def main(args):
# set up the logger
f = logging.getLogger('toplevel.logger')
h = logging.StreamHandler()
h.setFormatter(logging.Formatter('%(message)s %(asctime)s'))
f.addHandler(h)
if args.verbose:
f.setLevel(logging.DEBUG)
else:
f.setLevel(logging.WARNING)
f.info('(local) permute columns of the alignment')
header_seq_pairs = beasttut.get_456_col_permuted_header_seq_pairs()
f.info('(local) run BEAST serially locally and build the R stuff')
table_string, scripts = get_table_string_and_scripts(
g_start_stop_pairs, args.nsamples, header_seq_pairs)
f.info('(local) create the composite R script')
out = StringIO()
print >> out, 'library(ggplot2)'
print >> out, 'par(mfrow=c(3,1))'
for script in scripts:
print >> out, script
comboscript = out.getvalue()
f.info('(local) run R to create the pdf')
device_name = Form.g_imageformat_to_r_function['pdf']
retcode, r_out, r_err, image_data = RUtil.run_plotter(
table_string, comboscript, device_name, keep_intermediate=True)
if retcode:
raise RUtil.RError(r_err)
f.info('(local) write the .pdf file')
with open(args.outfile, 'wb') as fout:
fout.write(image_data)
f.info('(local) return from toplevel')
def get_response_content(fs):
start_pos = 1
stop_pos = fs.ncolumns
nsamples = fs.nsamples
header_seq_pairs = beasttut.get_456_col_permuted_header_seq_pairs()
arr = get_loganalysis_array(
start_pos, stop_pos, nsamples, header_seq_pairs)
s = '\n'.join('\t'.join(str(x) for x in row) for row in arr) + '\n'
return s
