def parse_metadata(self, data_dir):
samples_dict = defaultdict(list)
wf_conf_dict = {}
for r_ix, r in self.records.iterrows():
read_type = r['paired-end or single-end'].lower()
sample_info = {'treatment': r['name']}
wf_key = '-'.join([read_type])
if 'control' in r.keys() and r['control'] and type(r['control']) != float: # After reading this metadata info, this will contain a nan (float) if undetermined
sample_info['control'] = r['control']
wf_key += '-with-control'
wf_conf_dict[wf_key] = {'rt': read_type,
'st': sample_info.keys()}
genome = consts.GENOME # Default genome
if 'genome' in r.keys():
genome = r['genome']
samples_dict[wf_key].append([sample_info, genome])
for wf_key, samples_genomes in samples_dict.iteritems():
if self.obj.separate_jsons:
for si, s in enumerate(sorted(samples_genomes)):
sample, genome = s[0], s[1]
ref_dataset = consts.ReferenceDataset(genome)
self.update_paths(ref_dataset)
yield self.render_json(wf_conf_dict[wf_key], [sample], data_dir, self.experiment_type), wf_key, si
else:
samples_list, genomes_list = zip(*samples_genomes)
if len(set(genomes_list)) > 1:
raise Exception('More than one genome specified (%s). Please create a different metadata file'
' per genome or provide a sjdb and specify the --separate-jsons argument' %
', '.join(set(genomes_list)))
ref_dataset = consts.ReferenceDataset(genomes_list[0])
self.update_paths(ref_dataset)
yield self.render_json(wf_conf_dict[wf_key], sorted(samples_list), data_dir, self.experiment_type), wf_key, None
def parse_metadata(self, data_dir):
samples_dict = defaultdict(list)
wf_conf_dict = {}
for r in self.records:
read_type = r['Paired-end or single-end'].lower()
sample_name = r['Name']
strand_specific = r['Strand specificity']
genome = consts.GENOME # Default genome
if 'Genome' in r.keys():
genome = r['Genome']
kws = [read_type, strand_specific]
if self.skip_star_2pass:
kws.append('with-sjdb')
wf_key = '-'.join(kws)
wf_conf_dict[wf_key] = {'rt': read_type, 'sn': sample_name}
samples_dict[wf_key].append([sample_name, genome])
for wf_key, samples_gemomes in samples_dict.iteritems():
if self.obj.separate_jsons:
for si, s in enumerate(sorted(samples_gemomes)):
sample, genome = s[0], s[1]
ref_dataset = consts.ReferenceDataset(genome, read_length=self.read_length)
self.update_paths(ref_dataset)
yield self.render_json(wf_conf_dict[wf_key], [sample], data_dir), wf_key, si
else:
samples_list = [s[0] for s in samples_genomes]
genomes_list = [g[1] for g in samples_genomes]
if len(set(genomes_list)) > 1:
raise Exception(
'More than one genome specified (%s). Please create a different metadata file'
' per genome or provide a sjdb and specify the --separate-jsons argument' %
', '.join(set(genomes_list)))
ref_dataset = consts.ReferenceDataset(genomes_list[0], read_length=self.read_length)
self.update_paths(ref_dataset)
yield self.render_json(wf_conf_dict[wf_key], sorted(samples_list), data_dir), wf_key, None
def parse_metadata(self, data_dir):
samples_dict = defaultdict(list)
wf_conf_dict = {}
for rix, r in self.records.iterrows():
read_type = r['paired-end or single-end'].lower()
sample_name = r['name']
strand_specific = r['strand specificity']
genome = consts.GENOME # Default genome
if 'genome' in r.keys():
genome = r['genome']
ercc_spikein = False
if 'with ercc spike-in' in r.keys():
ercc_spikein = r['with ercc spike-in']
kws = [read_type, strand_specific]
if self.skip_star_2pass:
kws.append('with-sjdb')
wf_key = '-'.join(kws)
wf_conf_dict[wf_key] = {'rt': read_type, 'sn': sample_name}
read_length = self.read_length
if 'read length' in r.keys():
read_length = int(r['read length'])
samples_dict[wf_key].append([sample_name, genome, ercc_spikein, read_length])
for wf_key, samples_genomes in samples_dict.iteritems():
if self.obj.separate_jsons:
for si, s in enumerate(sorted(samples_genomes)):
sample, genome, ercc_spikein, read_length = s
ref_dataset = consts.ReferenceDataset(genome,
read_length=read_length,
with_ercc=ercc_spikein)
self.update_paths(ref_dataset)
yield self.render_json(wf_conf_dict[wf_key], [sample], data_dir), wf_key, si
else:
samples_list = [s[0] for s in samples_genomes]
genomes_list = [g[1] for g in samples_genomes]
ercc_list = [e[2] for e in samples_genomes]
read_length_list = [l[3] for l in samples_genomes]
if len(set(genomes_list)) > 1:
raise Exception(
'More than one genome specified (%s). Please create a different metadata file'
' per genome or provide a sjdb and specify the --separate-jsons argument' %
', '.join(set(genomes_list)))
if len(set(ercc_list)) > 1:
raise Exception(
'With and without ERCC spike-in specified. Please create a different metadata file'
' per ERCC choice or provide a sjdb and specify the --separate-jsons argument')
if len(set(read_length_list)) > 1:
raise Exception(
'More than one read length specified. Please create a different metadata file'
