def atacseq_summary(config, input, output, Cutadapt, Qualimap,
MarkDuplicates, InsertMetrics, AlignmentMetrics):
"""Make atacseq summary"""
# Dictionary of figures
d = {}
Cutadapt.read_aggregate_data()
d.update({'cutadapt': {'fig': Cutadapt.plot('cutadapt')[0]}})
Qualimap.read_aggregate_data()
d.update({'qualimap': {'fig': {'globals': Qualimap.plot("Globals")[0],
'coverage_per_contig': Qualimap.plot("Coverage_per_contig")[0]}}})
InsertMetrics.read_aggregate_data()
plist = [InsertMetrics.plot('metrics')[0]] + [x for sublist in InsertMetrics.plot("hist")[0].children for x in sublist]
gp = gridplot([plist[i:i+3] for i in range(0, len(plist), 3)])
d.update({'picard': {'InsertMetrics': {'atacseq' : {'fig': gp}}}})
MarkDuplicates.read_aggregate_data()
d['picard'].update({'DuplicationMetrics': {'atacseq':
{'fig':
gridplot([[MarkDuplicates.plot('metrics')[0],
MarkDuplicates.plot('hist')[0]]])}}})
d.update({'rulegraph' : {'fig' : input.rulegraph, 'uri': data_uri(input.rulegraph),
'target' : 'atacseq_all'}})
# Write the resulting html
tp = Env.get_template('workflow_atacseq_qc.html')
with open(output.html, "w") as fh:
fh.write(static_html(tp, template_variables=d, css_raw=css_files))
def scrnaseq_qc(config, input, output, results=None, rsem=None, rpkmforgenes=None, **kwargs):
"""Do QC of scrnaseq"""
# Collect results - subset by samples if applicable
results.read_aggregate_data()
results.filter_aggregate_data('alignrseqc', 'SM', config["samples"])
taptool_url = None
if not config['scrnaseq.workflow']['report']['annotation_url'] is None:
taptool_url = config['scrnaseq.workflow']['report']['annotation_url'] + "@gene_id"
# Brennecke args
# brennecke_args = {'plot_height':600, 'plot_width': 800, 'alpha':
# 0.3, 'taptool_url': config['scrnaseq.workflow']['report']['annotation_url'] + "@gene_id"}
# Alignment stats
d = {'align': {'fig': results.plot('alignrseqc')[0]['fig'], 'table': results.plot('alignrseqc')[0]['table']}}
# rsem plots
if rsem.run:
d.update({'rsem': plot_pca(rsem.targets['pca'][0],
config['scrnaseq.workflow']['metadata'],
rsem.targets['pca'][0].replace(".pca.csv", ".pcaobj.pickle"),
taptool_url= taptool_url)})
# # FIXME: Instead of re use list
# # d['rsem'].update({'brennecke': scrnaseq_brennecke_plot(infile=input.rsemgenes, spikein_re=re.compile("^ERCC"),
# # index=["SM", "gene_id", "transcript_id(s)", "gene_name"],
# # **brennecke_args)})
# rpkmforgenes plots
if rpkmforgenes.run:
d.update({'rpkmforgenes': plot_pca(rpkmforgenes.targets['pca'][0],
config['scrnaseq.workflow']['metadata'],
rpkmforgenes.targets['pca'][0].replace(".pca.csv", ".pcaobj.pickle"),
taptool_url= taptool_url)})
d.update({'version' : all_versions(), 'config' : {'uri' : data_uri(input.globalconf), 'file' : input.globalconf}})
d.update({'rulegraph': {'fig': input.rulegraph, 'uri': data_uri(input.rulegraph),
'target': 'scrnaseq_all'}})
tp = Env.get_template('workflow_scrnaseq_qc.html')
with open(output.html, "w") as fh:
fh.write(static_html(tp, template_variables=d, css_raw=bootstrap_css_files, js_raw=bootstrap_js_files))
