コード例 #1
0
def get_analysis_time(accession, repstr, project):

    result = list(dxpy.find_analyses(project=project, name='*'+accession+repstr+'*', name_mode='glob', describe=True, state='done'))
    if len(result) != 1:
        print "WARN: No single (%s) analysis found for %s%s" % (len(result), accession, repstr)
        return -999.99

    anl = result[0]['describe']
    start = anl['created']
    finish = [ t['setAt'] for t in anl['stateTransitions'] if t['newState'] == 'done'][0]

    #print start, finish, finish-start, (finish-start)/1000.0
    return (finish-start)/1000.0 # covert to secs.
コード例 #2
0
def main():

    args = get_args()
    if args.debug:
        logger.setLevel(logging.DEBUG)
    else:
        logger.setLevel(logging.INFO)

    authid, authpw, server = common.processkey(args.key, args.keyfile)
    keypair = (authid, authpw)

    if args.analysis_ids:
        ids = args.analysis_ids
    elif args.created_after:
        analyses = []
        for state in args.state:
            analyses.extend(
                dxpy.find_analyses(name="ENCSR*",
                                   name_mode='glob',
                                   state=state,
                                   include_subjobs=True,
                                   return_handler=True,
                                   created_after="%s" % (args.created_after)))
        ids = [
            analysis.get_id() for analysis in analyses
            if analysis.describe()['executableName'] == 'tf_chip_seq'
            or analysis.describe()['executableName'].startswith(
                'ENCSR783QUL Peaks')
        ]
    elif args.infile:
        ids = args.infile
    else:
        #never reached because inile defaults to stdin
        raise InputError(
            "Must supply analysis id's in arguments, --infile or supply search string in --created_after"
        )

    fieldnames = [
        'date', 'analysis', 'experiment', 'target', 'biosample_term_name',
        'biosample_type', 'lab', 'rfa', 'assembly', 'Nt', 'Np', 'N1', 'N2',
        'rescue_ratio', 'self_consistency_ratio', 'reproducibility_test',
        'state', 'total price', 'notes'
    ]
    writer = csv.DictWriter(sys.stdout,
                            fieldnames=fieldnames,
                            delimiter='\t',
                            quotechar='"')
    writer.writeheader()

    for (i, analysis_id) in enumerate(ids):
        if analysis_id.startswith('#'):
            continue
        analysis_id = analysis_id.rstrip()
        logger.debug('%s' % (analysis_id))
        analysis = dxpy.DXAnalysis(analysis_id)
        desc = analysis.describe()
        project = desc.get('project')

        m = re.match('^(ENCSR[0-9]{3}[A-Z]{3}) Peaks', desc['name'])
        if m:
            experiment_accession = m.group(1)
        else:
            logger.error("No accession in %s, skipping." % (desc['name']))
            continue

