset']
filesystem.add_project(project)
filesystem[project].add_dataset(dataset)
filesystem[project][dataset].add_file(
mongo_submission['data_filename'])
mongo_submission['data_filename']=\
change_data_filename("/dsde/working/somaticDB/master/data/%s/%s/"%(project,dataset),
mongo_submission['data_filename'])
bulk.insert(mongo_submission)
if bulk_count == 10000:
print "variants uploaded: %d (%.2f seconds since start of upload)." % (
n, time.time() - start_time)
bulk_count = 0
bulk.execute()
bulk = variants.initialize_unordered_bulk_op()
if bulk_count > 0:
print "variants uploaded: %d (%.2f seconds since start of upload)." % (
n, time.time() - start_time)
bulk.execute()
def VariantAssessor(query,tsv,output_file,outdir=""):
collection = connect_to_mongo()
caller_output = pd.read_csv(tsv,sep='\t')
known_true = {'snp': defaultdict(set),'indel': defaultdict(set)}
known_false = {'snp': defaultdict(set),'indel': defaultdict(set)}
found_variants = {'snp': defaultdict(set),'indel': defaultdict(set)}
false_positive = {'snp': defaultdict(set),'indel': defaultdict(set)}
query = query_processor(query)
logging.getLogger(__name__).info("Querying database for variants.")
# collect query information
for record in collection.find(ast.literal_eval(query)):
sample_information = get_entries_from_dict(record, keys=['project','dataset','sample'],return_type=tuple)
variant = get_entries_from_dict(record, keys=['chromosome','start','ref','alt'],return_type=tuple)
sample_information = tuple(map(str, sample_information))
variant = tuple(map(str, variant))
evidence_type = record['evidence_type']
if is_snp(record):
if 'TP' in evidence_type:
known_true['snp'][sample_information].add(variant)
if 'FP' in evidence_type:
known_false['snp'][sample_information].add(variant)
elif is_indel(record):
if 'TP' in evidence_type:
known_true['indel'][sample_information].add(variant)
if 'FP' in evidence_type:
known_false['indel'][sample_information].add(variant)
normal_normal = set([])
cm = set([])
#index the type of assessment to be done for each datatype.
for k,row in caller_output.iterrows():
sample_information = (row['project'],row['dataset'],row['sample'])
if row['evidence_type'] == 'NN':
normal_normal.add(sample_information)
elif row['evidence_type'] == 'CM':
cm.add(sample_information)
else:
cm.add(sample_information) #by default, ROC-like curves are used.
gather = DataGatherer(tsv)
logging.getLogger(__name__).info("Collection of variants from user submitted files.")
found_feature_data = defaultdict(dict)
#data from file (algorithm being tested)
for variant_dict in gather.data_iterator():
sample_information = get_entries_from_dict(variant_dict, keys=['project','dataset','sample'],return_type=tuple)
variant = get_entries_from_dict(variant_dict, keys=['chromosome','start','ref','alt'],return_type=tuple)
print sample_information, variant
#found_feature_data[sample_information][variant] = get_entries_from_dict(variant_dict, keys=['ECNT','HCNT','NLOD','TLOD'],return_type=dict)
if is_snp(variant_dict):
found_variants['snp'][sample_information].add(variant)
elif is_indel(variant_dict):
found_variants['indel'][sample_information].add(variant)
#print found_feature_data.keys()
caller_samples = caller_output[['project','dataset','sample']].values.tolist()
data = []
for feature in ['snp','indel']:
filename = {}; fp_fn = {}; fp_fp={}; all_dict={}; fp_tp= {}
filename[feature] = feature+".false_negatives.tsv"
