remove future import, left over iteritems
-from __future__ import print_function
import numpy as np
from collections import defaultdict
@@ -213,7 +212,7 @@ def read_vcf(vcf_file, ref_file):
recCalls[sname] = gt
#store the position and the alt
- for seq, gen in recCalls.iteritems():
+ for seq, gen in recCalls.items():
ref = REF
pos = POS-1 #VCF numbering starts from 1, but Reference seq numbering
#will be from 0 because it's python!
@@ -326,7 +325,7 @@ def write_vcf(tree_dict, file_name):#, compress=False):
i+=1
pi = positions[i]
pattern = []
- for k,v in sequences.iteritems():
+ for k,v in sequences.items():
try:
pattern.append(sequences[k][pi])
except KeyError, e:
