def get_loganalysis_text(xmldata):
# prepare the base path for the beast analysis
basepath = beast.prepare()
with open(os.path.join(basepath, 'myjob.xml'), 'w') as fout:
fout.write(xmldata + '\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()
return analysis_text
def get_loganalysis_text(xmldata):
# prepare the base path for the beast analysis
basepath = beast.prepare()
with open(os.path.join(basepath, 'myjob.xml'), 'w') as fout:
fout.write(xmldata + '\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()
return analysis_text
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 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