add missing import, arguments related to cht_data

CHT/cht_data.py

@@ -1,6 +1,6 @@
 import sys
 import gzip
-
+import os
 import numpy as np
 
 class TestSNP:
@@ -143,7 +143,8 @@ def open_input_files(in_filename):
 
 
 
-def read_count_matrices(input_filename, shuffle=False, skip=0, min_counts=0, min_as_counts=0):
+def read_count_matrices(input_filename, shuffle=False, skip=0,
+ min_counts=0, min_as_counts=0, sample=0):
  """Given an input file that contains paths to input files for all individuals, and returns 
  matrix of observed read counts, and matrix of expected read counts
  """
@@ -210,12 +211,12 @@ def read_count_matrices(input_filename, shuffle=False, skip=0, min_counts=0, min
  sys.stderr.write("expect_matrix dimension: %s\n" % str(expected_matrix.shape))
 
  nrow = count_matrix.shape[0]
- if (options.sample > 0) and (options.sample < count_matrix.shape):
+ if (sample > 0) and (sample < count_matrix.shape):
  # randomly sample subset of rows without replacement
- sys.stderr.write("randomly sampling %d target regions\n" % options.sample)
+ sys.stderr.write("randomly sampling %d target regions\n" % sample)
  samp_index = np.arange(nrow)
  np.random.shuffle(samp_index)
- samp_index = samp_index[:options.sample]
+ samp_index = samp_index[:sample]
  count_matrix = count_matrix[samp_index,]
  expected_matrix = expected_matrix[samp_index,]
 

CHT/fit_bnb_coefficients.py

@@ -152,7 +152,8 @@ def main():
  shuffle=False,
  skip=options.skip,
  min_counts=options.min_counts,
- min_as_counts=options.min_as_counts)
+ min_as_counts=options.min_as_counts,
+ sample=options.sample)
 
  gene_fits = [np.float64(0.005)] * count_matrix.shape[0]
  mean_fits = [np.float64(1)] * count_matrix.shape[0]