def main():
import argparse
import sys
parser = argparse.ArgumentParser()
parser.add_argument(
'--dryrun',
action="store_true",
default=False,
help="Run without making changes [default: %(default)s]")
parser.add_argument('--storetable', action="store_true", default=False)
parser.add_argument('--projectId', type=str)
args = parser.parse_args()
syn = synapseclient.login(silent=True)
annots = PCBCAnnotations.PCBCAllAnnotations(syn)
a = PCBCAnnotations.PCBCAllAnnotationTableUpdate(syn, annots)
my_synapse_id = None
if not args.dryrun:
my_synapse_id = synapseHelpers.thisCodeInSynapse(parentId='syn2758110',
syn=syn)
a.update_annots_synapse(executed=my_synapse_id, dryrun=args.dryrun)
if args.storetable:
tbl = a.update_annots_table_synapse(projectId=args.projectId,
dryrun=args.dryrun)
def main():
import argparse
import sys
parser = argparse.ArgumentParser()
parser.add_argument('--dryrun', action="store_true",
default=False,
help="Run without making changes [default: %(default)s]")
parser.add_argument('--storetable', action="store_true", default=False)
parser.add_argument('--projectId', type=str)
args = parser.parse_args()
syn = synapseclient.login(silent=True)
annots = PCBCAnnotations.PCBCAnnotations(syn)
a = PCBCAnnotations.PCBCAnnotationTableUpdate(syn, annots)
my_synapse_id = None
if not args.dryrun:
my_synapse_id = synapseHelpers.thisCodeInSynapse(parentId='syn2758110', syn=syn)
a.update_annots_synapse(executed=my_synapse_id, dryrun=args.dryrun)
if args.storetable:
tbl = a.update_annots_table_synapse(projectId=args.projectId, dryrun=args.dryrun)
if isUptodate(name, files, args.parentId):
print " is up to date"
continue
if list(set(filteredMeta.fileType))[0] in ["seg", "bed"]:
dfs = mp.map(lambda f: pd.read_csv(f.path, sep="\t"), files)
df = pd.concat(dfs, axis=0)
df.to_csv(args.filepath + name, sep="\t", index=False)
nSamples = len(set(df.Sample))
nFeatures = 0
else: # All other fileTypes
dfs = mp.map(lambda f: pd.read_csv(f.path, sep="\t", index_col=0), files)
df = pd.concat(dfs, axis=1)
df.to_csv(args.filepath + name, sep="\t")
nFeatures, nSamples = df.shape
print "Created", name, df.shape
# Add file to Synapse
entity = synapseclient.File(args.filepath + name, parentId=args.parentId)
# Set annotations
entity.platform = platform
entity.dataSubType = dataSubType
entity.acronym = "PANCAN"
entity.dataProducer = "TCGA"
entity.disease = "cancer"
entity.center = list(set(filteredMeta.center))
entity.centerTitle = list(set(filteredMeta.centerTitle))
entity.fileType = list(set(filteredMeta.fileType))
entity.platformTitle = list(set(filteredMeta.platformTitle))
entity.nSamples = nSamples
entity.nFeatures = nFeatures
entity = syn.store(entity, used=files, executed=thisCodeInSynapse(parentId=args.parentId))
if list(set(filteredMeta.fileType))[0] in ['seg', 'bed']:
dfs = mp.map(lambda f: pd.read_csv(f.path, sep='\t'), files)
df = pd.concat(dfs, axis=0)
df.to_csv(args.filepath + name, sep='\t', index=False)
nSamples = len(set(df.Sample))
nFeatures = 0
else: #All other fileTypes
dfs = mp.map(lambda f: pd.read_csv(f.path, sep='\t', index_col=0),
files)
df = pd.concat(dfs, axis=1)
df.to_csv(args.filepath + name, sep='\t')
nFeatures, nSamples = df.shape
print 'Created', name, df.shape
#Add file to Synapse
entity = synapseclient.File(args.filepath + name, parentId=args.parentId)
#Set annotations
entity.platform = platform
entity.dataSubType = dataSubType
entity.acronym = 'PANCAN'
entity.dataProducer = 'TCGA'
entity.disease = 'cancer'
entity.center = list(set(filteredMeta.center))
entity.centerTitle = list(set(filteredMeta.centerTitle))
entity.fileType = list(set(filteredMeta.fileType))
entity.platformTitle = list(set(filteredMeta.platformTitle))
entity.nSamples = nSamples
entity.nFeatures = nFeatures
entity = syn.store(entity,
used=files,
executed=thisCodeInSynapse(parentId=args.parentId))
to a specific platform."""
old_whitelist = syn.get(WHITELISTID, version=version)
whitelist = pd.read_csv(whitelistEntity.path, sep='\t')
oldToRemove = set(whitelist.ix[whitelist.Do_not_use & (whitelist.platform==platform),
'aliquot_barcode'])
return oldToRemove
#mp = Pool(8)
syn = synapseclient.login(silent=True)
whitelistEntity = syn.get(WHITELISTID)
whitelist = pd.read_csv(whitelistEntity.path, sep='\t')
inputFiles = synapseHelpers.query2df(syn.chunkedQuery(QUERY_STR))
code=synapseHelpers.thisCodeInSynapse(parentId='syn1774100')
for i, row in inputFiles.iterrows():
print row.id, row['name'],
inputFileEntity = syn.get(row.id)
outFileName = row['name'][:-4]+'_whitelisted'+row['name'][-4:]
toRemove = set(whitelist.ix[whitelist.Do_not_use & (whitelist.platform == row['platform']),
'aliquot_barcode'])
if isUptodate(outFileName, [inputFileEntity], toRemove, row['platform']):
print ' is up to date - but update provenance'
e = syn.get(getFileIdFromName(outFileName), downloadFile=False)
syn.store(e, used=[inputFileEntity, whitelistEntity], executed=code)
continue
if row.fileType =='bed5': #Do the filtering for bed files
df = pd.read_csv(inputFileEntity.path, sep='\t')
