def load(self, host="localhost", port=6499):
print "Tuner.load " + str(port)
# Calibrate page
self.calibrate = Calibrate(changefunc=self.onChange,
host=host,
port=port)
self.tabs.addTab(self.calibrate.get_widget(), "Calibrate")
# Preflight page
self.preflight = Preflight(changefunc=self.onChange,
host=host,
port=port)
self.tabs.addTab(self.preflight.get_widget(), "Preflight")
# Launch page
self.launch = Launch(changefunc=self.onChange, host=host, port=port)
self.tabs.addTab(self.launch.get_widget(), "Launch")
# Circle hold page
self.circle = Circle(changefunc=self.onChange, host=host, port=port)
self.tabs.addTab(self.circle.get_widget(), "Circle")
# Chirp page
self.chirp = Chirp(changefunc=self.onChange, host=host, port=port)
self.tabs.addTab(self.chirp.get_widget(), "Chirp")
# Land page
self.land = Land(changefunc=self.onChange, host=host, port=port)
self.tabs.addTab(self.land.get_widget(), "Land")
def launches(update, context):
pass
j = requests.get('https://fdo.rocketlaunch.live/json/launches/next/5')
n_results = 5
api_json = json.loads(j.text)['result']
txts = []
livestream = ""
for i in range(0, n_results):
padlocation = str(
api_json[i]['pad']['location']['statename']) + ', ' + str(
api_json[i]['pad']['location']['country'])
print(str(api_json[i]['pad']['location']['statename']))
if str(api_json[i]['pad']['location']['statename']) == "None":
padlocation = str(api_json[i]['pad']['location']['country'])
print(padlocation)
launch_date = str(api_json[i]['win_open'])
if launch_date == "None":
if str(api_json[i]['est_date']['month']) != "None":
day = '0'
month = '0'
if int(api_json[i]['est_date']['month']) < 10:
month = month + str(api_json[i]['est_date']['month'])
else:
month = str(api_json[i]['est_date']['month'])
if str(api_json[i]['est_date']['day']) != "None":
if int(api_json[i]['est_date']['day']) < 10:
day = day + str(api_json[i]['est_date']['day'])
else:
day = str(api_json[i]['est_date']['day'])
else:
day = "??"
launch_date = month + '-' + day + '-' + str(
api_json[i]['est_date']['year'])
l = Launch(str(api_json[i]['name']),
str(api_json[i]['provider']['name']),
str(api_json[i]['vehicle']['name']),
str(api_json[i]['pad']['location']['name']), padlocation,
'nodescforlist', launch_date, livestream)
txts.append(rocket + ' /' + str(i+1) + ' - <i>' + str(api_json[i]['name']) + '</i> ' + rocket \
+ '\n' + l.getFormattedText())
endtext = ""
for i in range(0, len(txts)):
endtext = endtext + txts[i]
context.bot.send_message(chat_id=update.effective_chat.id,
text=endtext,
disable_web_page_preview=True,
parse_mode=ParseMode.HTML)
def get_args(self):
'''Parse the input arguments.'''
ap = Launch.get_args(self,parse=False)
ap.add_argument('-rl', '--read_length',
help='The length of reads.',
type=int,
choices=['32', '36', '40', '50', '58', '72', '76', '100'],
default='100',
required=False)
ap.add_argument('--umi',
help='Treat fastqs as having UMI flags embedded.',
action='store_true',
required=False)
ap.add_argument('--no_hotspot',
help='Stop before calling hotspots (default: include all steps).',
action='store_true',
required=False)
# NOTE: Could override get_args() to have this non-generic control message
#ap.add_argument('-c', '--control',
# help='The control bam for peak calling.',
# required=False)
return ap.parse_args()
def pipeline_specific_vars(self, args, verbose=False):
'''Adds pipeline specific variables to a dict, for use building the workflow.'''
#args.pe = True # This is necessary to ensure templating does what it must.
psv = Launch.pipeline_specific_vars(self, args)
# Could be multiple annotations supported per genome
psv['annotation'] = args.annotation
if psv['genome'] != self.GENOME_DEFAULT and psv[
'annotation'] == self.ANNO_DEFAULT:
psv['annotation'] = self.ANNO_DEFAULTS[psv['genome']]
if psv['annotation'] not in self.ANNO_ALLOWED[psv['genome']]:
print psv['genome'] + " has no " + psv[
'annotation'] + " annotation."
sys.exit(1)
# Some specific settings
psv['assay_type'] = "rampage"
if self.exp["assay_term_name"] == "CAGE":
psv['assay_type'] = "cage"
psv['nthreads'] = 8
if not self.template:
psv['control'] = args.control
if psv['paired_end'] and psv['assay_type'] == "cage":
print "ERROR: CAGE is always expected to be single-end but mapping says otherwise."
sys.exit(1)
elif not psv['paired_end'] and psv['assay_type'] == "rampage":
print "Rampage is always expected to be paired-end but mapping says otherwise."
sys.exit(1)
if not psv["stranded"]:
print "Detected unstranded library"
# run will either be for combined or single rep.
if not self.combined_reps:
run = psv['reps'][
'a'] # If not combined then run will be for the first (only) replicate
else:
run = psv
# If annotation is not default, then add it to title
if psv['annotation'] != self.ANNO_DEFAULTS[psv['genome']]:
psv['title'] += ', ' + psv['annotation']
psv['name'] += '_' + psv['annotation']
if self.exp["assay_term_name"] == "CAGE":
psv['name'] = psv['assay_type'] + psv['name'][4:]
psv['title'] = "CAGE" + psv['title'][7:]
# Must override results location because of annotation
psv['resultsLoc'] = self.umbrella_folder(args.folder,self.FOLDER_DEFAULT,self.proj_name,psv['exp_type'], \
psv['genome'],psv['annotation'])
psv['resultsFolder'] = psv['resultsLoc']
if not self.template:
psv['resultsFolder'] += psv['experiment'] + '/'
self.update_rep_result_folders(psv)
if verbose:
print "Pipeline Specific Vars:"
print json.dumps(psv, indent=4)
return psv
def pipeline_specific_vars(self, args, verbose=False):
'''Adds pipeline specific variables to a dict, for use building the workflow.'''