        experiment = common.encoded_get(
            urlparse.urljoin(server,
                             '/experiments/%s' % (experiment_accession)),
            keypair)
        logger.debug('ENCODEd experiment %s' % (experiment['accession']))
        if args.lab and experiment['lab'].split('/')[2] not in args.lab:
            continue
        try:
            idr_stage = next(
                s['execution'] for s in desc['stages']
                if s['execution']['name'] == "Final IDR peak calls")
        except:
            logging.error('Failed to find final IDR stage in %s' %
                          (analysis_id))
        else:
            if idr_stage[
                    'state'] != 'done':  #Final IDR peak calls stage not done, so loop through intermediate IDR stages to find errors
                Np = N1 = N2 = Nt = rescue_ratio = self_consistency_ratio = reproducibility_test = None
                notes = []
                #note this list contains a mis-spelled form of IDR Pooled Pseudoreplicates because until 11/13/15 the pipeline stage name was misspelled - need to be able to report on those runs
                idr_stage_names = [
                    'IDR True Replicates', 'IDR Rep 1 Self-pseudoreplicates',
                    'IDR Rep 2 Self-pseudoreplicates',
                    'IDR Pooled Pseudoreplicates', 'IDR Pooled Pseudoeplicates'
                ]
                for stage_name in idr_stage_names:
                    try:
                        idr_stage = next(
                            s['execution'] for s in desc['stages']
                            if s['execution']['name'] == stage_name)
                    except StopIteration:
                        continue
                    except:
                        raise
                    if idr_stage['state'] == 'failed':
                        try:
                            job_log = subprocess.check_output(
                                'dx watch %s' % (idr_stage['id']),
                                shell=True,
                                stderr=subprocess.STDOUT)
                        except subprocess.CalledProcessError as e:
                            job_log = e.output
                        else:
                            job_log = None
                        if job_log:
                            patterns = [
                                r'Peak files must contain at least 20 peaks post-merge'
                            ]
                            for p in patterns:
                                m = re.search(p, job_log)
                                if m:
                                    notes.append("%s: %s" %
                                                 (stage_name, m.group(0)))
                        if not notes:
                            notes.append(idr_stage['failureMessage'])
                try:
                    done_time = next(transition['setAt']
                                     for transition in desc['stateTransitions']
                                     if transition['newState'] == "failed")
                except StopIteration:
                    done_time = "Not done or failed"
                except:
                    raise
            else:
                Np = idr_stage['output'].get('Np')
                N1 = idr_stage['output'].get('N1')
                N2 = idr_stage['output'].get('N2')
                Nt = idr_stage['output'].get('Nt')
                rescue_ratio = idr_stage['output'].get('rescue_ratio')
                self_consistency_ratio = idr_stage['output'].get(
                    'self_consistency_ratio')
                reproducibility_test = idr_stage['output'].get(
                    'reproducibility_test')
                notes = "IDR Complete"
                done_time = next(transition['setAt']
                                 for transition in desc['stateTransitions']
                                 if transition['newState'] == "done")

        if done_time:
            date = time.strftime("%Y-%m-%d %H:%M:%S",
                                 time.localtime(done_time / 1000))
        else:
            date = "Running"
        analysis_link = 'https://platform.dnanexus.com/projects/%s/monitor/analysis/%s' % (
            desc.get('project').split('-')[1], desc.get('id').split('-')[1])
        experiment_link = 'https://www.encodeproject.org/experiments/%s' % (
            experiment.get('accession'))
        row = {
            'date':
            date,
            'analysis':
            analysis_link,
            'experiment':
            experiment_link,
            'target':
            experiment['target'].split('/')[2],
            'biosample_term_name':
            experiment.get('biosample_term_name'),
            'biosample_type':
            experiment.get('biosample_type'),
            'lab':
            experiment['lab'].split('/')[2],
            'rfa':
            common.encoded_get(server + experiment.get('award'),
                               keypair).get('rfa'),
            'assembly':
            args.assembly,  #TODO ... derive this from the analysis
            'Np':
            Np,
            'N1':
            N1,
            'N2':
            N2,
            'Nt':
            Nt,
            'rescue_ratio':
            rescue_ratio,
            'self_consistency_ratio':
            self_consistency_ratio,
            'reproducibility_test':
            reproducibility_test,
            'state':
            desc.get('state'),
            'total price':
            desc.get('totalPrice')
        }

        if notes:
            row.update({'notes': '%s' % (notes)})
        else:
            row.update({'notes': '%s' % ('OK')})
        #log = subprocess.check_output('dx watch %s' %(analysis.))
        writer.writerow(row)
コード例 #3
0
def main():

	args = get_args()
	if args.debug:
		logger.setLevel(logging.DEBUG)
	else:
		logger.setLevel(logging.INFO)

	authid, authpw, server = common.processkey(args.key, args.keyfile)
	keypair = (authid,authpw)

	if args.analysis_ids:
		ids = args.analysis_ids
	elif args.created_after:
		analyses = []
		for state in args.state:
			analyses.extend(dxpy.find_analyses(name="ENCSR*",name_mode='glob',state=state,include_subjobs=True,return_handler=True,created_after="%s" %(args.created_after)))
		ids = [analysis.get_id() for analysis in analyses if analysis.describe()['executableName'] == 'tf_chip_seq' or analysis.describe()['executableName'].startswith('ENCSR783QUL Peaks')]
	elif args.infile:
		ids = args.infile
	else:
		#never reached because inile defaults to stdin
		raise InputError("Must supply analysis id's in arguments, --infile or supply search string in --created_after")

