def sample_paths_jamo(samp):
'''
Find paths to h5 files using JAMO
'''
# Load JAMO module and import sdm_curl
import EnvironmentModules as EnvMod
EnvMod.module(['load', 'jamo'])
# EnvMod.module(['load','hdf5'])
for x in os.getenv("PYTHONPATH").split(":"):
if x not in sys.path:
sys.path.append(x)
from sdm_curl import Curl
curl = Curl(JAMO_URL)
files = curl.post('api/metadata/query',
data={
'file_type': 'h5',
'metadata.sample_name': {
'$regex': samp
}
})
if len(files) == 0:
print >> sys.stderr, '[ERROR] No samples matching "%s"' % samp
sys.exit(1)
h5_paths = (os.path.join(f['file_path'], f['file_name']) for f in files
if f['file_name'].endswith('bax.h5'))
return sorted(h5_paths)
def find_smrtcells_jamo_dna(sample_name):
''' Returns absolute path for all H5 files matching sample_name '''
from sdm_curl import Curl
filenames = []
curl = Curl('https://sdm2.jgi-psf.org')
files = curl.post('api/metadata/query',data={'metadata.sample_name':sample_name,'file_type':'h5'})
if not files:
return None
return [os.path.join(f['file_path'],f['file_name']) for f in files]
def find_smrtcells_jamo(sample_name):
''' Returns absolute path for all H5 files matching sample_name '''
from sdm_curl import Curl
filenames = []
curl = Curl('https://sdm2.jgi-psf.org')
files = curl.post('api/metadata/query',data={'metadata.sample_name':sample_name,'file_type':'h5'})
if not files:
return None
locations = list(set(f['metadata']['sdm_smrt_cell']['fs_location'] for f in files))
return locations
def sample_paths_jamo(samp):
"""
Find paths to h5 files using JAMO
"""
# Load JAMO module and import sdm_curl
import EnvironmentModules as EnvMod
EnvMod.module(["load", "jamo"])
# EnvMod.module(['load','hdf5'])
for x in os.getenv("PYTHONPATH").split(":"):
if x not in sys.path:
sys.path.append(x)
from sdm_curl import Curl
curl = Curl(JAMO_URL)
files = curl.post("api/metadata/query", data={"file_type": "h5", "metadata.sample_name": {"$regex": samp}})
if len(files) == 0:
print >>sys.stderr, '[ERROR] No samples matching "%s"' % samp
sys.exit(1)
h5_paths = (os.path.join(f["file_path"], f["file_name"]) for f in files if f["file_name"].endswith("bax.h5"))
return sorted(h5_paths)