psv = Launch.pipeline_specific_vars(self, args)
# Some specific settings
psv['nthreads'] = 8
psv['map_thresh'] = 10
psv['sample_size'] = 15000000
psv['read_length'] = args.read_length
psv['pe_or_se'] = "pe"
for ltr in sorted(psv['reps'].keys()):
rep = psv['reps'][ltr]
if not rep['paired_end']:
psv['pe_or_se'] = "se"
if rep['paired_end'] and 'barcode' in rep and rep[
'barcode'] == "undetected":
del rep['barcode']
if args.umi:
psv['umi'] = "yes"
psv['upper_limit'] = 0
# Crawford fastqs require trimming
psv["trim_len"] = 0
if not self.template and not psv['paired_end'] and "crawford" in psv[
'lab']:
print "Detected that fastqs will be trimmed to 20"
psv["trim_len"] = 20
self.multi_rep = True # For DNase, a single tech_rep moves on to merge/filter.
self.combined_reps = True
if verbose:
print "Pipeline Specific Vars:"
print json.dumps(psv, indent=4)
return psv
def load(self, host="localhost", port=6499):
print "Tuner.load " + str(port)
# Recalibrate page
self.recalibrate = Recalibrate(changefunc=self.onChange, host=host,
port=port)
self.tabs.addTab( self.recalibrate.get_widget(), "Recalibrate" )
# Preflight page
self.preflight = Preflight(changefunc=self.onChange, host=host,
port=port)
self.tabs.addTab( self.preflight.get_widget(), "Preflight" )
# Launch page
self.launch = Launch(changefunc=self.onChange, host=host, port=port)
self.tabs.addTab( self.launch.get_widget(), "Launch" )
# Circle hold page
self.circle = Circle(changefunc=self.onChange, host=host, port=port)
self.tabs.addTab( self.circle.get_widget(), "Circle" )
# Chirp page
self.chirp = Chirp(changefunc=self.onChange, host=host, port=port)
self.tabs.addTab( self.chirp.get_widget(), "Chirp" )
# Land page
self.land = Land(changefunc=self.onChange, host=host, port=port)
self.tabs.addTab( self.land.get_widget(), "Land" )
def __init__(self, root):
self.root = root
self.manifest = PackageXML(self.root + '/package.xml')
self.name = self.manifest.name
self.cmake = parse_file(self.root + '/CMakeLists.txt')
package_structure = get_package_structure(root)
self.source_code = SourceCode(package_structure['source'], self.name)
self.source_code.setup_tags(self.cmake)
self.launches = []
self.plugin_configs = []
for rel_fn, file_path in package_structure['launch'].iteritems():
self.launches.append(Launch(rel_fn, file_path))
for rel_fn, file_path in package_structure['plugin_config'].iteritems(
):
self.plugin_configs.append(PluginXML(rel_fn, file_path))
self.setup_py = None
if 'setup.py' in package_structure['key']:
self.setup_py = SetupPy(self.name,
package_structure['key']['setup.py'])
self.generators = collections.defaultdict(list)
for rel_fn, path in package_structure['generators'].iteritems():
gen = ROSGenerator(rel_fn, path)
self.generators[gen.type].append(gen)
self.dynamic_reconfigs = package_structure['cfg'].keys()
self.misc_files = package_structure[None].keys()
def pipeline_specific_vars(self,args,verbose=False):
'''Adds pipeline specific variables to a dict, for use building the workflow.'''
psv = Launch.pipeline_specific_vars(self,args)
# Some specific settings
psv['nthreads'] = 8
psv['map_thresh'] = 10
psv['sample_size'] = 15000000
psv['read_length'] = args.read_length
psv['pe_or_se'] = "pe"
for ltr in sorted( psv['reps'].keys() ):
rep = psv['reps'][ltr]
if not rep['paired_end']:
psv['pe_or_se'] = "se"
if rep['paired_end'] and 'barcode' in rep and rep['barcode'] == "undetected":
del rep['barcode']
if args.umi:
psv['umi'] = "yes"
psv['upper_limit'] = 0
# Crawford fastqs require trimming
psv["trim_len"] = 0
if not self.template and not psv['paired_end'] and "crawford" in psv['lab']:
print "Detected that fastqs will be trimmed to 20"
psv["trim_len"] = 20
self.multi_rep = True # For DNase, a single tech_rep moves on to merge/filter.
self.combined_reps = True
if verbose:
print "Pipeline Specific Vars:"
print json.dumps(psv,indent=4)
return psv
def pipeline_specific_vars(self,args,verbose=False):
'''Adds pipeline specific variables to a dict, for use building the workflow.'''
psv = Launch.pipeline_specific_vars(self,args)
# Could be multiple annotations supported per genome
psv['annotation'] = args.annotation
if psv['genome'] != self.GENOME_DEFAULT and psv['annotation'] == self.ANNO_DEFAULT:
psv['annotation'] = self.ANNO_DEFAULTS[psv['genome']]
if psv['annotation'] not in self.ANNO_ALLOWED[psv['genome']]:
print psv['genome']+" has no "+psv['annotation']+" annotation."
sys.exit(1)
# Some specific settings
psv['nthreads'] = 8
psv['rnd_seed'] = 12345
# If annotation is not default, then add it to title
if psv['annotation'] != self.ANNO_DEFAULTS[psv['genome']]:
psv['title'] += ', ' + psv['annotation']
psv['name'] += '_' + psv['annotation']
self.no_tophat = args.no_tophat
if not self.no_tophat:
self.PRUNE_STEPS = []
# Must override results location because of annotation
psv['resultsLoc'] = dxencode.umbrella_folder(args.folder,self.FOLDER_DEFAULT,self.proj_name,psv['exp_type'], \
psv['genome'],psv['annotation'])
psv['resultsFolder'] = psv['resultsLoc'] + psv['experiment'] + '/'
self.update_rep_result_folders(psv)
if verbose:
print "Pipeline Specific Vars:"
print json.dumps(psv,indent=4)
return psv
def test20_execute_feedback(self):
self.ctl = Control(db='sqlite.db')
self.ctl.initialize()
self.ctl.reserve()
self.lnc = Launch(db='sqlite.db',
feedpath='/tmp',
taskid=1,
info1='INFO1',
info2='INFO2',
info3='INFO3',
timeout=10,
debug=True)
command = "tests/testprog.py --scenario progressing --feedback /tmp/feedback_1.log --delay 0.002 --debug"
result = self.lnc.execute(command=command)
print("test20 result={}".format(result))
self.assertTrue(result)
def pipeline_specific_vars(self, args, verbose=False):
'''Adds pipeline specific variables to a dict, for use building the workflow.'''