fp_fn[feature] = csv.DictWriter(open( os.path.join(outdir,filename[feature]) ,'w'),
delimiter='\t',
fieldnames=['project','dataset','sample','chromosome','start','ref','alt','variant_type'])
#fieldnames=['project','dataset','sample','chromosome','start','ref','alt','ECNT','HCNT','NLOD','TLOD','variant_type']
fieldnames=['project','dataset','sample','chromosome','start','ref','alt','variant_type']
filename[feature] = feature+".false_positives.tsv"
fp_fp[feature] = csv.DictWriter(open( os.path.join(outdir,filename[feature]) ,'w'),
delimiter='\t',
fieldnames=fieldnames)
#fieldnames=['project','dataset','sample','chromosome','start','ref','alt','ECNT','HCNT','NLOD','TLOD','variant_type']
fieldnames=['project','dataset','sample','chromosome','start','ref','alt','variant_type']
filename[feature] = feature+".true_positives.tsv"
fp_tp[feature] = csv.DictWriter(open( os.path.join(outdir,filename[feature]) ,'w'),
delimiter='\t',
fieldnames=fieldnames)
fp_fn[feature].writeheader()
fp_fp[feature].writeheader()
fp_tp[feature].writeheader()
for eval_type in ['CM','NN']:
all_dict[eval_type] = {'project': 'all',
'dataset': 'all',
'sample' : 'all',
'false_positives': 0,
'true_positives': 0,
'false_negatives': 0,
'tpr': np.nan,
'fpr': np.nan,
'precision': np.nan,
'evidence_type': eval_type,
'variant_type': feature }
for sample_information in map(tuple,caller_samples):
if sample_information in normal_normal:
assessment_type = 'NN'
elif sample_information in cm:
assessment_type = 'CM'
else:
assessment_type = 'CM'
row_dict = {'project': sample_information[0],
'dataset': sample_information[1],
'sample' : sample_information[2],
'false_positives': 0,
'true_positives': 0,
'false_negatives': 0,
'tpr': np.nan,
'fpr': np.nan,
'precision': np.nan,
'evidence_type': assessment_type,
'variant_type': feature}
if assessment_type == 'NN':
FN = len(found_variants[feature][sample_information])
row_dict['false_positives'] = FN
row_dict['precision'] = 0
if assessment_type == 'CM':
TP = np.float(len(found_variants[feature][sample_information].intersection(known_true[feature][sample_information])))
FN = np.float(len(known_true[feature][sample_information].difference(found_variants[feature][sample_information])))
FP = np.float(len(found_variants[feature][sample_information].difference(known_true[feature][sample_information])))
print TP, FN, FP
try:
row_dict['tpr'] = TP/(TP+FN)
except:
row_dict['tpr'] = np.nan
row_dict['true_positives'] = TP
row_dict['false_negatives'] = FN
row_dict['false_positives'] = FP
all_dict['CM']['true_positives'] += TP
all_dict['CM']['false_negatives'] += FN
all_dict['CM']['false_positives'] += FP
try:
row_dict['precision'] = TP/(TP+FP)
except:
row_dict['precision'] = np.nan
row_dict['dream_accuracy'] = (row_dict['tpr'] + row_dict['precision'])/2.0
print row_dict['tpr'], row_dict['precision'], row_dict['dream_accuracy']
row_dict['variant_type'] = feature
data.append(row_dict)
true_positives = list(found_variants[feature][sample_information].intersection(known_true[feature][sample_information]))
false_positives = list(found_variants[feature][sample_information].difference(known_true[feature][sample_information]))
false_negatives = list(known_true[feature][sample_information].difference(found_variants[feature][sample_information]))
for variant in true_positives:
fp_tp[feature].writerow({'project': sample_information[0],
'dataset':sample_information[1],
'sample':sample_information[2],
'chromosome':variant[0],
'start':variant[1],
'ref':variant[2],
'alt':variant[3],
#'ECNT':found_feature_data[sample_information][variant]['ECNT'],
#'HCNT':found_feature_data[sample_information][variant]['HCNT'],
#'NLOD':found_feature_data[sample_information][variant]['NLOD'],
#'TLOD':found_feature_data[sample_information][variant]['TLOD'],
'variant_type':feature})
for variant in false_positives:
fp_fp[feature].writerow({'project': sample_information[0],
'dataset':sample_information[1],
'sample':sample_information[2],
'chromosome':variant[0],
'start':variant[1],
'ref':variant[2],
'alt':variant[3],
#'ECNT':found_feature_data[sample_information][variant]['ECNT'],
#'HCNT':found_feature_data[sample_information][variant]['HCNT'],
#'NLOD':found_feature_data[sample_information][variant]['NLOD'],
#'TLOD':found_feature_data[sample_information][variant]['TLOD'],
'variant_type':feature})
for variant in false_negatives:
fp_fn[feature].writerow({'project': sample_information[0],
'dataset':sample_information[1],
'sample':sample_information[2],
'chromosome':variant[0],
'start':variant[1],
'ref':variant[2],
'alt':variant[3],
'variant_type':feature})
try:
all_dict['CM']['tpr'] = all_dict['CM']['true_positives']/(all_dict['CM']['true_positives']+all_dict['CM']['false_negatives'])
except:
all_dict['CM']['tpr'] = np.nan
all_dict['CM']['dream_accuracy'] = (all_dict['CM']['tpr'] + 1 -all_dict['CM']['precision'])/2.0
try:
all_dict['CM']['precision'] = all_dict['CM']['true_positives']/(all_dict['CM']['true_positives']+all_dict['CM']['false_positives'])
except:
all_dict['CM']['precision'] = np.nan
all_dict['CM']['dream_accuracy'] = (all_dict['CM']['tpr'] + all_dict['CM']['precision'])/2.0
all_dict['CM']['variant_type'] = feature
#data.append(all_dict['CM'])
#data.append(all_dict['NN'])
fieldnames=['project','dataset','sample' ,'false_positives','true_positives','false_negatives','tpr','precision','evidence_type','dream_accuracy','variant_type']
pd.DataFrame(data).to_csv(output_file, sep='\t',index=False,columns=fieldnames,na_rep='nan')
def BamAggregator(query, normal_bam_list_name, tumor_bam_list_name,
interval_list_name, metadata_list_name, folder):
collection = connect_to_mongo()
query = query_processor(query)
interval_list = defaultdict(set)
metadata_list = {}
query = query.strip('"')
query = ast.literal_eval(query)
print query
print type(query)
print "query dictionary:", query.items()
print "directory:" + os.getcwd()
doesrecordloop = False
for record in collection.find(query):
if doesrecordloop == False:
print "Contains at least one record."
doesrecordloop = True
if not record.has_key('tumor_bam'):
print record
continue
#print record['tumor_bam']
record['tumor_bam'] = picard_version_to_current(record['tumor_bam'])
record['normal_bam'] = picard_version_to_current(record['normal_bam'])
#print record['tumor_bam']
#print
tumor_bam = record['tumor_bam']
normal_bam = record['normal_bam']
interval = "%s:%s-%s" % (record['chromosome'], record['start'],
record['end'])
interval_list[(tumor_bam, normal_bam)].add(interval)
field_names = [
'tumor_bam', 'normal_bam', 'data_filename', 'project', 'dataset',
'sample'
]
metadata_list[(tumor_bam,
normal_bam)] = get_entries_from_dict(record,
keys=field_names,
return_type=dict)
metadata_list[(tumor_bam, normal_bam)]['evidence_type'] = '.'
metadata_list[(tumor_bam, normal_bam)]['author'] = '.'
print 'OPENNING FILES HERE.'