	fieldnames = [	'date','analysis','experiment','target','biosample_term_name','biosample_type','lab','rfa','assembly',
					'Nt','Np','N1','N2','rescue_ratio','self_consistency_ratio','reproducibility_test',
					'state','total price','notes']
	writer = csv.DictWriter(sys.stdout, fieldnames=fieldnames, delimiter='\t', quotechar='"')
	writer.writeheader()

	for (i, analysis_id) in enumerate(ids):
		if analysis_id.startswith('#'):
			continue
		analysis_id = analysis_id.rstrip()
		logger.debug('%s' %(analysis_id))
		analysis = dxpy.DXAnalysis(analysis_id)
		desc = analysis.describe()
		project = desc.get('project')

		m = re.match('^(ENCSR[0-9]{3}[A-Z]{3}) Peaks',desc['name'])
		if m:
			experiment_accession = m.group(1)
		else:
			logger.error("No accession in %s, skipping." %(desc['name']))
			continue

		experiment = common.encoded_get(urlparse.urljoin(server,'/experiments/%s' %(experiment_accession)), keypair)
		logger.debug('ENCODEd experiment %s' %(experiment['accession']))
		if args.lab and experiment['lab'].split('/')[2] not in args.lab:
			continue
		try:
			idr_stage = next(s['execution'] for s in desc['stages'] if s['execution']['name'] == "Final IDR peak calls")
		except:
			logging.error('Failed to find final IDR stage in %s' %(analysis_id))
		else:
			if idr_stage['state'] != 'done': #Final IDR peak calls stage not done, so loop through intermediate IDR stages to find errors
				Np = N1 = N2 = Nt = rescue_ratio = self_consistency_ratio = reproducibility_test = None
				notes = []
				#note this list contains a mis-spelled form of IDR Pooled Pseudoreplicates because until 11/13/15 the pipeline stage name was misspelled - need to be able to report on those runs
				idr_stage_names = ['IDR True Replicates', 'IDR Rep 1 Self-pseudoreplicates', 'IDR Rep 2 Self-pseudoreplicates', 'IDR Pooled Pseudoreplicates', 'IDR Pooled Pseudoeplicates']
				for stage_name in idr_stage_names:
					try:
						idr_stage = next(s['execution'] for s in desc['stages'] if s['execution']['name'] == stage_name)
					except StopIteration:
						continue
					except:
						raise
					if idr_stage['state'] == 'failed':
						try:
							job_log = subprocess.check_output('dx watch %s' %(idr_stage['id']), shell=True, stderr=subprocess.STDOUT)
						except subprocess.CalledProcessError as e:
							job_log = e.output
						else:
							job_log = None
						if job_log:
							patterns = [r'Peak files must contain at least 20 peaks post-merge']
							for p in patterns:
								m = re.search(p,job_log)
								if m:
									notes.append("%s: %s" %(stage_name,m.group(0)))
						if not notes:
							notes.append(idr_stage['failureMessage'])
				try:
					done_time = next(transition['setAt'] for transition in desc['stateTransitions'] if transition['newState'] == "failed")
				except StopIteration:
					done_time = "Not done or failed"
				except:
					raise
			else:
				Np = idr_stage['output'].get('Np')
				N1 = idr_stage['output'].get('N1')
				N2 = idr_stage['output'].get('N2')
				Nt = idr_stage['output'].get('Nt')
				rescue_ratio = idr_stage['output'].get('rescue_ratio')
				self_consistency_ratio = idr_stage['output'].get('self_consistency_ratio')
				reproducibility_test = idr_stage['output'].get('reproducibility_test')
				notes = "IDR Complete"
				done_time = next(transition['setAt'] for transition in desc['stateTransitions'] if transition['newState'] == "done")

