def get_response_content(fs):
header_sequence_pairs = beasttut.get_header_seq_pairs()
interval_xml_data = beasttut.get_xml_string(
fs.start_pos, fs.stop_pos, fs.nsamples, 'myjob.log',
header_sequence_pairs)
arr = get_loganalysis_array(interval_xml_data)
s = '\n'.join('\t'.join(str(x) for x in row) for row in arr) + '\n'
return s
def get_response_content(fs):
header_sequence_pairs = beasttut.get_header_seq_pairs()
interval_xml_data = beasttut.get_xml_string(fs.start_pos, fs.stop_pos,
fs.nsamples, 'myjob.log',
header_sequence_pairs)
arr = get_loganalysis_array(interval_xml_data)
s = '\n'.join('\t'.join(str(x) for x in row) for row in arr) + '\n'
return s
def get_loganalysis_array(start_pos, stop_pos, nsamples, header_seq_pairs):
# get the xml contents
xml_string = beasttut.get_xml_string(
start_pos, stop_pos, nsamples, 'myjob.log', header_seq_pairs)
# prepare the base path for the beast analysis
basepath = beast.prepare()
with open(os.path.join(basepath, 'myjob.xml'), 'w') as fout:
fout.write(xml_string + '\n')
beast.run_beast(basepath, g_beast_jar_path)
beast.run_loganalyser(basepath)
# read the analysis
with open(os.path.join(basepath, 'myjob-loganalyser.txt')) as fin:
analysis_text = fin.read()
# parse the analysis
arr = beast.loganalyser_to_array(analysis_text)
return arr
def preprocess(self):
# for each (start_pos, stop_pos) pair
# define a log filename and
# create a beast xml and a bsub script
self.local_log_paths = []
for i, start_stop_pair in enumerate(self.start_stop_pairs):
start_pos, stop_pos = start_stop_pair
# define the log file paths
log_name = 'primate-tut-%d-%d.log' % start_stop_pair
local_log_path = os.path.join(
self.local.get_out(), log_name)
remote_log_path = os.path.join(
self.remote.get_out(), log_name)
self.local_log_paths.append(local_log_path)
# define the xml file paths
xml_name = 'primate-tut-%d-%d.xml' % start_stop_pair
local_xml_path = os.path.join(
self.local.get_in_contents(), xml_name)
remote_xml_path = os.path.join(
self.remote.get_in_contents(), xml_name)
# define the local bsub path
bsub_name = 'primate-tut-%d-%d.bsub' % start_stop_pair
local_bsub_path = os.path.join(
self.local.get_in_bsubs(), bsub_name)
# create the xml file
with open(local_xml_path, 'w') as fout:
print >> fout, beasttut.get_xml_string(
start_pos, stop_pos, self.nsamples, remote_log_path)
# create the bsub file
with open(local_bsub_path, 'w') as fout:
stdout_path = os.path.join(self.remote.get_out(),
'out.tut-%d-%d' % start_stop_pair)
stderr_path = os.path.join(self.remote.get_out(),
'err.tut-%d-%d' % start_stop_pair)
# name the job
print >> fout, '#BSUB -J tut-%d-%d' % start_stop_pair
# suggest the brc queue
print >> fout, '#BSUB -q brc'
# redirect stdout
print >> fout, '#BSUB -o', stdout_path
# redirect stderr
print >> fout, '#BSUB -e', stderr_path
# run BEAST using a java path suggested by Gary Howell
print >> fout, g_remote_java_path, '-jar'
print >> fout, g_remote_beast_jar_path, remote_xml_path
def __call__(self, conn):
# for each (start_pos, stop_pos) pair
# define a log filename and
# create a beast xml and a bsub script
self.local_log_paths = []
for i, start_stop_pair in enumerate(self.start_stop_pairs):
start_pos, stop_pos = start_stop_pair
# define the log file paths
log_name = 'primate-tut-%d-%d.log' % start_stop_pair
local_log_path = os.path.join(
conn.local.get_out(), log_name)
remote_log_path = os.path.join(
conn.remote.get_out(), log_name)
self.local_log_paths.append(local_log_path)
# define the xml file paths
xml_name = 'primate-tut-%d-%d.xml' % start_stop_pair
local_xml_path = os.path.join(
conn.local.get_in_contents(), xml_name)
remote_xml_path = os.path.join(
conn.remote.get_in_contents(), xml_name)
# define the local bsub path
bsub_name = 'primate-tut-%d-%d.bsub' % start_stop_pair
local_bsub_path = os.path.join(
conn.local.get_in_bsubs(), bsub_name)
# create the xml file
with open(local_xml_path, 'w') as fout:
print >> fout, beasttut.get_xml_string(
start_pos, stop_pos, self.nsamples, remote_log_path)
# create the bsub file
with open(local_bsub_path, 'w') as fout:
stdout_path = os.path.join(conn.remote.get_out(),
'out.tut-%d-%d' % start_stop_pair)
stderr_path = os.path.join(conn.remote.get_out(),
'err.tut-%d-%d' % start_stop_pair)
# name the job
print >> fout, '#BSUB -J tut-%d-%d' % start_stop_pair
# suggest the brc queue
print >> fout, '#BSUB -q brc'
# redirect stdout
print >> fout, '#BSUB -o', stdout_path
# redirect stderr
print >> fout, '#BSUB -e', stderr_path
# run BEAST using a java path suggested by Gary Howell
print >> fout, g_remote_java_path, '-jar'
print >> fout, g_remote_beast_jar_path, remote_xml_path
def __call__(self, conn):
# for each (start_pos, stop_pos) pair
# define a log filename and
# create a beast xml and a bsub script
self.local_log_paths = []
for i, start_stop_pair in enumerate(self.start_stop_pairs):
start_pos, stop_pos = start_stop_pair
# define the log file paths
log_name = "primate-tut-%d-%d.log" % start_stop_pair
local_log_path = os.path.join(conn.local.get_out(), log_name)
remote_log_path = os.path.join(conn.remote.get_out(), log_name)
self.local_log_paths.append(local_log_path)
# define the xml file paths
xml_name = "primate-tut-%d-%d.xml" % start_stop_pair
local_xml_path = os.path.join(conn.local.get_in_contents(), xml_name)
remote_xml_path = os.path.join(conn.remote.get_in_contents(), xml_name)
# define the local bsub path
bsub_name = "primate-tut-%d-%d.bsub" % start_stop_pair
local_bsub_path = os.path.join(conn.local.get_in_bsubs(), bsub_name)
# create the xml file
with open(local_xml_path, "w") as fout:
print >> fout, beasttut.get_xml_string(start_pos, stop_pos, self.nsamples, remote_log_path)
# create the bsub file
with open(local_bsub_path, "w") as fout:
stdout_path = os.path.join(conn.remote.get_out(), "out.tut-%d-%d" % start_stop_pair)
stderr_path = os.path.join(conn.remote.get_out(), "err.tut-%d-%d" % start_stop_pair)
# name the job
print >> fout, "#BSUB -J tut-%d-%d" % start_stop_pair
# suggest the brc queue
print >> fout, "#BSUB -q brc"
# redirect stdout
print >> fout, "#BSUB -o", stdout_path
# redirect stderr
print >> fout, "#BSUB -e", stderr_path
# run BEAST using a java path suggested by Gary Howell
print >> fout, g_remote_java_path, "-jar"
print >> fout, g_remote_beast_jar_path, remote_xml_path
def get_response_content(fs):
# init the response and get the user variables
start_pos = fs.start
stop_pos = fs.stop
nsamples = fs.nsamples
out = StringIO()
# get the xml contents
xml_string = beasttut.get_xml_string(
start_pos, stop_pos, nsamples, 'myjob.log',
beasttut.get_header_seq_pairs())
# prepare the base path for the beast analysis
basepath = beast.prepare()
with open(os.path.join(basepath, 'myjob.xml'), 'w') as fout:
fout.write(xml_string + '\n')
beast.run_beast(basepath, g_beast_jar_path)
beast.run_loganalyser(basepath)
# read the analysis
with open(os.path.join(basepath, 'myjob-loganalyser.txt')) as fin:
analysis_text = fin.read()
# parse the analysis
arr = beast.loganalyser_to_array(analysis_text)
s = '\n'.join('\t'.join(str(x) for x in row) for row in arr) + '\n'
# return the response
return s
def get_response_content(fs):
# init the response and get the user variables
start_pos = fs.start
stop_pos = fs.stop
nsamples = fs.nsamples
out = StringIO()
# get the xml contents
xml_string = beasttut.get_xml_string(start_pos, stop_pos, nsamples,
'myjob.log',
beasttut.get_header_seq_pairs())
# prepare the base path for the beast analysis
basepath = beast.prepare()
with open(os.path.join(basepath, 'myjob.xml'), 'w') as fout:
fout.write(xml_string + '\n')
beast.run_beast(basepath, g_beast_jar_path)
beast.run_loganalyser(basepath)
# read the analysis
with open(os.path.join(basepath, 'myjob-loganalyser.txt')) as fin:
analysis_text = fin.read()
# parse the analysis
arr = beast.loganalyser_to_array(analysis_text)
s = '\n'.join('\t'.join(str(x) for x in row) for row in arr) + '\n'
# return the response
return s