print 'tumor_bam_file: ' + tumor_bam_list_name
print 'normal_bam_file: ' + normal_bam_list_name
print 'interval file:' + interval_list_name
tumor_bam_file = open(tumor_bam_list_name, 'w')
normal_bam_file = open(normal_bam_list_name, 'w')
interval_file = open(interval_list_name, 'w')
location = os.path.dirname(tumor_bam_list_name)
fname = os.path.join(location, 'test.txt')
print "test:" + fname
f = open(fname, 'w')
f.close()
for filename in os.listdir(location):
if filename.endswith("list"): print filename
fieldnames = [
'tumor_bam', 'normal_bam', 'data_filename', 'project', 'dataset',
'sample', 'evidence_type', 'author'
]
metadata_file = csv.DictWriter(open(metadata_list_name, 'w'),
fieldnames=fieldnames,
delimiter='\t')
metadata_file.writeheader()
current_dir = os.getcwd()
for pair in interval_list:
tumor_bam, normal_bam = pair
tumor_bam_file.write(tumor_bam + '\n')
normal_bam_file.write(normal_bam + '\n')
metadata_file.writerow(metadata_list[(tumor_bam, normal_bam)])
sample =\
"".join([random.choice('abcdef0123456789') for k in range(40)])
intervals_dir = folder
current_filename = ".".join([
"intervals",
os.path.splitext(os.path.basename(tumor_bam))[0],
os.path.splitext(os.path.basename(normal_bam))[0], "list"
])
current_filename = os.path.join(intervals_dir, current_filename)
if not os.path.exists(intervals_dir): os.mkdir(intervals_dir)
print "made this folder:", intervals_dir, os.path.exists(intervals_dir)
current_interval_file = open(current_filename, 'w')
sorted_intervals = sorted(
list(interval_list[pair]),
key=lambda x: int(x.split(':')[1].split('-')[0]))
sorted_intervals = sorted(sorted_intervals, key=lambda x: x.split(':'))
for interval in sorted_intervals:
current_interval_file.write(interval + "\n")
current_interval_file.close()
interval_file.write(current_filename + '\n')
for thing in os.listdir(intervals_dir):
print "file in dir:", thing
tumor_bam_file.close()
normal_bam_file.close()
interval_file.close()
def VariantUploader(tsv, submit_to_filesystem=False):
gather = DataGatherer(tsv)
variants = connect_to_mongo()
if submit_to_filesystem:
filesystem = SomaticFileSystem("/dsde/working/somaticDB/master/data")
S = SubmissionFile(tsv)
S.change_file_dir()
S.to_csv(os.path.join("/dsde/working/somaticDB/master/records", os.path.basename(tsv)))
else:
filesystem = None
bulk_count = 0
bulk = variants.initialize_unordered_bulk_op()
start_time = time.time()
n = 0
for variant_dict in gather.data_iterator():
n += 1
bulk_count += 1
additional_data_dict = {}
mongo_submission = merge_dicts(variant_dict, additional_data_dict)
# if the user is uploading a mutect1 maf ... rename fields
if mongo_submission.has_key("contig"):
mongo_submission["chromosome"] = mongo_submission.pop("contig")
if mongo_submission.has_key("position"):
mongo_submission["start"] = mongo_submission.pop("position")
if mongo_submission.has_key("ref_allele"):
mongo_submission["ref"] = mongo_submission.pop("ref_allele")
if mongo_submission.has_key("alt_allele"):
mongo_submission["alt"] = mongo_submission.pop("alt_allele")
unique_data = get_entries_from_dict(
mongo_submission,
keys=["chromosome", "start", "ref", "alt", "project", "dataset", "evidence_type"],
return_type=dict,
)
if filesystem:
project = mongo_submission["project"]
dataset = mongo_submission["dataset"]
filesystem.add_project(project)
filesystem[project].add_dataset(dataset)
filesystem[project][dataset].add_file(mongo_submission["data_filename"])
mongo_submission["data_filename"] = change_data_filename(
"/dsde/working/somaticDB/master/data/%s/%s/" % (project, dataset), mongo_submission["data_filename"]
)
bulk.insert(mongo_submission)
if bulk_count == 10000:
print "variants uploaded: %d (%.2f seconds since start of upload)." % (n, time.time() - start_time)
bulk_count = 0
bulk.execute()
bulk = variants.initialize_unordered_bulk_op()
if bulk_count > 0:
print "variants uploaded: %d (%.2f seconds since start of upload)." % (n, time.time() - start_time)
bulk.execute()
def VariantAssessor(query, tsv, output_file, outdir=""):
collection = connect_to_mongo()
caller_output = pd.read_csv(tsv, sep='\t')
known_true = {'snp': defaultdict(set), 'indel': defaultdict(set)}
known_false = {'snp': defaultdict(set), 'indel': defaultdict(set)}
found_variants = {'snp': defaultdict(set), 'indel': defaultdict(set)}
false_positive = {'snp': defaultdict(set), 'indel': defaultdict(set)}
query = query_processor(query)
logging.getLogger(__name__).info("Querying database for variants.")
