#
from __future__ import division
import _config
import sys, os, fnmatch, datetime, subprocess
sys.path.append('/home/unix/maxwshen/')
import numpy as np
from collections import defaultdict
from mylib import util, compbio
import pandas as pd
# Default params
inp_dir = _config.OUT_PLACE + f'pb_d_major_subset/'
NAME = util.get_fn(__file__)
out_dir = _config.OUT_PLACE + NAME + '/'
util.ensure_dir_exists(out_dir)
exp_design = pd.read_csv(_config.DATA_DIR + f'Badran2015_SraRunTable.csv')
pacbio_nms = exp_design[exp_design['Instrument'] ==
'PacBio RS II']['Library Name']
pacbio_nms = sorted(pacbio_nms)
params = {
# 'mutations': 'VIWASDNGERIPYCDKSKL',
# 'wt': 'AACVFGTEAQTSDSNENES',
'mutations': 'VIWSGDNGERIPYCDKSKL',
'wt': 'AACFRGTEAQTSDSNENES',
'wt_dots': '...................',
'sim_read_lens': [
1,
50,
75,
import _config
import sys, os, fnmatch, datetime, subprocess
import nltk, pattern.en
from nltk.stem import WordNetLemmatizer
wnl = WordNetLemmatizer()
from pattern.en import conjugate
from mylib import util
# Default params
# DEFAULT_INP_DIR = _config.DATA_DIR + 'google10k/google-10000-english-usa.txt'
DEFAULT_INP_DIR = [_config.NOUN_FN, _config.VERB_FN]
NAME = util.get_fn(__file__)
# Functions
def pluralize(word):
lemma = wnl.lemmatize(word, 'n')
plural = True if word is not lemma else False
if not plural:
out = pattern.en.pluralize(word)
else:
out = word
return out
def make_nouns(inp_fn, out_dir):
nouns = set()
with open(inp_fn) as f:
