def main(argv = None):
via = "lsf"
limspath = None
ms_limspath = "/data/htsstation/mapseq/mapseq_minilims"
hts_key = None
working_dir = None
config = None
if argv is None:
argv = sys.argv
try:
try:
opts,args = getopt.getopt(sys.argv[1:],"hu:k:d:w:m:c:",
["help","via","key","minilims",
"mapseq_minilims",
"working-directory","config"])
except getopt.error, msg:
raise Usage(msg)
for o, a in opts:
if o in ("-h", "--help"):
print __doc__
print usage
sys.exit(0)
elif o in ("-u", "--via"):
if a=="local":
via = "local"
elif a=="lsf":
via = "lsf"
else:
raise Usage("Via (-u) can only be \"local\" or \"lsf\", got %s." % (a,))
elif o in ("-w", "--working-directory"):
if os.path.exists(a):
os.chdir(a)
working_dir = a
else:
raise Usage("Working directory '%s' does not exist." % a)
elif o in ("-d", "--minilims"):
limspath = a
elif o in ("-m", "--mapseq_minilims"):
ms_limspath = a
elif o in ("-k", "--key"):
hts_key = a
elif o in ("-c", "--config"):
config_file = a
else:
raise Usage("Unhandled option: " + o)
M = MiniLIMS( limspath )
if len(hts_key)>1:
gl = use_pickle( M, "global variables" )
htss = frontend.Frontend( url=gl['hts_4cseq']['url'] )
job = htss.job( hts_key )
elif os.path.exists(config_file):
(job,gl) = frontend.parseConfig( config_file )
else:
raise ValueError("Need either a job key (-k) or a configuration file (-c).")
mapseq_url = None
if 'hts_mapseq' in gl:
mapseq_url = gl['hts_mapseq']['url']
job.options['ucsc_bigwig'] = True
g_rep = genrep.GenRep( gl["genrep_url"], gl.get("bwt_root") )
assembly = g_rep.assembly( job.assembly_id )
primers_file='/scratch/cluster/monthly/htsstation/4cseq/'+str(job.id)+'/primers.fa'
primers_dict=c4seq.loadPrimers(primers_file)
with execution( M, description=hts_key, remote_working_directory=working_dir ) as ex:
(mapseq_files, job) = mapseq.get_bam_wig_files( ex, job, ms_limspath, mapseq_url, suffix=['merged'],script_path=gl['script_path'], via=via )
c4seq_files = c4seq.workflow_groups( ex, job, primers_dict, g_rep,
mapseq_files, mapseq_url,
gl['script_path'])
ucscfiles = common.get_files( ex.id, M, select_param={'ucsc':'1'} )
with open(hts_key+".bed",'w') as ucscbed:
for ftype,fset in ucscfiles.iteritems():
for ffile,descr in fset.iteritems():
ucscbed.write(common.track_header(descr,ftype,gl['hts_4cseq']['download'],ffile))
allfiles = common.get_files( ex.id, M )
# gdv_project = gdv.create_gdv_project( gl['gdv']['key'], gl['gdv']['email'],
# job.description,
# assembly.nr_assembly_id,
# gdv_url=gl['gdv']['url'], public=True )
# add_pickle( ex, gdv_project, description='py:gdv_json' )
# if 'sql' in allfiles:
# allfiles['url'] = {gdv_project['public_url']: 'GDV view'}
# download_url = gl['hts_4cseq']['download']
# [gdv.add_gdv_track( gl['gdv']['key'], gl['gdv']['email'],
# gdv_project['project_id'],
# url=download_url+str(k),
# name = re.sub('\.sql','',str(f)),
# gdv_url=gl['gdv']['url'])
# for k,f in allfiles['sql'].iteritems()]
print json.dumps(allfiles)
with open(hts_key+".done",'w') as done:
json.dump(allfiles,done)
if 'email' in gl:
r = email.EmailReport( sender=gl['email']['sender'],
to=str(job.email),
subject="4cseq job "+str(job.description),
smtp_server=gl['email']['smtp'] )
r.appendBody('''
Your 4C-seq job is finished.
The description was:
'''+str(job.description)+'''
and its unique key is '''+hts_key+'''.
You can retrieve the results at this url:
'''+gl['hts_4cseq']['url']+"jobs/"+hts_key+"/get_results")
r.send()
sys.exit(0)
def main(argv = None):
via = "lsf"
limspath = None
hts_key = ''
working_dir = None
config_file = None
if argv is None:
argv = sys.argv
try:
try:
opts,args = getopt.getopt(sys.argv[1:],"hu:k:d:w:c:",
["help","via=","key=","minilims=",
"working-directory=","config="])
except getopt.error, msg:
raise Usage(msg)
for o, a in opts:
if o in ("-h", "--help"):
print __doc__
print usage
return 0
elif o in ("-u", "--via"):
if a=="local":
via = "local"
elif a=="lsf":
via = "lsf"
else:
raise Usage("Via (-u) can only be \"local\" or \"lsf\", got %s." % (a,))
elif o in ("-w", "--working-directory"):
if os.path.exists(a):
os.chdir(a)
working_dir = a
else:
raise Usage("Working directory '%s' does not exist." % a)
elif o in ("-d", "--minilims"):
limspath = a
elif o in ("-k", "--key"):
hts_key = a
elif o in ("-c", "--config"):
config_file = a
else:
raise Usage("Unhandled option: " + o)
if not(limspath and os.path.exists(limspath)
and (hts_key != None or (config_file and os.path.exists(config_file)))):
raise Usage("Need a minilims and a job key or a configuration file")
M = MiniLIMS( limspath )
if len(hts_key)>1:
gl = use_pickle(M, "global variables")
htss = frontend.Frontend( url=gl['hts_mapseq']['url'] )
job = htss.job( hts_key )
[M.delete_execution(x) for x in M.search_executions(with_description=hts_key,fails=True)]
elif os.path.exists(config_file):
(job,gl) = frontend.parseConfig( config_file )
hts_key = job.description
else:
raise ValueError("Need either a job key (-k) or a configuration file (-c).")
g_rep = genrep.GenRep( url=gl["genrep_url"], root=gl["bwt_root"],
intype=job.options.get('input_type_id') or 0 )
assembly = g_rep.assembly( job.assembly_id )
if 'lims' in gl:
dafl = dict((loc,daflims.DAFLIMS( username=gl['lims']['user'], password=pwd ))
for loc,pwd in gl['lims']['passwd'].iteritems())
else:
dafl = None
if not('compute_densities' in job.options):
job.options['compute_densities'] = True
elif isinstance(job.options['compute_densities'],str):
job.options['compute_densities'] = job.options['compute_densities'].lower() in ['1','true','t']
if not('ucsc_bigwig' in job.options):
job.options['ucsc_bigwig'] = True
elif isinstance(job.options['ucsc_bigwig'],str):
job.options['ucsc_bigwig'] = job.options['ucsc_bigwig'].lower() in ['1','true','t']
job.options['ucsc_bigwig'] = job.options['ucsc_bigwig'] and job.options['compute_densities']
if not('create_gdv_project' in job.options):
job.options['create_gdv_project'] = False
elif isinstance(job.options['create_gdv_project'],str):
job.options['create_gdv_project'] = job.options['create_gdv_project'].lower() in ['1','true','t']
if job.options.get('read_extension'):
job.options['read_extension'] = int(job.options['read_extension'])
if job.options.get('merge_strands'):
job.options['merge_strands'] = int(job.options['merge_strands'])
logfile = open(hts_key+".log",'w')
with execution( M, description=hts_key, remote_working_directory=working_dir ) as ex:
logfile.write("Enter execution, fetch fastq files.\n");logfile.flush()
job = get_fastq_files( job, ex.working_directory, dafl )
logfile.write("Map reads.\n");logfile.flush()
mapped_files = map_groups( ex, job, ex.working_directory, assembly, {'via': via} )
logfile.write("Make stats:\n");logfile.flush()
for k,v in job.groups.iteritems():
logfile.write(str(k)+str(v['name'])+"\t");logfile.flush()
pdf = add_pdf_stats( ex, mapped_files,
{k:v['name']},
gl.get('script_path') or '',
description=set_file_descr(v['name']+"_mapping_report.pdf",groupId=k,step='stats',type='pdf') )
if job.options['compute_densities']:
logfile.write("computing densities.\n");logfile.flush()
if not(job.options.get('read_extension')>0):
job.options['read_extension'] = mapped_files.values()[0].values()[0]['stats']['read_length']
density_files = densities_groups( ex, job, mapped_files, assembly.chromosomes, via=via )
logfile.write("Finished computing densities.\n");logfile.flush()
if job.options['create_gdv_project']:
logfile.write("Creating GDV project.\n");logfile.flush()
gdv_project = gdv.create_gdv_project( gl['gdv']['key'], gl['gdv']['email'],
job.description,
assembly.nr_assembly_id,
gdv_url=gl['gdv']['url'], public=True )
logfile.write("GDV project: "+str(gdv_project['project_id']+"\n"));logfile.flush()
add_pickle( ex, gdv_project, description=set_file_descr("gdv_json",step='gdv',type='py',view='admin') )
allfiles = get_files( ex.id, M )
if 'ucsc_bigwig' and g_rep.intype == 0:
ucscfiles = get_files( ex.id, M, select_param={'ucsc':'1'} )
with open(hts_key+".bed",'w') as ucscbed:
for ftype,fset in ucscfiles.iteritems():
for ffile,descr in fset.iteritems():
if re.search(r' \(.*\)',descr): continue
ucscbed.write(track_header(descr,ftype,gl['hts_mapseq']['download'],ffile))
if job.options['create_gdv_project']:
allfiles['url'] = {gdv_project['public_url']: 'GDV view'}
download_url = gl['hts_mapseq']['download']
[gdv.add_gdv_track( gl['gdv']['key'], gl['gdv']['email'],
gdv_project['project_id'],
url=download_url+str(k),
name = re.sub('\.sql','',str(f)),
gdv_url=gl['gdv']['url'] )
for k,f in allfiles['sql'].iteritems()]
logfile.close()
print json.dumps(allfiles)
with open(hts_key+".done",'w') as done:
json.dump(allfiles,done)
if 'email' in gl:
r = email.EmailReport( sender=gl['email']['sender'],
to=str(job.email),
subject="Mapseq job "+str(job.description),
smtp_server=gl['email']['smtp'] )
r.appendBody('''
Your mapseq job has finished.
The description was:
'''+str(job.description)+'''
and its unique key is '''+hts_key+'''.
You can now retrieve the results at this url:
'''+gl['hts_mapseq']['url']+"jobs/"+hts_key+"/get_results")
r.send()
return 0