def rna_seq_wrapper(assembly, taxon_id):
url = 'https://www.encodeproject.org/search/?type=experiment&assay_term_name=RNA-seq'
# Used to set is_main
track_hierarchy = {
'signal_forward': [
'plus strand signal of unique reads',
'plus strand signal of all reads', 'plus strand signal',
'raw plus strand signal'
],
'signal_reverse': [
'minus strand signal of unique reads',
'minus strand signal of all reads', 'minus strand signal',
'raw minus strand signal'
],
'signal': [
'signal of unique reads', 'signal of all reads', 'signal',
'raw signal', 'splice junctions'
],
'contigs': ['contigs']
}
size_range_to_experiment_type = {'>200': 'mRNA-seq', '<200': 'smRNA-seq'}
def dataset_additions_f(experiment, json_object):
#Set experiment_type
size_range = None
if 'size_range' in experiment['replicates'][0]['library']:
size_range = experiment['replicates'][0]['library']['size_range']
if size_range is None:
print 'Could not find size_range ' + experiment['accession']
json_object['experiment_attributes']['experiment_type'] = 'RNA-seq'
json_object['experiment_attributes']['assay_type'] = 'RNA-seq'
elif size_range not in size_range_to_experiment_type:
print 'Size range not found: ' + experiment['replicates'][0][
'library']['size_range']
json_object['experiment_attributes']['experiment_type'] = 'RNA-seq'
json_object['experiment_attributes']['assay_type'] = 'RNA-seq'
else:
json_object['experiment_attributes'][
'experiment_type'] = size_range_to_experiment_type[size_range]
json_object['experiment_attributes'][
'assay_type'] = size_range_to_experiment_type[size_range]
return json_object
return convert_to_IHEC_format(url, assembly, taxon_id, track_hierarchy,
dataset_additions_f)
def bisulfite_wrapper(assembly, taxon_id):
url = 'https://www.encodeproject.org/search/?type=experiment&assay_term_name=whole-genome%20shotgun%20bisulfite%20sequencing'
# Used to set is_main
track_hierarchy = {'methylation_profile': ['methylation state at CpG', 'methylation state at CHH']}
def dataset_additions_f(experiment, json_object):
#Set experiment_type
json_object['experiment_attributes']['experiment_type'] = 'DNA Methylation'
json_object['experiment_attributes']['assay_type'] = 'WGB-Seq'
return json_object
return convert_to_IHEC_format(url, assembly, taxon_id, track_hierarchy, dataset_additions_f)
def chip_seq_wrapper(assembly, taxon_id, target):
url = 'https://www.encodeproject.org/search/?type=experiment&assay_term_name=ChIP-seq&target.name=%s-human' % target
# Used to set is_main
track_hierarchy = {'peak_calls': ['optimal idr thresholded peaks', 'conservative idr thresholded peaks',
'replicated peaks', 'peaks', 'hotspots'],
'signal': ['signal p-value', 'fold change over control', 'signal', 'raw signal']}
def dataset_additions_f(experiment, json_object):
#Set experiment_type
json_object['experiment_attributes']['experiment_type'] = experiment['target']['label']
return json_object
return convert_to_IHEC_format(url, assembly, taxon_id, track_hierarchy, dataset_additions_f)
def chip_seq_wrapper(target, version):
url = 'https://www.encodeproject.org/search/?type=experiment&assay_term_name=ChIP-seq&target.name=%s-human' % target
assembly = 'hg19'
taxon_id = 9606
# Used to set is_main
track_hierarchy = {'peak_calls': ['optimal idr thresholded peaks', 'conservative idr thresholded peaks',
'replicated peaks', 'peaks', 'hotspots'],
'signal': ['signal p-value', 'fold change over control', 'signal', 'raw signal']}
def dataset_additions_f(experiment, json_object):
#Set experiment_type
json_object['experiment_attributes']['experiment_type'] = experiment['target']['label']
return json_object
with open('../output/%s_v%s.json' % (target, version), 'w+') as outfile:
json.dump(convert_to_IHEC_format(url, assembly, taxon_id, track_hierarchy, dataset_additions_f), outfile, indent=4)
def bisulfite_wrapper(assembly, taxon_id):
url = 'https://www.encodeproject.org/search/?type=experiment&assay_term_name=whole-genome%20shotgun%20bisulfite%20sequencing'
# Used to set is_main
track_hierarchy = {
'methylation_profile':
['methylation state at CpG', 'methylation state at CHH']
}
def dataset_additions_f(experiment, json_object):
#Set experiment_type
json_object['experiment_attributes'][
'experiment_type'] = 'DNA Methylation'
json_object['experiment_attributes']['assay_type'] = 'WGB-Seq'
return json_object
return convert_to_IHEC_format(url, assembly, taxon_id, track_hierarchy,
dataset_additions_f)
def rna_seq_wrapper(version):
url = 'https://www.encodeproject.org/search/?type=experiment&assay_term_name=RNA-seq'
assembly = 'hg19'
taxon_id = 9606
# Used to set is_main
track_hierarchy = {'signal_forward': ['plus strand signal of unique reads', 'plus strand signal of all reads',
'plus strand signal', 'raw plus strand signal'],
'signal_reverse': ['minus strand signal of unique reads', 'minus strand signal of all reads',
'minus strand signal', 'raw minus strand signal'],
'signal': ['signal of unique reads', 'signal of all reads', 'signal', 'raw signal', 'splice junctions'],
'contigs': ['contigs']}
size_range_to_experiment_type = {
'>200': 'mRNA-seq',
'<200': 'smRNA-seq'
}
def dataset_additions_f(experiment, json_object):
#Set experiment_type
size_range = None
if 'size_range' in experiment['replicates'][0]['library']:
size_range = experiment['replicates'][0]['library']['size_range']
if size_range is None:
print 'Could not find size_range ' + experiment['accession']
json_object['experiment_attributes']['experiment_type'] = 'RNA-seq'
json_object['experiment_attributes']['assay_type'] = 'RNA-seq'
elif size_range not in size_range_to_experiment_type:
print 'Size range not found: ' + experiment['replicates'][0]['library']['size_range']
json_object['experiment_attributes']['experiment_type'] = 'RNA-seq'
json_object['experiment_attributes']['assay_type'] = 'RNA-seq'
else:
json_object['experiment_attributes']['experiment_type'] = size_range_to_experiment_type[size_range]
json_object['experiment_attributes']['assay_type'] = size_range_to_experiment_type[size_range]
return json_object
with open('../output/RNAseq_v%s.json' % version, 'w+') as outfile:
json.dump(convert_to_IHEC_format(url, assembly, taxon_id, track_hierarchy, dataset_additions_f), outfile, indent=4)
def chip_seq_wrapper(assembly, taxon_id, target):
url = 'https://www.encodeproject.org/search/?type=experiment&assay_term_name=ChIP-seq&target.name=%s-human' % target
# Used to set is_main
track_hierarchy = {
'peak_calls': [
'optimal idr thresholded peaks',
'conservative idr thresholded peaks', 'replicated peaks', 'peaks',
'hotspots'
],
'signal':
['signal p-value', 'fold change over control', 'signal', 'raw signal']
}
def dataset_additions_f(experiment, json_object):
#Set experiment_type
json_object['experiment_attributes']['experiment_type'] = experiment[
'target']['label']
return json_object
return convert_to_IHEC_format(url, assembly, taxon_id, track_hierarchy,
dataset_additions_f)