' per read length choice or provide a sjdb and specify the --separate-jsons argument')
ref_dataset = consts.ReferenceDataset(genomes_list[0],
read_length=read_length_list[0],
with_ercc=ercc_list[0])
self.update_paths(ref_dataset)
yield self.render_json(wf_conf_dict[wf_key], sorted(samples_list), data_dir), wf_key, None
def parse_metadata(self, data_dir):
samples_dict = defaultdict(list)
wf_conf_dict = {}
for rix, r in self.records.iterrows():
read_type = r['paired-end or single-end'].lower()
sample_name = r['name']
genome = consts.GENOME # Default genome
if 'genome' in r.keys():
genome = r['genome']
kws = [read_type]
wf_key = '-'.join(kws)
with_umis = 'umis' in r.keys() and not is_false(r['umis'])
if with_umis:
wf_key += '-umis'
wf_conf_dict[wf_key] = {
'rt': read_type,
'sn': sample_name,
'umis': with_umis
}
samples_dict[wf_key].append([sample_name, genome])
for wf_key, samples_genomes in samples_dict.iteritems():
if self.obj.separate_jsons:
for si, s in enumerate(sorted(samples_genomes)):
sample, genome = s[0], s[1]
ref_dataset = consts.ReferenceDataset(
genome,
read_length=self.read_length,
umis='umis' in wf_key)
self.update_paths(ref_dataset)
yield self.render_json(wf_conf_dict[wf_key], [sample],
data_dir), wf_key, si
else:
samples_list = [s[0] for s in samples_genomes]
genomes_list = [g[1] for g in samples_genomes]
if len(set(genomes_list)) > 1:
raise Exception(
'More than one genome specified (%s). Please create a different metadata file'
' per genome or provide a sjdb and specify the --separate-jsons argument'
% ', '.join(set(genomes_list)))
ref_dataset = consts.ReferenceDataset(
genomes_list[0],
read_length=self.read_length,
umis='umis' in wf_key)
self.update_paths(ref_dataset)
yield self.render_json(wf_conf_dict[wf_key],
sorted(samples_list),
data_dir), wf_key, None
def parse_metadata(self, data_dir):
samples_dict = defaultdict(list)
wf_conf_dict = {}
for r in self.records:
read_type = r['Paired-end or single-end'].lower()
peak_type = r['Peak type'].lower()
sample_info = {'treatment': r['Name'], 'iter': r['Iter num']}
wf_key = '-'.join([read_type, peak_type])
if 'Control' in r.keys(
) and r['Control'] and r['Control'].upper() != 'NA':
sample_info['control'] = r['Control']
wf_key += '-with-control'
wf_conf_dict[wf_key] = {
'rt': read_type,
'pt': peak_type,
'st': sample_info.keys()
}
genome = 'hg38' # Default genome
if 'Genome' in r.keys():
genome = r['Genome']
samples_dict[wf_key].append([sample_info, genome])
for wf_key, samples_genomes in samples_dict.iteritems():
if self.obj.separate_jsons:
for si, s in enumerate(sorted(samples_genomes)):
sample, genome = s[0], s[1]
ref_dataset = consts.ReferenceDataset(genome)
self.update_paths(ref_dataset)
yield self.render_json(wf_conf_dict[wf_key], [sample],
data_dir,
self.experiment_type), wf_key, si
else:
samples_list, genomes_list = zip(*samples_genomes)
if len(set(genomes_list)) > 1:
raise Exception(
'More than one genome specified (%s). Please create a different metadata file'
' per genome or provide a sjdb and specify the --separate-jsons argument'
% ', '.join(set(genomes_list)))
ref_dataset = consts.ReferenceDataset(genomes_list[0])
self.update_paths(ref_dataset)
yield self.render_json(wf_conf_dict[wf_key],
sorted(samples_list), data_dir,
self.experiment_type), wf_key, None
def parse_metadata(self, data_dir):
samples_dict = defaultdict(list)
wf_conf_dict = {}
for r in self.records:
read_type = r['Paired-end or single-end'].lower()
sample_info = {'treatment': r['Name'], 'iter': r['Iter num']}
wf_key = '-'.join([read_type])
genome = 'hg38' # Default genome
if 'Genome' in r.keys():
genome = r['Genome']
if not ('Blacklist removal' in r.keys()
and is_false(r['Blacklist removal'])):
wf_key += '-blacklist-removal'
wf_conf_dict[wf_key] = {'rt': read_type}
samples_dict[wf_key].append([sample_info, genome])
for wf_key, samples_genomes in samples_dict.iteritems():
if self.obj.separate_jsons:
for si, s in enumerate(sorted(samples_genomes)):
sample, genome = s[0], s[1]
ref_dataset = consts.ReferenceDataset(genome)
if 'blacklist-removal' not in wf_key:
ref_dataset.encode_blacklist_bedfile = None
self.update_paths(ref_dataset)
yield self.render_json(wf_conf_dict[wf_key], [sample],
data_dir,
self.experiment_type), wf_key, si
else:
samples_list = [s[0] for s in samples_genomes]
genomes_list = [g[1] for g in samples_genomes]
if len(set(genomes_list)) > 1:
raise Exception(
'More than one genome specified (%s). Please create a different metadata file'
' per genome or provide a sjdb and specify the --separate-jsons argument'
% ', '.join(set(genomes_list)))
ref_dataset = consts.ReferenceDataset(genomes_list[0])
if 'blacklist-removal' not in wf_key:
ref_dataset.encode_blacklist_bedfile = None
self.update_paths(ref_dataset)
yield self.render_json(wf_conf_dict[wf_key],
sorted(samples_list), data_dir,
self.experiment_type), wf_key, None