psv = Launch.pipeline_specific_vars(self, args)
# Could be multiple annotations supported per genome
psv['annotation'] = args.annotation
if psv['genome'] != self.GENOME_DEFAULT and psv['annotation'] == self.ANNO_DEFAULT:
psv['annotation'] = self.ANNO_DEFAULTS[psv['genome']]
if psv['annotation'] not in self.ANNO_ALLOWED[psv['genome']]:
print psv['genome']+" has no "+psv['annotation']+" annotation."
sys.exit(1)
# Some specific settings
psv['nthreads'] = 8
psv['rnd_seed'] = 12345
# If paired-end then read_strand might vary TruSeq or ScriptSeq, but only for quant-rsem
psv["read_strand"] = "unstranded" # SE experiments are all unstranded
if psv["paired_end"]:
psv["read_strand"] = "reverse" # Usual ENCODE LRNA experiments are rd1-/rd2+ (AKA reverse)
if not psv["stranded"]:
psv["read_strand"] = "unstranded" # "ScriptSeq" experiments are rd1+/rd2- (AKA forward)
print "Detected unstranded library"
elif psv.get('ScriptSeq', False): # file.replicate.library.document contains "/documents/F17c31e10-1542-42c6-8b4c-3afff95564cf%2F"
psv["read_strand"] = "ScriptSeq" # "ScriptSeq" experiments are rd1+/rd2- (AKA forward)
print "Detected ScriptSeq"
else: # SE
if psv["stranded"]:
psv["read_strand"] = psv.get("strand_direction", "unstranded")
else:
psv["read_strand"] = "unstranded"
if psv["stranded"]:
print "Strand orientation is '%s'" % (psv["read_strand"])
# print "Detected special cases"
# If annotation is not default, then add it to title
if psv['annotation'] != self.ANNO_DEFAULTS[psv['genome']]:
psv['title'] += ', ' + psv['annotation']
psv['name'] += '_' + psv['annotation']
self.no_tophat = True
if args.tophat_also:
self.no_tophat = False
self.PRUNE_STEPS = [] # This blocks pruning... keeping tophat
# Must override results location because of annotation
psv['resultsLoc'] = self.umbrella_folder(args.folder, self.FOLDER_DEFAULT, self.proj_name,
psv['exp_type'], psv['genome'], psv['annotation'])
psv['resultsFolder'] = psv['resultsLoc']
if not self.template:
psv['resultsFolder'] += psv['experiment'] + '/'
self.update_rep_result_folders(psv)
if verbose:
print "Pipeline Specific Vars:"
print json.dumps(psv, indent=4)
return psv
def pipeline_specific_vars(self, args, verbose=False):
'''Adds pipeline specific variables to a dict, for use building the workflow.'''
psv = Launch.pipeline_specific_vars(self, args)
# Now add pipline specific variables and tests
# Could be multiple annotations supported per genome
psv['annotation'] = args.annotation
if psv['genome'] != self.GENOME_DEFAULT and psv[
'annotation'] == self.ANNO_DEFAULT:
psv['annotation'] = self.ANNO_DEFAULTS[psv['genome']]
if psv['annotation'] not in self.ANNO_ALLOWED[psv['genome']]:
print psv['genome'] + " has no " + psv[
'annotation'] + " annotation."
sys.exit(1)
# Paired ends?
if psv['paired_end']:
print "Small-RNA is always expected to be single-end but mapping says otherwise."
#print json.dumps(psv,indent=4,sort_keys=True)
sys.exit(1)
# Some specific settings
psv['nthreads'] = 8
# By replicate:
for ltr in psv['reps'].keys():
if len(ltr) != 1: # only simple reps
continue
rep = psv['reps'][ltr]
rep["clipping_model"] = "ENCODE3" # Default
if "a_tailing" in rep:
rep["clipping_model"] = "A_Tailing_" + rep["a_tailing"]
print "%s detected for %s" % (rep["clipping_model"],
rep["rep_tech"])
# If annotation is not default, then add it to title
if psv['annotation'] != self.ANNO_DEFAULTS[psv['genome']]:
psv['title'] += ', ' + psv['annotation']
psv['name'] += '_' + psv['annotation']
# Must override results location because of annotation
genome = psv['genome']
if self.no_refs: # (no_refs is only True when templating)
genome = None # If templating with no refs then this will hide genome and annotation
psv['resultsLoc'] = self.umbrella_folder(args.folder,self.FOLDER_DEFAULT,self.proj_name,psv['exp_type'], \
psv['genome'],psv['annotation'])
psv['resultsFolder'] = psv['resultsLoc']
if not self.template:
psv['resultsFolder'] += psv['experiment'] + '/'
self.update_rep_result_folders(psv)
if verbose:
print "Pipeline Specific Vars:"
print json.dumps(psv, indent=4)
return psv
def get_args(self):
'''Parse the input arguments.'''
ap = Launch.get_args(self,parse=False)
# NOTE: Could override get_args() to have this non-generic control message
#ap.add_argument('-c', '--control',
# help='The control bam for peak calling.',
# required=False)
return ap.parse_args()
def get_args(self):
'''Parse the input arguments.'''
ap = Launch.get_args(self,parse=False)
# NOTE: Could override get_args() to have this non-generic control message
#ap.add_argument('-c', '--control',
# help='The control bam for peak calling.',
# required=False)
return ap.parse_args()
def get_args(self):
'''Parse the input arguments.'''
ap = Launch.get_args(self,parse=False)
ap.add_argument('-a', '--annotation',
help="Label of annotation (default: '" + self.ANNO_DEFAULT + "')",
choices=[self.ANNO_DEFAULT, 'M2','M3','M4'],
default=self.ANNO_DEFAULT,
required=False)
return ap.parse_args()
def pipeline_specific_vars(self,args,verbose=False):
'''Adds pipeline specific variables to a dict, for use building the workflow.'''
#args.pe = True # This is necessary to ensure templating does what it must.
psv = Launch.pipeline_specific_vars(self,args)
# Could be multiple annotations supported per genome
psv['annotation'] = args.annotation
if psv['genome'] != self.GENOME_DEFAULT and psv['annotation'] == self.ANNO_DEFAULT:
psv['annotation'] = self.ANNO_DEFAULTS[psv['genome']]
if psv['annotation'] not in self.ANNO_ALLOWED[psv['genome']]:
print psv['genome']+" has no "+psv['annotation']+" annotation."
sys.exit(1)
# Some specific settings
psv['assay_type'] = "rampage"
if self.exp["assay_term_name"] == "CAGE":
psv['assay_type'] = "cage"
psv['nthreads'] = 8
if not self.template:
psv['control'] = args.control
if psv['paired_end'] and psv['assay_type'] == "cage":
print "ERROR: CAGE is always expected to be single-end but mapping says otherwise."
sys.exit(1)
elif not psv['paired_end'] and psv['assay_type'] == "rampage":
print "Rampage is always expected to be paired-end but mapping says otherwise."
sys.exit(1)
# run will either be for combined or single rep.
if not self.combined_reps:
run = psv['reps']['a'] # If not combined then run will be for the first (only) replicate
else:
run = psv
# If annotation is not default, then add it to title
if psv['annotation'] != self.ANNO_DEFAULTS[psv['genome']]:
psv['title'] += ', ' + psv['annotation']
psv['name'] += '_' + psv['annotation']
if self.exp["assay_term_name"] == "CAGE":
psv['name'] = psv['assay_type'] + psv['name'][4:]
psv['title'] = "CAGE" + psv['title'][7:]
# Must override results location because of annotation
psv['resultsLoc'] = self.umbrella_folder(args.folder,self.FOLDER_DEFAULT,self.proj_name,psv['exp_type'], \
psv['genome'],psv['annotation'])
psv['resultsFolder'] = psv['resultsLoc']
if not self.template:
psv['resultsFolder'] += psv['experiment'] + '/'
self.update_rep_result_folders(psv)
if verbose:
print "Pipeline Specific Vars:"
print json.dumps(psv,indent=4)
return psv
def pipeline_specific_vars(self,args,verbose=False):
'''Adds pipeline specific variables to a dict, for use building the workflow.'''
psv = Launch.pipeline_specific_vars(self,args)
# Could be multiple annotations supported per genome
psv['annotation'] = args.annotation
if psv['genome'] != self.GENOME_DEFAULT and psv['annotation'] == self.ANNO_DEFAULT:
psv['annotation'] = self.ANNO_DEFAULTS[psv['genome']]
if psv['annotation'] not in self.ANNO_ALLOWED[psv['genome']]:
print psv['genome']+" has no "+psv['annotation']+" annotation."
sys.exit(1)
if not psv['paired_end']:
print "Rampage is always expected to be paired-end but mapping says otherwise."
sys.exit(1)
# Some specific settings
psv['nthreads'] = 8
psv['control'] = args.control
# run will either be for combined or single rep.
if not psv['combined']:
run = psv['reps']['a'] # If not combined then run will be for the first (only) replicate
else:
run = psv
# workflow labeling
psv['description'] = "The ENCODE Rampage RNA pipeline for long RNAs"
run['name'] = "rampage_"+psv['genome']
if psv['genome'] == 'mm10':
run['name'] += psv['annotation']
if psv['gender'] == 'female':
run['name'] += "XX"
else:
run['name'] += "XY"
run['title'] = "Rampage RNA " + psv['experiment'] + " - " + run['rep_tech']
run['name'] += "_"+psv['experiment']+"_" + run['rep_tech']
if not psv['combined']:
run['title'] += " [library '"+run['library_id']+"']"
run['title'] += " on " + psv['genome']+" - "+psv['gender']
# Must override results location because of annotation
psv['resultsLoc'] = dxencode.umbrella_folder(args.folder,self.FOLDER_DEFAULT,self.proj_name,psv['exp_type'], \
psv['genome'],psv['annotation'])
psv['resultsFolder'] = psv['resultsLoc'] + psv['experiment'] + '/'
psv['reps']['a']['resultsFolder'] = psv['resultsLoc'] + psv['experiment'] + '/' + \
psv['reps']['a']['rep_tech'] + '/'
if psv['combined']:
psv['reps']['b']['resultsFolder'] = psv['resultsLoc'] + psv['experiment'] + '/' + \
psv['reps']['b']['rep_tech'] + '/'
if verbose:
print "Pipeline Specific Vars:"
print json.dumps(psv,indent=4)
return psv
def pipeline_specific_vars(self,args,verbose=False):
'''Adds pipeline specific variables to a dict, for use building the workflow.'''
psv = Launch.pipeline_specific_vars(self,args)
# Now add pipline specific variables and tests
# Could be multiple annotations supported per genome
psv['annotation'] = args.annotation
if psv['genome'] != self.GENOME_DEFAULT and psv['annotation'] == self.ANNO_DEFAULT:
psv['annotation'] = self.ANNO_DEFAULTS[psv['genome']]
if psv['annotation'] not in self.ANNO_ALLOWED[psv['genome']]:
print psv['genome']+" has no "+psv['annotation']+" annotation."
sys.exit(1)
# Paired ends?
if psv['paired_end']:
print "Small-RNA is always expected to be single-end but mapping says otherwise."
#print json.dumps(psv,indent=4,sort_keys=True)
sys.exit(1)
# Some specific settings
psv['nthreads'] = 8
# By replicate:
for ltr in psv['reps'].keys():
if len(ltr) != 1: # only simple reps
continue
rep = psv['reps'][ltr]
rep["clipping_model"] = "ENCODE3" # Default
if "a_tailing" in rep:
rep["clipping_model"] = "A_Tailing_" + rep["a_tailing"]
print "%s detected for %s" % (rep["clipping_model"],rep["rep_tech"])
# If annotation is not default, then add it to title
if psv['annotation'] != self.ANNO_DEFAULTS[psv['genome']]:
psv['title'] += ', ' + psv['annotation']
psv['name'] += '_' + psv['annotation']
# Must override results location because of annotation
genome = psv['genome']
if self.no_refs: # (no_refs is only True when templating)
genome = None # If templating with no refs then this will hide genome and annotation
psv['resultsLoc'] = self.umbrella_folder(args.folder,self.FOLDER_DEFAULT,self.proj_name,psv['exp_type'], \
psv['genome'],psv['annotation'])
psv['resultsFolder'] = psv['resultsLoc']
if not self.template:
psv['resultsFolder'] += psv['experiment'] + '/'
self.update_rep_result_folders(psv)
if verbose:
print "Pipeline Specific Vars:"
print json.dumps(psv,indent=4)
return psv
def process_launch(self, launch_obj, conf, testItems):
return Launch(
str(launch_obj["_id"]), launch_obj["projectRef"],
launch_obj["name"],
launch_obj["description"] if "description" in launch_obj else "",
conf,
launch_obj["statistics"] if "statistics" in launch_obj else {},
launch_obj["start_time"],
launch_obj["end_time"] if "end_time" in launch_obj else None,
launch_obj["last_modified"]
if "last_modified" in launch_obj else None,
launch_obj["number"] if "number" in launch_obj else 0, testItems)
def get_args(self):
'''Parse the input arguments.'''
ap = Launch.get_args(self, parse=False)
ap.add_argument('-a',
'--annotation',
help="Label of annotation (default: '" +
self.ANNO_DEFAULT + "')",
choices=[self.ANNO_DEFAULT, 'M2', 'M3', 'M4'],
default=self.ANNO_DEFAULT,
required=False)
return ap.parse_args()
def pipeline_specific_vars(self, args, verbose=False):
'''Adds pipeline specific variables to a dict, for use building the workflow.'''
psv = Launch.pipeline_specific_vars(self, args)
# Could be multiple annotations supported per genome
psv['annotation'] = args.annotation
if psv['genome'] != self.GENOME_DEFAULT and psv[
'annotation'] == self.ANNO_DEFAULT:
psv['annotation'] = self.ANNO_DEFAULTS[psv['genome']]
if psv['annotation'] not in self.ANNO_ALLOWED[psv['genome']]:
print psv['genome'] + " has no " + psv[
'annotation'] + " annotation."
sys.exit(1)
# Some specific settings
psv['nthreads'] = 8
psv['rnd_seed'] = 12345
# Override paired-end with TruSeq or ScriptSeq, but only for quant-rsem
psv["paired_type"] = "true"
if not psv["paired_end"]:
psv["paired_type"] = "false"
else:
if psv.get(
'ScriptSeq', False
): # file.replicate.library.document contains "/documents/F17c31e10-1542-42c6-8b4c-3afff95564cf%2F"
psv["paired_type"] = "ScriptSeq"
print "Detected ScriptSeq"
else:
psv["paired_type"] = "TruSeq"
# If annotation is not default, then add it to title
if psv['annotation'] != self.ANNO_DEFAULTS[psv['genome']]:
psv['title'] += ', ' + psv['annotation']
psv['name'] += '_' + psv['annotation']
self.no_tophat = args.no_tophat
if not self.no_tophat:
self.PRUNE_STEPS = []
# Must override results location because of annotation
psv['resultsLoc'] = self.umbrella_folder(args.folder,self.FOLDER_DEFAULT,self.proj_name,psv['exp_type'], \
psv['genome'],psv['annotation'])
psv['resultsFolder'] = psv['resultsLoc']
if not self.template:
psv['resultsFolder'] += psv['experiment'] + '/'
self.update_rep_result_folders(psv)
if verbose:
print "Pipeline Specific Vars:"
print json.dumps(psv, indent=4)
return psv
def pipeline_specific_vars(self,args,verbose=False):
'''Adds pipeline specific variables to a dict, for use building the workflow.'''
psv = Launch.pipeline_specific_vars(self,args)
# Some specific settings
psv['nthreads'] = 8
psv['min_insert'] = 0
psv['max_insert'] = 500
if verbose:
print "Pipeline Specific Vars:"
print json.dumps(psv,indent=4)
return psv
def pipeline_specific_vars(self,args,verbose=False):
'''Adds pipeline specific variables to a dict, for use building the workflow.'''
psv = Launch.pipeline_specific_vars(self,args)
# Some specific settings
psv['nthreads'] = 8
psv['min_insert'] = 0
psv['max_insert'] = 500
if verbose:
print "Pipeline Specific Vars:"
print json.dumps(psv,indent=4)
return psv
def get_args(self):
"""Parse the input arguments."""
ap = Launch.get_args(self, parse=False)
ap.add_argument(
"-a",
"--annotation",
help="Label of annotation (default: '" + self.ANNO_DEFAULT + "')",
choices=[self.ANNO_DEFAULT, "M2", "M3", "M4"],
default=self.ANNO_DEFAULT,
required=False,
)
return ap.parse_args()
def pipeline_specific_vars(self, args, verbose=False):
'''Adds pipeline specific variables to a dict, for use building the workflow.'''
psv = Launch.pipeline_specific_vars(self, args)
# Could be multiple annotations supported per genome
psv['annotation'] = args.annotation
if psv['genome'] != self.GENOME_DEFAULT and psv['annotation'] == self.ANNO_DEFAULT:
psv['annotation'] = self.ANNO_DEFAULTS[psv['genome']]
if psv['annotation'] not in self.ANNO_ALLOWED[psv['genome']]:
print psv['genome']+" has no "+psv['annotation']+" annotation."
sys.exit(1)
# Some specific settings
psv['nthreads'] = 8
psv['rnd_seed'] = 12345
# If paired-end then read_strand might vary TruSeq or ScriptSeq, but only for quant-rsem
psv["read_strand"] = "unstranded" # SE experiments are all unstranded
if psv["paired_end"]:
psv["read_strand"] = "reverse" # Usual ENCODE LRNA experiments are rd1-/rd2+ (AKA reverse)
if not psv["stranded"]:
psv["read_strand"] = "unstranded" # "ScriptSeq" experiments are rd1+/rd2- (AKA forward)
print "Detected unstranded library"
elif psv.get('ScriptSeq', False): # file.replicate.library.document contains "/documents/F17c31e10-1542-42c6-8b4c-3afff95564cf%2F"
psv["read_strand"] = "ScriptSeq" # "ScriptSeq" experiments are rd1+/rd2- (AKA forward)
print "Detected ScriptSeq"
# print "Detected special cases"
# If annotation is not default, then add it to title
if psv['annotation'] != self.ANNO_DEFAULTS[psv['genome']]:
psv['title'] += ', ' + psv['annotation']
psv['name'] += '_' + psv['annotation']
self.no_tophat = True
if args.tophat_also:
self.no_tophat = False
self.PRUNE_STEPS = [] # This blocks pruning... keeping tophat
# Must override results location because of annotation
psv['resultsLoc'] = self.umbrella_folder(args.folder, self.FOLDER_DEFAULT, self.proj_name,
psv['exp_type'], psv['genome'], psv['annotation'])
psv['resultsFolder'] = psv['resultsLoc']
if not self.template:
psv['resultsFolder'] += psv['experiment'] + '/'
self.update_rep_result_folders(psv)
if verbose:
print "Pipeline Specific Vars:"
print json.dumps(psv, indent=4)
return psv
def get_args(self):
'''Parse the input arguments.'''
