#!/usr/bin/env python
import os
import csv
import time
import sys
from subprocess import check_call
import utils
from opener import opener
import plotting
from mutefreqer import MuteFreqer
has_root = plotting.check_root()
# ----------------------------------------------------------------------------------------
class ParameterCounter(object):
""" class to keep track of how many times we've seen each gene version, erosion length,
insertion (length and base content), and mutation """
def __init__(self, germline_seqs): #, base_outdir='', plotdir='', write_parameters=True, plot_parameters=True):
self.total = 0
self.counts = {}
self.counts['all'] = {}
for column in utils.column_dependencies:
self.counts[column] = {}
for bound in utils.boundaries:
self.counts[bound + '_insertion_content'] = {'A':0, 'C':0, 'G':0, 'T':0} # base content of each insertion
self.counts['seq_content'] = {'A':0, 'C':0, 'G':0, 'T':0}
self.mutefreqer = MuteFreqer(germline_seqs) #, self.base_outdir, self.plotdir, write_parameters=self.write_parameters, plot_parameters=self.plot_parameters)
# ----------------------------------------------------------------------------------------
def clean(self):
""" remove all the parameter files """
#!/usr/bin/env python
import os
import csv
import time
import sys
from subprocess import check_call
import utils
from opener import opener
import plotting
from mutefreqer import MuteFreqer
has_root = plotting.check_root()
# ----------------------------------------------------------------------------------------
class ParameterCounter(object):
""" class to keep track of how many times we've seen each gene version, erosion length,
insertion (length and base content), and mutation """
def __init__(
self, germline_seqs
): #, base_outdir='', plotdir='', write_parameters=True, plot_parameters=True):
self.total = 0
self.counts = {}
self.counts['all'] = {}
for column in utils.column_dependencies:
self.counts[column] = {}
for bound in utils.boundaries:
self.counts[bound + '_insertion_content'] = {
'A': 0,
'C': 0,
import sys
import utils
import plotting
from hist import Hist
from subprocess import check_call
assert plotting.check_root()
# Columns for which we just want to know, Did we guess the right value? (for other columns, we store guess - true)
bool_columns = ('v_gene', 'd_gene', 'j_gene')
class PerformancePlotter(object):
# ----------------------------------------------------------------------------------------
def __init__(self, germlines, plotdir, name):
self.germlines = germlines
self.plotdir = plotdir
self.name = name
utils.prep_dir(self.plotdir + '/plots', wildling=None, multilings=['*.csv', '*.svg', '*.root'])
self.values = {}
for column in utils.index_columns:
if column == 'cdr3_length': # kind of finicky to figure out what this is, so I don't always set it
continue
self.values[column] = {}
if column in bool_columns:
self.values[column]['right'] = 0
self.values[column]['wrong'] = 0
self.values['hamming_to_true_naive'] = {}
for region in utils.regions:
self.values[region + '_hamming_to_true_naive'] = {}
self.values[region + '_hamming_to_true_naive_normed'] = {}
# for bound in utils.boundaries:
