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python3.5 can run this method #193

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python3.5 can run this method #193

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7f3e7de
subprocess.PIPE is a bytes
loganylchen Dec 3, 2018
92470fd
this method can fit python 3.5
loganylchen Dec 3, 2018
8b18161
update .gitignore
loganylchen Dec 3, 2018
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4 changes: 3 additions & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -27,4 +27,6 @@ hisat2_test/kim_example*.malignment.gcsa
hisat2_test/genome*
hisat2_test/2*
hisat2_test/snp142*
hisat2_test/testset*
hisat2_test/testset*

.idea/
9 changes: 5 additions & 4 deletions hisat2_extract_snps_haplotypes_UCSC.py
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Expand Up @@ -23,7 +23,7 @@
import sys, subprocess
import re
from argparse import ArgumentParser, FileType

from functools import cmp_to_key

"""
"""
Expand Down Expand Up @@ -129,7 +129,7 @@ def generate_haplotypes(snp_file,
assert len(vars) > 0

# Sort variants and remove redundant variants
vars = sorted(vars, cmp=compare_vars)
vars = sorted(vars, key=cmp_to_key(compare_vars))
tmp_vars = []
v = 0
while v < len(vars):
Expand Down Expand Up @@ -289,7 +289,7 @@ def cmp_haplotype(a, b):
return a_begin - b_begin
return a_end - b_end

haplotypes = sorted(list(haplotypes2), cmp=cmp_haplotype)
haplotypes = sorted(list(haplotypes2), key=cmp_to_key(cmp_haplotype))

# Write haplotypes
for h_i in range(len(haplotypes)):
Expand Down Expand Up @@ -353,7 +353,8 @@ def main(genome_file,
snp_cmd = ["cat", snp_fname]
snp_proc = subprocess.Popen(snp_cmd,
stdout=subprocess.PIPE,
stderr=open("/dev/null", 'w'))
stderr=open("/dev/null", 'w'),
universal_newlines=True)
ids_seen = set()
for line in snp_proc.stdout:
if not line or line.startswith('#'):
Expand Down