parser.add_argument('--markersizes')
parser.add_argument('--dont-calculate-mean-info', action='store_true')
parser.add_argument('--normalize', action='store_true')
parser.add_argument('--graphify', action='store_true')
parser.add_argument('--strings-to-ignore') # remove this string from the plot names in each dir (e.g. '-mean-bins') NOTE replaces '_' with '-'
args = parser.parse_args()
if args.strings_to_ignore is not None:
args.strings_to_ignore = args.strings_to_ignore.replace('_', '-')
args.plotdirs = utils.get_arg_list(args.plotdirs)
args.scale_errors = utils.get_arg_list(args.scale_errors)
args.colors = utils.get_arg_list(args.colors, intify=True)
args.linestyles = utils.get_arg_list(args.linestyles, intify=True)
args.names = utils.get_arg_list(args.names)
args.leaves_per_tree = utils.get_arg_list(args.leaves_per_tree, intify=True)
args.strings_to_ignore = utils.get_arg_list(args.strings_to_ignore)
args.markersizes = utils.get_arg_list(args.markersizes, intify=True)
args.linewidths = utils.get_arg_list(args.linewidths, intify=True)
for iname in range(len(args.names)):
args.names[iname] = args.names[iname].replace('@', ' ')
assert len(args.plotdirs) == len(args.names)
with opener('r')(args.datadir + '/v-meta.json') as json_file: # get location of <begin> cysteine in each v region
args.cyst_positions = json.load(json_file)
with opener('r')(args.datadir + '/j_tryp.csv') as csv_file: # get location of <end> tryptophan in each j region (TGG)
tryp_reader = csv.reader(csv_file)
args.tryp_positions = {row[0]:row[1] for row in tryp_reader} # WARNING: this doesn't filter out the header line
plotting.compare_directories(args)
del_3p = len(self.germline_seqs[region][match_name]) - del_5p - len(gl_match_seq)
if region == 'j' and del_5p < 0:
print ' WARNING adding to right side of germline j'
# assert len(gl_match_seq) > len(self.germline_seqs[region][match_name])
self.germline_seqs[region][match_name] = gl_match_seq
del_5p = self.germline_seqs[region][match_name].find(gl_match_seq)
del_3p = len(self.germline_seqs[region][match_name]) - del_5p - len(gl_match_seq)
if del_5p < 0 or del_3p < 0:
print 'ERROR couldn\'t figure out deletions in', region
print ' germline', self.germline_seqs[region][match_name], match_name
print ' germline match', gl_match_seq
print ' ', del_5p, del_3p
return
line[region + '_5p_del'] = del_5p
line[region + '_3p_del'] = del_3p
line[region + '_gene'] = match_name
line[region + '_gl_seq'] = gl_match_seq
line[region + '_qr_seq'] = region_query_seq
if __name__ == "__main__":
filelist = [ '/home/dralph/Dropbox/join-output-' + str(ifile) + '.xml' for ifile in range(1,6)]
# jparser = JoinParser('caches/recombinator/simu.csv', filelist, datadir='./data')
# plotting.compare_directories('/var/www/sharing/dralph/partis/performance/plots/', 'hmm', '/var/www/sharing/dralph/partis/joinsolver_performance/plots/', 'jsolver', xtitle='inferred - true', stats='')
base_plotdir = '/var/www/sharing/dralph/partis'
plotting.compare_directories(base_plotdir + '/performance/plots', 'partis',
base_plotdir + '/imgt_performance/plots', 'imgt',
dir3=base_plotdir + '/joinsolver_performance/plots', name3='joinsolver')
if del_5p < 0 or del_3p < 0:
print 'ERROR couldn\'t figure out deletions in', region
print ' germline', self.germline_seqs[region][
match_name], match_name
print ' germline match', gl_match_seq
print ' ', del_5p, del_3p
return
line[region + '_5p_del'] = del_5p
line[region + '_3p_del'] = del_3p
line[region + '_gene'] = match_name
line[region + '_gl_seq'] = gl_match_seq
line[region + '_qr_seq'] = region_query_seq
if __name__ == "__main__":
filelist = [
'/home/dralph/Dropbox/join-output-' + str(ifile) + '.xml'
for ifile in range(1, 6)
]
# jparser = JoinParser('caches/recombinator/simu.csv', filelist, datadir='./data')
# plotting.compare_directories('/var/www/sharing/dralph/partis/performance/plots/', 'hmm', '/var/www/sharing/dralph/partis/joinsolver_performance/plots/', 'jsolver', xtitle='inferred - true', stats='')
base_plotdir = '/var/www/sharing/dralph/partis'
plotting.compare_directories(base_plotdir + '/performance/plots',
'partis',
base_plotdir + '/imgt_performance/plots',
'imgt',
dir3=base_plotdir +
'/joinsolver_performance/plots',
name3='joinsolver')
del_5p = self.germline_seqs[region][match_name].find(gl_match_seq)
del_3p = len(self.germline_seqs[region][match_name]) - del_5p - len(gl_match_seq)
if del_5p < 0 or del_3p < 0:
print "ERROR couldn't figure out deletions in", region
print " germline", self.germline_seqs[region][match_name], match_name
print " germline match", gl_match_seq
print " ", del_5p, del_3p
return
line[region + "_5p_del"] = del_5p
line[region + "_3p_del"] = del_3p
line[region + "_gene"] = match_name
line[region + "_gl_seq"] = gl_match_seq
line[region + "_qr_seq"] = region_query_seq
if __name__ == "__main__":
filelist = ["/home/dralph/Dropbox/join-output-" + str(ifile) + ".xml" for ifile in range(1, 6)]
# jparser = JoinParser('caches/recombinator/simu.csv', filelist, datadir='./data')
# plotting.compare_directories('/var/www/sharing/dralph/partis/performance/plots/', 'hmm', '/var/www/sharing/dralph/partis/joinsolver_performance/plots/', 'jsolver', xtitle='inferred - true', stats='')
base_plotdir = "/var/www/sharing/dralph/partis"
plotting.compare_directories(
base_plotdir + "/performance/plots",
"partis",
base_plotdir + "/imgt_performance/plots",
"imgt",
dir3=base_plotdir + "/joinsolver_performance/plots",
name3="joinsolver",
)