ap = Launch.get_args(self,parse=False)
# NOTE: Could override get_args() to have this non-generic control message
#ap.add_argument('-c', '--control',
# help='The control bam for peak calling.',
# required=False)
ap.add_argument('-a', '--annotation',
help="Label of annotation (default: '" + self.ANNO_DEFAULT + "')",
choices=[self.ANNO_DEFAULT, 'M2','M3','M4'],
default=self.ANNO_DEFAULT,
required=False)
return ap.parse_args()
def get_args(self):
'''Parse the input arguments.'''
ap = Launch.get_args(self,parse=False)
# NOTE: Could override get_args() to have this non-generic control message
#ap.add_argument('-c', '--control',
# help='The control bam for peak calling.',
# required=False)
ap.add_argument('-a', '--annotation',
help="Label of annotation (default: '" + self.ANNO_DEFAULT + "')",
choices=[self.ANNO_DEFAULT, 'M2','M3','M4'],
default=self.ANNO_DEFAULT,
required=False)
return ap.parse_args()
def get_args(self):
'''Parse the input arguments.'''
ap = Launch.get_args(self,parse=False)
ap.add_argument('-a', '--annotation',
help="Label of annotation (default: '" + self.ANNO_DEFAULT + "')",
choices=[self.ANNO_DEFAULT, 'M2','M3','M4'],
default=self.ANNO_DEFAULT,
required=False)
ap.add_argument('--no_tophat',
help='Do not include TopHat steps in pipeline (default: include TopHat steps).',
action='store_true',
required=False)
return ap.parse_args()
def pipeline_specific_vars(self, args, verbose=False):
"""Adds pipeline specific variables to a dict, for use building the workflow."""
psv = Launch.pipeline_specific_vars(self, args)
# Now add pipline specific variables and tests
# Could be multiple annotations supported per genome
psv["annotation"] = args.annotation
if psv["genome"] != self.GENOME_DEFAULT and psv["annotation"] == self.ANNO_DEFAULT:
psv["annotation"] = self.ANNO_DEFAULTS[psv["genome"]]
if psv["annotation"] not in self.ANNO_ALLOWED[psv["genome"]]:
print psv["genome"] + " has no " + psv["annotation"] + " annotation."
sys.exit(1)
# Paired ends?
if psv["paired_end"]:
print "Small-RNA is always expected to be single-end but mapping says otherwise."
# print json.dumps(psv,indent=4,sort_keys=True)
sys.exit(1)
# Some specific settings
psv["nthreads"] = 8
# If annotation is not default, then add it to title
if psv["annotation"] != self.ANNO_DEFAULTS[psv["genome"]]:
psv["title"] += ", " + psv["annotation"]
psv["name"] += "_" + psv["annotation"]
# Must override results location because of annotation
genome = psv["genome"]
if self.no_refs: # (no_refs is only True when templating)
genome = None # If templating with no refs then this will hide genome and annotation
psv["resultsLoc"] = self.umbrella_folder(
args.folder, self.FOLDER_DEFAULT, self.proj_name, psv["exp_type"], psv["genome"], psv["annotation"]
)
psv["resultsFolder"] = psv["resultsLoc"]
if not self.template:
psv["resultsFolder"] += psv["experiment"] + "/"
self.update_rep_result_folders(psv)
if verbose:
print "Pipeline Specific Vars:"
print json.dumps(psv, indent=4)
return psv
def get_args(self):
'''Parse the input arguments.'''
ap = Launch.get_args(self, parse=False)
ap.add_argument('-a',
'--annotation',
help="Label of annotation (default: '" +
self.ANNO_DEFAULT + "')",
choices=[self.ANNO_DEFAULT, 'M2', 'M3', 'M4'],
default=self.ANNO_DEFAULT,
required=False)
ap.add_argument(
'--no_tophat',
help=
'Do not include TopHat steps in pipeline (default: include TopHat steps).',
action='store_true',
required=False)
return ap.parse_args()
def get_args(self):
'''Parse the input arguments.'''
ap = Launch.get_args(self,parse=False)
ap.add_argument('-rl', '--read_length',
help='The length of reads.',
type=int,
choices=['32', '36', '40', '50', '58', '72', '76', '100'],
default='100',
required=False)
ap.add_argument('--umi',
help='Treat fastqs as having UMI flags embedded.',
action='store_true',
required=False)
# NOTE: Could override get_args() to have this non-generic control message
#ap.add_argument('-c', '--control',
# help='The control bam for peak calling.',
# required=False)
return ap.parse_args()
def pipeline_specific_vars(self, args, verbose=False):
'''Adds pipeline specific variables to a dict, for use building the workflow.'''
psv = Launch.pipeline_specific_vars(self, args)
# Could be multiple annotations supported per genome
psv['annotation'] = args.annotation
if psv['genome'] != self.GENOME_DEFAULT and psv[
'annotation'] == self.ANNO_DEFAULT:
psv['annotation'] = self.ANNO_DEFAULTS[psv['genome']]
if psv['annotation'] not in self.ANNO_ALLOWED[psv['genome']]:
print psv['genome'] + " has no " + psv[
'annotation'] + " annotation."
sys.exit(1)
# Some specific settings
psv['nthreads'] = 8
psv['rnd_seed'] = 12345
# If annotation is not default, then add it to title
if psv['annotation'] != self.ANNO_DEFAULTS[psv['genome']]:
psv['title'] += ', ' + psv['annotation']
psv['name'] += '_' + psv['annotation']
self.no_tophat = args.no_tophat
if not self.no_tophat:
self.PRUNE_STEPS = []
# Must override results location because of annotation
psv['resultsLoc'] = self.umbrella_folder(args.folder,self.FOLDER_DEFAULT,self.proj_name,psv['exp_type'], \
psv['genome'],psv['annotation'])
psv['resultsFolder'] = psv['resultsLoc']
if not self.template:
psv['resultsFolder'] += psv['experiment'] + '/'
self.update_rep_result_folders(psv)
if verbose:
print "Pipeline Specific Vars:"
print json.dumps(psv, indent=4)
return psv
def pipeline_specific_vars(self,args,verbose=False):
'''Adds pipeline specific variables to a dict, for use building the workflow.'''
psv = Launch.pipeline_specific_vars(self,args)
# Now add pipline specific variables and tests
# Could be multiple annotations supported per genome
psv['annotation'] = args.annotation
if psv['genome'] != self.GENOME_DEFAULT and psv['annotation'] == self.ANNO_DEFAULT:
psv['annotation'] = self.ANNO_DEFAULTS[psv['genome']]
if psv['annotation'] not in self.ANNO_ALLOWED[psv['genome']]:
print psv['genome']+" has no "+psv['annotation']+" annotation."
sys.exit(1)
# Paired ends?
if psv['paired_end']:
print "Small-RNA is always expected to be single-end but mapping says otherwise."