# collect query information
for record in collection.find(ast.literal_eval(query)):
sample_information = get_entries_from_dict(
record, keys=['project', 'dataset', 'sample'], return_type=tuple)
variant = get_entries_from_dict(
record,
keys=['chromosome', 'start', 'ref', 'alt'],
return_type=tuple)
sample_information = tuple(map(str, sample_information))
variant = tuple(map(str, variant))
evidence_type = record['evidence_type']
if is_snp(record):
if 'TP' in evidence_type:
known_true['snp'][sample_information].add(variant)
if 'FP' in evidence_type:
known_false['snp'][sample_information].add(variant)
elif is_indel(record):
if 'TP' in evidence_type:
known_true['indel'][sample_information].add(variant)
if 'FP' in evidence_type:
known_false['indel'][sample_information].add(variant)
normal_normal = set([])
cm = set([])
#index the type of assessment to be done for each datatype.
for k, row in caller_output.iterrows():
sample_information = (row['project'], row['dataset'], row['sample'])
if row['evidence_type'] == 'NN':
normal_normal.add(sample_information)
elif row['evidence_type'] == 'CM':
cm.add(sample_information)
else:
cm.add(sample_information) #by default, ROC-like curves are used.
gather = DataGatherer(tsv)
logging.getLogger(__name__).info(
"Collection of variants from user submitted files.")
found_feature_data = defaultdict(dict)
#data from file (algorithm being tested)
for variant_dict in gather.data_iterator():
sample_information = get_entries_from_dict(
variant_dict,
keys=['project', 'dataset', 'sample'],
return_type=tuple)
variant = get_entries_from_dict(
variant_dict,
keys=['chromosome', 'start', 'ref', 'alt'],
return_type=tuple)
print sample_information, variant
#found_feature_data[sample_information][variant] = get_entries_from_dict(variant_dict, keys=['ECNT','HCNT','NLOD','TLOD'],return_type=dict)
if is_snp(variant_dict):
found_variants['snp'][sample_information].add(variant)
elif is_indel(variant_dict):
found_variants['indel'][sample_information].add(variant)
#print found_feature_data.keys()
caller_samples = caller_output[['project', 'dataset',
'sample']].values.tolist()
data = []
for feature in ['snp', 'indel']:
filename = {}
fp_fn = {}
fp_fp = {}
all_dict = {}
fp_tp = {}
filename[feature] = feature + ".false_negatives.tsv"
fp_fn[feature] = csv.DictWriter(
open(os.path.join(outdir, filename[feature]), 'w'),
delimiter='\t',
fieldnames=[
'project', 'dataset', 'sample', 'chromosome', 'start', 'ref',
'alt', 'variant_type'
])
#fieldnames=['project','dataset','sample','chromosome','start','ref','alt','ECNT','HCNT','NLOD','TLOD','variant_type']
fieldnames = [
'project', 'dataset', 'sample', 'chromosome', 'start', 'ref',
'alt', 'variant_type'
]
filename[feature] = feature + ".false_positives.tsv"
fp_fp[feature] = csv.DictWriter(open(
os.path.join(outdir, filename[feature]), 'w'),
delimiter='\t',
fieldnames=fieldnames)
#fieldnames=['project','dataset','sample','chromosome','start','ref','alt','ECNT','HCNT','NLOD','TLOD','variant_type']
fieldnames = [
'project', 'dataset', 'sample', 'chromosome', 'start', 'ref',
'alt', 'variant_type'
]
filename[feature] = feature + ".true_positives.tsv"
fp_tp[feature] = csv.DictWriter(open(
os.path.join(outdir, filename[feature]), 'w'),
delimiter='\t',
fieldnames=fieldnames)
fp_fn[feature].writeheader()
fp_fp[feature].writeheader()
fp_tp[feature].writeheader()
for eval_type in ['CM', 'NN']:
all_dict[eval_type] = {
'project': 'all',
'dataset': 'all',
'sample': 'all',
'false_positives': 0,
'true_positives': 0,
'false_negatives': 0,
'tpr': np.nan,
'fpr': np.nan,
'precision': np.nan,
'evidence_type': eval_type,
'variant_type': feature
}
for sample_information in map(tuple, caller_samples):
if sample_information in normal_normal:
assessment_type = 'NN'
elif sample_information in cm:
assessment_type = 'CM'
else:
assessment_type = 'CM'
row_dict = {
'project': sample_information[0],
'dataset': sample_information[1],
'sample': sample_information[2],
'false_positives': 0,
'true_positives': 0,
'false_negatives': 0,
'tpr': np.nan,
'fpr': np.nan,
'precision': np.nan,
'evidence_type': assessment_type,
'variant_type': feature
}
if assessment_type == 'NN':
FN = len(found_variants[feature][sample_information])
row_dict['false_positives'] = FN
row_dict['precision'] = 0
if assessment_type == 'CM':
TP = np.float(
len(found_variants[feature]
[sample_information].intersection(
known_true[feature][sample_information])))
FN = np.float(
len(known_true[feature][sample_information].difference(
found_variants[feature][sample_information])))
FP = np.float(
len(found_variants[feature][sample_information].difference(
known_true[feature][sample_information])))
print TP, FN, FP
try:
row_dict['tpr'] = TP / (TP + FN)
except:
row_dict['tpr'] = np.nan
row_dict['true_positives'] = TP
row_dict['false_negatives'] = FN
row_dict['false_positives'] = FP
all_dict['CM']['true_positives'] += TP
all_dict['CM']['false_negatives'] += FN
all_dict['CM']['false_positives'] += FP
try:
row_dict['precision'] = TP / (TP + FP)
except:
row_dict['precision'] = np.nan
row_dict['dream_accuracy'] = (row_dict['tpr'] +
row_dict['precision']) / 2.0
print row_dict['tpr'], row_dict['precision'], row_dict[
'dream_accuracy']
row_dict['variant_type'] = feature
data.append(row_dict)
true_positives = list(
found_variants[feature][sample_information].intersection(
known_true[feature][sample_information]))
false_positives = list(
found_variants[feature][sample_information].difference(
known_true[feature][sample_information]))
false_negatives = list(
known_true[feature][sample_information].difference(
found_variants[feature][sample_information]))
for variant in true_positives:
fp_tp[feature].writerow({
'project': sample_information[0],
'dataset': sample_information[1],
'sample': sample_information[2],
'chromosome': variant[0],
'start': variant[1],
'ref': variant[2],
'alt': variant[3],
#'ECNT':found_feature_data[sample_information][variant]['ECNT'],
#'HCNT':found_feature_data[sample_information][variant]['HCNT'],
#'NLOD':found_feature_data[sample_information][variant]['NLOD'],
#'TLOD':found_feature_data[sample_information][variant]['TLOD'],
'variant_type': feature
})
for variant in false_positives:
fp_fp[feature].writerow({
'project': sample_information[0],
'dataset': sample_information[1],
'sample': sample_information[2],
'chromosome': variant[0],
'start': variant[1],
'ref': variant[2],
'alt': variant[3],
#'ECNT':found_feature_data[sample_information][variant]['ECNT'],
#'HCNT':found_feature_data[sample_information][variant]['HCNT'],
#'NLOD':found_feature_data[sample_information][variant]['NLOD'],
#'TLOD':found_feature_data[sample_information][variant]['TLOD'],
'variant_type': feature
})
for variant in false_negatives:
fp_fn[feature].writerow({
'project': sample_information[0],
'dataset': sample_information[1],
'sample': sample_information[2],
'chromosome': variant[0],
'start': variant[1],
'ref': variant[2],
'alt': variant[3],
'variant_type': feature
})
try:
all_dict['CM']['tpr'] = all_dict['CM']['true_positives'] / (
all_dict['CM']['true_positives'] +
all_dict['CM']['false_negatives'])
except:
all_dict['CM']['tpr'] = np.nan
all_dict['CM']['dream_accuracy'] = (all_dict['CM']['tpr'] + 1 -
all_dict['CM']['precision']) / 2.0
try:
all_dict['CM']['precision'] = all_dict['CM']['true_positives'] / (
all_dict['CM']['true_positives'] +
all_dict['CM']['false_positives'])
except:
all_dict['CM']['precision'] = np.nan
all_dict['CM']['dream_accuracy'] = (all_dict['CM']['tpr'] +
all_dict['CM']['precision']) / 2.0
all_dict['CM']['variant_type'] = feature
#data.append(all_dict['CM'])
#data.append(all_dict['NN'])
fieldnames = [
'project', 'dataset', 'sample', 'false_positives', 'true_positives',
'false_negatives', 'tpr', 'precision', 'evidence_type',
'dream_accuracy', 'variant_type'
]
pd.DataFrame(data).to_csv(output_file,
sep='\t',
index=False,
columns=fieldnames,
na_rep='nan')
def BamAggregator(query, normal_bam_list_name, tumor_bam_list_name, interval_list_name, metadata_list_name, folder):
collection = connect_to_mongo()
query = query_processor(query)
interval_list = defaultdict(set)
metadata_list = {}
query = query.strip('"')
query = ast.literal_eval(query)
print query
print type(query)
print "query dictionary:", query.items()
print "directory:" + os.getcwd()
doesrecordloop = False
for record in collection.find(query):
if doesrecordloop == False:
print "Contains at least one record."