		if done_time:
			date = time.strftime("%Y-%m-%d %H:%M:%S",time.localtime(done_time/1000))
		else:
			date = "Running"
		analysis_link = 'https://platform.dnanexus.com/projects/%s/monitor/analysis/%s' %(desc.get('project').split('-')[1], desc.get('id').split('-')[1])
		experiment_link = 'https://www.encodeproject.org/experiments/%s' %(experiment.get('accession'))
		row = {
			'date': date,
			'analysis':		analysis_link,
			'experiment': 	experiment_link,
			'target':		experiment['target'].split('/')[2],
			'biosample_term_name':	experiment.get('biosample_term_name'),
			'biosample_type':	experiment.get('biosample_type'),
			'lab':			experiment['lab'].split('/')[2],
			'rfa':			common.encoded_get(server+experiment.get('award'),keypair).get('rfa'),
			'assembly':		args.assembly, #TODO ... derive this from the analysis
			'Np':			Np,
			'N1':			N1,
			'N2':			N2,
			'Nt':			Nt,
			'rescue_ratio':	rescue_ratio,
			'self_consistency_ratio': self_consistency_ratio,
			'reproducibility_test': reproducibility_test,
			'state': 		desc.get('state'),
			'total price': 	desc.get('totalPrice')
		}

		if notes:
			row.update({'notes': '%s' %(notes)})
		else:
			row.update({'notes': '%s' %('OK')})
		#log = subprocess.check_output('dx watch %s' %(analysis.))
		writer.writerow(row)
コード例 #4
0
def main():

	args = get_args()
	if args.debug:
		logger.setLevel(logging.DEBUG)
	else:
		logger.setLevel(logging.INFO)

	authid, authpw, server = common.processkey(args.key, args.keyfile)
	keypair = (authid,authpw)

	if args.analysis_ids:
		ids = args.analysis_ids
	elif args.created_after:
		analyses = dxpy.find_analyses(name="ENCSR*",name_mode='glob',state='done',include_subjobs=True,return_handler=True,created_after="%s" %(args.created_after))
		ids = [analysis.get_id() for analysis in analyses if analysis.describe()['executableName'] == 'tf_chip_seq']
	elif args.infile:
		ids = args.infile
	else:
		#never reached because inile defaults to stdin
		raise InputError("Must supply analysis id's in arguments, --infile or supply search string in --created_after")

	fieldnames = [	'date','analysis','experiment','target','biosample_term_name','biosample_type','lab','rfa','assembly',
					'Nt','Np','N1','N2','rescue_ratio','self_consistency_ratio','reproducibility_test',
					'state','total price','notes']
	writer = csv.DictWriter(sys.stdout, fieldnames=fieldnames, delimiter='\t', quotechar='"')
	writer.writeheader()

	for (i, analysis_id) in enumerate(ids):
		if analysis_id.startswith('#'):
			continue
		analysis_id = analysis_id.rstrip()
		logger.debug('%s' %(analysis_id))
		analysis = dxpy.DXAnalysis(analysis_id)
		desc = analysis.describe()
		project = desc.get('project')

		m = re.match('^(ENCSR[0-9]{3}[A-Z]{3}) Peaks',desc['name'])
		if m:
			experiment_accession = m.group(1)
		else:
			logger.error("No accession in %s, skipping." %(desc['name']))
			continue

		experiment = common.encoded_get(urlparse.urljoin(server,'/experiments/%s' %(experiment_accession)), keypair)
		logger.debug('ENCODEd experiment %s' %(experiment['accession']))
		try:
			idr_stage = next(s['execution'] for s in desc['stages'] if s['execution']['name'] == "Final IDR peak calls")
		except:
			logging.error('Failed to find IDR stage in %s' %(analysis_id))
		else:
			Np = idr_stage['output'].get('Np')
			N1 = idr_stage['output'].get('N1')
			N2 = idr_stage['output'].get('N2')
			Nt = idr_stage['output'].get('Nt')
			rescue_ratio = idr_stage['output'].get('rescue_ratio')
			self_consistency_ratio = idr_stage['output'].get('self_consistency_ratio')
			reproducibility_test = idr_stage['output'].get('reproducibility_test')

		done_time = next(transition['setAt'] for transition in desc['stateTransitions'] if transition['newState'] == "done")

		row = {
			'date': time.strftime("%Y-%m-%d %H:%M:%S",time.localtime(done_time/1000)),
			'analysis':		analysis.get_id(),
			'experiment': 	experiment.get('accession'),
			'target':		experiment['target'].split('/')[2],
			'biosample_term_name':	experiment.get('biosample_term_name'),
			'biosample_type':	experiment.get('biosample_type'),
			'lab':			experiment['lab'].split('/')[2],
			'rfa':			common.encoded_get(server+experiment.get('award'),keypair).get('rfa'),
			'assembly':		args.assembly, #TODO ... derive this from the analysis
			'Np':			Np,
			'N1':			N1,
			'N2':			N2,
			'Nt':			Nt,
			'rescue_ratio':	rescue_ratio,
			'self_consistency_ratio': self_consistency_ratio,
			'reproducibility_test': reproducibility_test,
			'state': 		desc.get('state'),
			'total price': 	desc.get('totalPrice')
		}
		notes = []

		# if int(np_stage.get('output').get('npeaks_in')) - int(np_stage.get('output').get('npeaks_out')) != int(np_stage.get('output').get('npeaks_rejected')):
		# 	notes.append("in-out!=rej delta=%i" %(int(np_stage.get('output').get('npeaks_in')) - int(np_stage.get('output').get('npeaks_out'))))
		# else:
		# 	notes.append("in-out=rej OK")

		# bb_check_notes = []
		# for stage in [np_stage, gp_stage]:
		# 	bb_dxf = dxpy.DXFile(stage['output']['overlapping_peaks_bb'])
		# 	if int(bb_dxf.describe()['size']) < 200000:
		# 		bb_check_notes.append("%s bb size=%i" %(stage['name'], int(bb_dxf.describe()['size'])))
		# if not bb_check_notes:
		# 	notes.append("bb check OK")
		# else:
		# 	notes.append(bb_check_notes)




		if notes:
			row.update({'notes': '%s' %(notes)})
		else:
			row.update({'notes': '%s' %('OK')})
		#log = subprocess.check_output('dx watch %s' %(analysis.))
		writer.writerow(row)
コード例 #5
0
def main():

    args = get_args()
    if args.debug:
        logger.setLevel(logging.DEBUG)
    else:
        logger.setLevel(logging.INFO)

    authid, authpw, server = common.processkey(args.key, args.keyfile)
    keypair = (authid, authpw)

    if args.analysis_ids:
        ids = args.analysis_ids
    elif args.created_after:
        analyses = []
        for state in args.state:
            analyses.extend(
                dxpy.find_analyses(
                    name="ENCSR*",
                    name_mode="glob",
                    state=state,
                    include_subjobs=True,
                    return_handler=True,
                    created_after="%s" % (args.created_after),
                )
            )
        ids = [
            analysis.get_id()
            for analysis in analyses
            if analysis.describe()["executableName"] == "tf_chip_seq"
            or analysis.describe()["executableName"].startswith("ENCSR783QUL Peaks")
        ]
    elif args.infile:
        ids = args.infile
    else:
        # never reached because inile defaults to stdin
        raise InputError("Must supply analysis id's in arguments, --infile or supply search string in --created_after")

    fieldnames = [
        "name",
        "date",
        "analysis",
        "experiment",
        "target",
        "biosample_term_name",
        "biosample_type",
        "lab",
        "rfa",
        "assembly",
        "Nt",
        "Np",
        "N1",
        "N2",
        "rescue_ratio",
        "self_consistency_ratio",
        "reproducibility_test",
        "state",
        "release",
        "total price",
        "notes",
    ]
    writer = csv.DictWriter(sys.stdout, fieldnames=fieldnames, delimiter="\t", quotechar='"')
    writer.writeheader()

    for (i, analysis_id) in enumerate(ids):
        if analysis_id.startswith("#"):
            continue
        analysis_id = analysis_id.rstrip()
        logger.debug("%s" % (analysis_id))
        analysis = dxpy.DXAnalysis(analysis_id)
        desc = analysis.describe()
        project = desc.get("project")

        m = re.match("^(ENCSR[0-9]{3}[A-Z]{3}) Peaks", desc["name"])
        if m:
            experiment_accession = m.group(1)
        else:
            logger.error("No accession in %s, skipping." % (desc["name"]))
            continue

        experiment = common.encoded_get(urlparse.urljoin(server, "/experiments/%s" % (experiment_accession)), keypair)
        logger.debug("ENCODEd experiment %s" % (experiment["accession"]))
        if args.lab and experiment["lab"].split("/")[2] not in args.lab:
            continue
        try:
            idr_stage = next(s["execution"] for s in desc["stages"] if s["execution"]["name"] == "Final IDR peak calls")
        except:
            logging.error("Failed to find final IDR stage in %s" % (analysis_id))
        else:
            if (
                idr_stage["state"] != "done"
            ):  # Final IDR peak calls stage not done, so loop through intermediate IDR stages to find errors
                Np = N1 = N2 = Nt = rescue_ratio = self_consistency_ratio = reproducibility_test = None
                notes = []
                # note this list contains a mis-spelled form of IDR Pooled Pseudoreplicates because until 11/13/15 the pipeline stage name was misspelled - need to be able to report on those runs
                idr_stage_names = [
                    "IDR True Replicates",
                    "IDR Rep 1 Self-pseudoreplicates",
                    "IDR Rep 2 Self-pseudoreplicates",
                    "IDR Pooled Pseudoreplicates",
                    "IDR Pooled Pseudoeplicates",
                ]
                for stage_name in idr_stage_names:
                    try:
                        idr_stage = next(s["execution"] for s in desc["stages"] if s["execution"]["name"] == stage_name)
                    except StopIteration:
                        continue
                    except:
                        raise
                    if idr_stage["state"] == "failed":
                        try:
                            job_log = subprocess.check_output(
                                "dx watch %s" % (idr_stage["id"]), shell=True, stderr=subprocess.STDOUT
                            )
                        except subprocess.CalledProcessError as e:
                            job_log = e.output
                        else:
                            job_log = None
                        if job_log:
                            patterns = [r"Peak files must contain at least 20 peaks post-merge"]
                            for p in patterns:
                                m = re.search(p, job_log)
                                if m:
                                    notes.append("%s: %s" % (stage_name, m.group(0)))
                        if not notes:
                            notes.append(idr_stage["failureMessage"])
                try:
                    done_time = next(
                        transition["setAt"]
                        for transition in desc["stateTransitions"]
                        if transition["newState"] == "failed"
                    )
                except StopIteration:
                    done_time = "Not done or failed"
                except:
                    raise
            else:
                Np = idr_stage["output"].get("Np")
                N1 = idr_stage["output"].get("N1")
                N2 = idr_stage["output"].get("N2")
                Nt = idr_stage["output"].get("Nt")
                rescue_ratio = idr_stage["output"].get("rescue_ratio")
                self_consistency_ratio = idr_stage["output"].get("self_consistency_ratio")
                reproducibility_test = idr_stage["output"].get("reproducibility_test")
                notes = "IDR Complete"
                done_time = next(
                    transition["setAt"] for transition in desc["stateTransitions"] if transition["newState"] == "done"
                )

        if done_time:
            date = time.strftime("%Y-%m-%d %H:%M:%S", time.localtime(done_time / 1000))
        else:
            date = "Running"
        analysis_link = "https://platform.dnanexus.com/projects/%s/monitor/analysis/%s" % (
            desc.get("project").split("-")[1],
            desc.get("id").split("-")[1],
        )
        experiment_link = "https://www.encodeproject.org/experiments/%s" % (experiment.get("accession"))
        row = {
            "name": desc.get("name"),
            "date": date,
            "analysis": analysis_link,
            "experiment": experiment_link,
            "target": experiment["target"].split("/")[2],
            "biosample_term_name": experiment.get("biosample_term_name"),
            "biosample_type": experiment.get("biosample_type"),
            "lab": experiment["lab"].split("/")[2],
            "rfa": common.encoded_get(server + experiment.get("award"), keypair).get("rfa"),
            "assembly": args.assembly,  # TODO ... derive this from the analysis
            "Np": Np,
            "N1": N1,
            "N2": N2,
            "Nt": Nt,
            "rescue_ratio": rescue_ratio,
            "self_consistency_ratio": self_consistency_ratio,
            "reproducibility_test": reproducibility_test,
            "state": desc.get("state"),
            "release": experiment["status"],
            "total price": desc.get("totalPrice"),
        }

        if notes:
            row.update({"notes": "%s" % (notes)})
        else:
            row.update({"notes": "%s" % ("OK")})
            # log = subprocess.check_output('dx watch %s' %(analysis.))
        writer.writerow(row)