#print json.dumps(psv,indent=4,sort_keys=True)
sys.exit(1)
# Some specific settings
psv['nthreads'] = 8
# If annotation is not default, then add it to title
if psv['annotation'] != self.ANNO_DEFAULTS[psv['genome']]:
psv['title'] += ', ' + psv['annotation']
psv['name'] += '_' + psv['annotation']
# Must override results location because of annotation
psv['resultsLoc'] = dxencode.umbrella_folder(args.folder,self.FOLDER_DEFAULT,self.proj_name,psv['exp_type'], \
psv['genome'],psv['annotation'])
psv['resultsFolder'] = psv['resultsLoc'] + psv['experiment'] + '/'
self.update_rep_result_folders(psv)
if verbose:
print "Pipeline Specific Vars:"
print json.dumps(psv,indent=4)
return psv
def pipeline_specific_vars(self,args,verbose=False):
'''Adds pipeline specific variables to a dict, for use building the workflow.'''
psv = Launch.pipeline_specific_vars(self,args)
# Now add pipline specific variables and tests
# Paired ends?
if psv['paired_end']:
print "Small-RNA is always expected to be single-end but mapping says otherwise."
#print json.dumps(psv,indent=4,sort_keys=True)
sys.exit(1)
# Some specific settings
psv['nthreads'] = 8
# run will either be for combined or single rep.
if self.combined_reps:
print "Small-RNA-seq pipeline currently does not support combined-replicate processing."
sys.exit(1)
if verbose:
print "Pipeline Specific Vars:"
print json.dumps(psv,indent=4)
return psv
def pipeline_specific_vars(self,args,verbose=False):
'''Adds pipeline specific variables to a dict, for use building the workflow.'''
psv = Launch.pipeline_specific_vars(self,args)
# Now add pipline specific variables and tests
# Paired ends?
if psv['paired_end']:
print "Small-RNA is always expected to be single-end but mapping says otherwise."
sys.exit(1)
# Some specific settings
psv['nthreads'] = 8
# run will either be for combined or single rep.
if not psv['combined']:
run = psv['reps']['a'] # If not combined then run will be for the first (only) replicate
else:
run = psv
print "Small-RNA-seq pipeline currently does not support combined-replicate processing."
sys.exit(1)
# workflow labeling
psv['description'] = "The ENCODE RNA Seq pipeline for short RNA"
genderToken = "XY"
if psv['gender'] == 'female':
genderToken = "XX"
run['title'] = "short RNA-seq " + psv['experiment'] + " - "+run['rep_tech'] + \
" (library '"+run['library_id']+"') on " + psv['genome'] + \
" - "+psv['gender']
run['name'] = "srna_"+psv['genome']+genderToken+"_"+psv['experiment'] + "_"+run['rep_tech']
if verbose:
print "Pipeline Specific Vars:"
print json.dumps(psv,indent=4)
return psv
def __init__(self):
Launch.__init__(self)
def nextLaunch(n_results):
pass
providers_list = [
"spacex", "ula", "nasa", "roscosmos", "jaxa", "china", "astra",
"virgin", "rocketlab", "grumman"
]
selected = ""
j = requests.get('https://fdo.rocketlaunch.live/json/launches/next/5')
#change this to select the right launch
if n_results > 0 and n_results < 6:
api_json = json.loads(j.text)['result']
txts = []
livestream = ""
for i in range(n_results - 1, n_results):
padlocation = str(
api_json[i]['pad']['location']['statename']) + ', ' + str(
api_json[i]['pad']['location']['country'])
print(str(api_json[i]['pad']['location']['statename']))
if str(api_json[i]['pad']['location']['statename']) == "None":
padlocation = str(api_json[i]['pad']['location']['country'])
print(padlocation)
launch_date = str(api_json[i]['win_open'])
if launch_date == "None":
if str(api_json[i]['est_date']['month']) != "None":
day = '0'
month = '0'
if int(api_json[i]['est_date']['month']) < 10:
month = month + str(api_json[i]['est_date']['month'])
else:
month = str(api_json[i]['est_date']['month'])
if str(api_json[i]['est_date']['day']) != "None":
if int(api_json[i]['est_date']['day']) < 10:
day = day + str(api_json[i]['est_date']['day'])
else:
day = str(api_json[i]['est_date']['day'])
else:
day = "??"
launch_date = month + '-' + day + '-' + str(
api_json[i]['est_date']['year'])
if str(api_json[i]['quicktext']) != "None":
parts = str(api_json[i]['quicktext']).split('- ')
for x in parts:
if "https" in x:
livestream = x
print("Livestream link: " + livestream)
l = Launch(str(api_json[i]['name']),
str(api_json[i]['provider']['name']),
str(api_json[i]['vehicle']['name']),
str(api_json[i]['pad']['location']['name']),
padlocation, str(api_json[i]['launch_description']),
launch_date, livestream)
txts.append(rocket + ' #' + str(i+1) + ' - <i>' + str(api_json[i]['name']) + '</i> ' + rocket \
+ '\n' + l.getFormattedText())
for k in range(0, len(providers_list)):
print("Lower data: " +
str(api_json[i]['provider']['name']).lower())
print("Item in list: " + providers_list[k])
if providers_list[k] in str(
api_json[i]['provider']['name']).lower():
selected = providers_list[k] + '.jpg'
break
return txts[0], selected, livestream
#button_list = [
# InlineKeyboardButton("Watch Livestream (if available)", url=livestream)
#]
#reply_markup = InlineKeyboardMarkup(build_menu(button_list, n_cols=1))
#if selected == "":
# context.bot.send_message(chat_id=update.effective_chat.id,
# text=txts[0],
# parse_mode=ParseMode.HTML)
#else:
# context.bot.send_photo(chat_id=update.effective_chat.id,
# photo=open('imgs/' + selected, 'rb'),
# caption=txts[0],
# parse_mode=ParseMode.HTML,
# reply_markup=reply_markup)
else:
print("param not in range\nn_results: " + str(n_results) + "\n")
def __init__(self):
Launch.__init__(self)
class Tuner(QtGui.QWidget):
def __init__(self, host="localhost", port=6499):
super(Tuner, self).__init__()
self.default_title = "Aura Tasks"
#self.chirp = None
#self.circle = None
#self.land = None
self.initUI()
self.load(host=host, port=port)
self.clean = True
def initUI(self):
self.setWindowTitle(self.default_title)
layout = QtGui.QVBoxLayout()
self.setLayout(layout)
# Main work area
self.tabs = QtGui.QTabWidget()
layout.addWidget(self.tabs)
#self.overview = Overview(changefunc=self.onChange)
#self.tabs.addTab( self.overview.get_widget(), "Overview" );
# 'File' button bar
file_group = QtGui.QFrame()
layout.addWidget(file_group)
file_layout = QtGui.QHBoxLayout()
file_group.setLayout(file_layout)
save = QtGui.QPushButton('Save')
save.clicked.connect(self.save)
file_layout.addWidget(save)
quit = QtGui.QPushButton('Quit')
quit.clicked.connect(self.quit)
file_layout.addWidget(quit)
file_layout.addStretch(1)
self.resize(800, 700)
self.show()
def load(self, host="localhost", port=6499):
print "Tuner.load " + str(port)
# Calibrate page
self.calibrate = Calibrate(changefunc=self.onChange,
host=host,
port=port)
self.tabs.addTab(self.calibrate.get_widget(), "Calibrate")
# Preflight page
self.preflight = Preflight(changefunc=self.onChange,
host=host,
port=port)
self.tabs.addTab(self.preflight.get_widget(), "Preflight")
# Launch page
self.launch = Launch(changefunc=self.onChange, host=host, port=port)
self.tabs.addTab(self.launch.get_widget(), "Launch")
# Circle hold page
self.circle = Circle(changefunc=self.onChange, host=host, port=port)
self.tabs.addTab(self.circle.get_widget(), "Circle")
# Chirp page
self.chirp = Chirp(changefunc=self.onChange, host=host, port=port)
self.tabs.addTab(self.chirp.get_widget(), "Chirp")
# Land page
self.land = Land(changefunc=self.onChange, host=host, port=port)
self.tabs.addTab(self.land.get_widget(), "Land")
def save(self):
print "called for save, but does nothing yet"
def quit(self):
QtCore.QCoreApplication.instance().quit()
def onChange(self):
#print "parent onChange() called!"
#result = self.rebuildTabNames()
#if result:
# self.rebuildWingLists()
self.clean = False
def isClean(self):
return self.clean
def setClean(self):
self.clean = True
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
import os
import sys
import cherrypy
from launch import Launch
"""
if hasattr(sys, "frozen"):
cwd = os.path.dirname(os.path.abspath(unicode(sys.executable, sys.getfilesystemencoding())))
else:
cwd = os.path.dirname(os.path.abspath(__file__))
sys.path.append(cwd)
"""
if __name__ == '__main__':
if os.name == "posix":
launchyc = Launch()
launchyc.handle_args()
elif os.name == "nt":
#importing here so that if the user isnt running windows
#they wont get an import error from the win only libs
from yamcatWin import LaunchWin
launchyc = LaunchWin()
launchyc.handle_args()
def __init__(self):
Launch.__init__(self)
self.detect_umi = True # Only in DNase is there a umi setting buried in the fastq metadata.
class Tuner(QtGui.QWidget):
def __init__(self, host="localhost", port=6499):
super(Tuner, self).__init__()
self.default_title = "Aura Tasks"
#self.chirp = None
#self.circle = None
#self.land = None
self.initUI()
self.load(host=host, port=port)
self.clean = True
def initUI(self):
self.setWindowTitle( self.default_title )
layout = QtGui.QVBoxLayout()
self.setLayout(layout)
# Main work area
self.tabs = QtGui.QTabWidget()
layout.addWidget( self.tabs )
#self.overview = Overview(changefunc=self.onChange)
#self.tabs.addTab( self.overview.get_widget(), "Overview" );
# 'File' button bar
file_group = QtGui.QFrame()
layout.addWidget(file_group)
file_layout = QtGui.QHBoxLayout()
file_group.setLayout( file_layout )
save = QtGui.QPushButton('Save')
save.clicked.connect(self.save)
file_layout.addWidget(save)
quit = QtGui.QPushButton('Quit')
quit.clicked.connect(self.quit)
file_layout.addWidget(quit)
file_layout.addStretch(1)
self.resize(800, 700)
self.show()
def load(self, host="localhost", port=6499):
print "Tuner.load " + str(port)
# Recalibrate page
self.recalibrate = Recalibrate(changefunc=self.onChange, host=host,
port=port)
self.tabs.addTab( self.recalibrate.get_widget(), "Recalibrate" )
# Preflight page
self.preflight = Preflight(changefunc=self.onChange, host=host,
port=port)
self.tabs.addTab( self.preflight.get_widget(), "Preflight" )
# Launch page
self.launch = Launch(changefunc=self.onChange, host=host, port=port)
self.tabs.addTab( self.launch.get_widget(), "Launch" )
# Circle hold page
self.circle = Circle(changefunc=self.onChange, host=host, port=port)
self.tabs.addTab( self.circle.get_widget(), "Circle" )
# Chirp page
self.chirp = Chirp(changefunc=self.onChange, host=host, port=port)
self.tabs.addTab( self.chirp.get_widget(), "Chirp" )
# Land page
self.land = Land(changefunc=self.onChange, host=host, port=port)
self.tabs.addTab( self.land.get_widget(), "Land" )
def save(self):
print "called for save, but does nothing yet"
def quit(self):
global data_fetcher_quit
data_fetcher_quit = True
QtCore.QCoreApplication.instance().quit()
def onChange(self):
#print "parent onChange() called!"
#result = self.rebuildTabNames()
#if result:
# self.rebuildWingLists()
self.clean = False
def isClean(self):
return self.clean
def setClean(self):
self.clean = True
def __init__(self):
Launch.__init__(self)
self.detect_umi = True # Only in DNase is there a umi setting buried in the fastq metadata.
def test10_execute_nofeedback(self):
self.lnc = Launch(db='sqlite.db', debug=True)
command = "tests/testprog.py --scenario sleeping --sleep 1 --debug"
result = self.lnc.execute(command=command)
print("test10 result={}".format(result))
self.assertTrue(result)