def main():
cmnd = get_args()
## resolve projects
project = dxencode.resolve_project(PROJECT_NAME)
print 'Project: ' + project.describe()['name']
pid = project.get_id()
applet = dxencode.find_applet_by_name('fastqc-exp', pid )
(AUTHID, AUTHPW, SERVER) = dxencode.processkey('www')
query = '/search/?type=experiment&assay_term_id=%s&award.rfa=ENCODE3&limit=all&frame=embedded&replicates.library.biosample.donor.organism.name=mouse&files.file_format=fastq' % ASSAY_TERM_ID
res = dxencode.encoded_get(SERVER+query, AUTHID=AUTHID, AUTHPW=AUTHPW)
exps = res.json()['@graph']
n = 0
for exp in exps:
acc = exp['accession']
if len(exp['replicates']) > 0:
if exp['replicates'][0]['library'].get('size_range', "") != '>200':
print "Skipping %s with wrong library size (%s)" % (acc, exp['replicates'][0]['library'].get('size_range', ""))
#print json.dumps(exp['replicates'][0]['library'], sort_keys=True, indent=4, separators=(',',': '))
continue
if exp['replicates'][0]['library'].get('nucleic_acid_starting_quantity_units', "") == "cells":
ncells = float(exp['replicates'][0]['library'].get('nucleic_acid_starting_quantity', 0.0))
if ncells < 20:
print "Skipping %s as single-cell (%s %s)" % (acc, exp['replicates'][0]['library'].get('nucleic_acid_starting_quantity_units', ""), ncells)
#print json.dumps(exp['replicates'][0]['library'], sort_keys=True, indent=4, separators=(',',': '))
continue
run = applet.run({ "accession": acc}, project=pid)
print "Running: %s for %s" % (run, acc)
n = n + 1
if n > cmnd.number:
break
else:
print "Skipping %s (0 replicates)" % acc
def main():
cmnd = get_args()
## resolve projects
project = dxencode.resolve_project(PROJECT_NAME)
print 'Project: ' + project.describe()['name']
pid = project.get_id()
counts = {}
n = 0
summaries = dxpy.find_data_objects(classname='file',
folder='/runs',
name='*_summary.txt',
recurse=True,
name_mode='glob',
project=pid,
return_handler=False)
while summaries:
try:
flink = dxpy.dxlink(summaries.next())
n = n + 1
except StopIteration:
break
fd = dxpy.describe(flink)
fn = "fastqc/%s" % fd['name']
if not os.path.isfile(fn):
print 'Downloading: %s from %s' % (fn, fd['folder'])
try:
dxpy.download_dxfile(flink, fn)
except Exception, e:
print "Error %s" % e
parse_summary(fn, counts)
def main():
cmnd = get_args()
## resolve projects
project = dxencode.resolve_project(PROJECT_NAME)
print 'Project: ' + project.describe()['name']
pid = project.get_id()
counts = {}
n = 0
summaries = dxpy.find_data_objects(classname='file', folder='/runs', name='*_summary.txt', recurse=True, name_mode='glob', project=pid, return_handler=False)
while summaries:
try:
flink = dxpy.dxlink(summaries.next())
n = n+1
except StopIteration:
break
fd = dxpy.describe(flink)
fn = "fastqc/%s" % fd['name']
if not os.path.isfile(fn):
print 'Downloading: %s from %s' % (fn, fd['folder'])
try:
dxpy.download_dxfile(flink, fn)
except Exception, e:
print "Error %s" % e
parse_summary(fn, counts)
def main():
cmnd = get_args()
## resolve projects
project = dxencode.resolve_project(PROJECT_NAME)
print 'Project: ' + project.describe()['name']
pid = project.get_id()
applet = dxencode.find_applet_by_name('fastqc-exp', pid)
(AUTHID, AUTHPW, SERVER) = dxencode.processkey('www')
query = '/search/?type=experiment&assay_term_id=%s&award.rfa=ENCODE3&limit=all&frame=embedded&replicates.library.biosample.donor.organism.name=mouse&files.file_format=fastq' % ASSAY_TERM_ID
res = dxencode.encoded_get(SERVER + query, AUTHID=AUTHID, AUTHPW=AUTHPW)
exps = res.json()['@graph']
n = 0
for exp in exps:
acc = exp['accession']
if len(exp['replicates']) > 0:
if exp['replicates'][0]['library'].get('size_range', "") != '>200':
print "Skipping %s with wrong library size (%s)" % (
acc, exp['replicates'][0]['library'].get('size_range', ""))
#print json.dumps(exp['replicates'][0]['library'], sort_keys=True, indent=4, separators=(',',': '))
continue
if exp['replicates'][0]['library'].get(
'nucleic_acid_starting_quantity_units', "") == "cells":
ncells = float(exp['replicates'][0]['library'].get(
'nucleic_acid_starting_quantity', 0.0))
if ncells < 20:
print "Skipping %s as single-cell (%s %s)" % (
acc, exp['replicates'][0]['library'].get(
'nucleic_acid_starting_quantity_units',
""), ncells)
#print json.dumps(exp['replicates'][0]['library'], sort_keys=True, indent=4, separators=(',',': '))
continue
run = applet.run({"accession": acc}, project=pid)
print "Running: %s for %s" % (run, acc)
n = n + 1
if n > cmnd.number:
break
else:
print "Skipping %s (0 replicates)" % acc