doesrecordloop = True
if not record.has_key("tumor_bam"):
print record
continue
# print record['tumor_bam']
record["tumor_bam"] = picard_version_to_current(record["tumor_bam"])
record["normal_bam"] = picard_version_to_current(record["normal_bam"])
# print record['tumor_bam']
# print
tumor_bam = record["tumor_bam"]
normal_bam = record["normal_bam"]
interval = "%s:%s-%s" % (record["chromosome"], record["start"], record["end"])
interval_list[(tumor_bam, normal_bam)].add(interval)
field_names = ["tumor_bam", "normal_bam", "data_filename", "project", "dataset", "sample"]
metadata_list[(tumor_bam, normal_bam)] = get_entries_from_dict(record, keys=field_names, return_type=dict)
metadata_list[(tumor_bam, normal_bam)]["evidence_type"] = "."
metadata_list[(tumor_bam, normal_bam)]["author"] = "."
print "OPENNING FILES HERE."
print "tumor_bam_file: " + tumor_bam_list_name
print "normal_bam_file: " + normal_bam_list_name
print "interval file:" + interval_list_name
tumor_bam_file = open(tumor_bam_list_name, "w")
normal_bam_file = open(normal_bam_list_name, "w")
interval_file = open(interval_list_name, "w")
location = os.path.dirname(tumor_bam_list_name)
fname = os.path.join(location, "test.txt")
print "test:" + fname
f = open(fname, "w")
f.close()
for filename in os.listdir(location):
if filename.endswith("list"):
print filename
fieldnames = ["tumor_bam", "normal_bam", "data_filename", "project", "dataset", "sample", "evidence_type", "author"]
metadata_file = csv.DictWriter(open(metadata_list_name, "w"), fieldnames=fieldnames, delimiter="\t")
metadata_file.writeheader()
current_dir = os.getcwd()
for pair in interval_list:
tumor_bam, normal_bam = pair
tumor_bam_file.write(tumor_bam + "\n")
normal_bam_file.write(normal_bam + "\n")
metadata_file.writerow(metadata_list[(tumor_bam, normal_bam)])
sample = "".join([random.choice("abcdef0123456789") for k in range(40)])
intervals_dir = folder
current_filename = ".".join(
[
"intervals",
os.path.splitext(os.path.basename(tumor_bam))[0],
os.path.splitext(os.path.basename(normal_bam))[0],
"list",
]
)
current_filename = os.path.join(intervals_dir, current_filename)
if not os.path.exists(intervals_dir):
os.mkdir(intervals_dir)
print "made this folder:", intervals_dir, os.path.exists(intervals_dir)
current_interval_file = open(current_filename, "w")
sorted_intervals = sorted(list(interval_list[pair]), key=lambda x: int(x.split(":")[1].split("-")[0]))
sorted_intervals = sorted(sorted_intervals, key=lambda x: x.split(":"))
for interval in sorted_intervals:
current_interval_file.write(interval + "\n")
current_interval_file.close()
interval_file.write(current_filename + "\n")
for thing in os.listdir(intervals_dir):
print "file in dir:", thing
tumor_bam_file.close()
normal_bam_file.close()
interval_file.close()
