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': {
'$regex': samp
}
})
if len(files) == 0:
print >> sys.stderr, '[ERROR] No samples matching "%s"' % samp
sys.exit(1)
h5_paths = (os.path.join(f['file_path'], f['file_name']) for f in files
if f['file_name'].endswith('bax.h5'))
return sorted(h5_paths)
def sample_paths_jamo(samp):
"""
Find paths to h5 files using JAMO
"""
# Load JAMO module and import sdm_curl
import EnvironmentModules as EnvMod
EnvMod.module(["load", "jamo"])
# EnvMod.module(['load','hdf5'])
for x in os.getenv("PYTHONPATH").split(":"):
if x not in sys.path:
sys.path.append(x)
from sdm_curl import Curl
curl = Curl(JAMO_URL)
files = curl.post("api/metadata/query", data={"file_type": "h5", "metadata.sample_name": {"$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)
import os
import sys
import glob
import urllib2
import json
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)
"""
Following is the resulting XML file for SMRT Pipe v2.1:
<?xml version="1.0"?>
<pacbioAnalysisInputs>
<dataReferences>
<url ref="run:0000000-0000"><location>/mnt/data/2770276/0006/Analysis_Results/m130512_050747_42209_c100524
962550000001823079609281357_s1_p0.2.bax.h5</location></url>
<url ref="run:0000000-0001"><location>/mnt/data/2770276/0006/Analysis_Results/m130512_050747_42209_c100524
962550000001823079609281357_s1_p0.3.bax.h5</location></url>
<url ref="run:0000000-0002"><location>/mnt/data/2770276/0006/Analysis_Results/m130512_050747_42209_c100524
962550000001823079609281357_s1_p0.1.bax.h5</location></url>
</dataReferences>
</pacbioAnalysisInputs>
For SMRT Pipe versions before v2.1:
