From e6a8ad6a6e9440b3ed759af790cc5c07524f7fc9 Mon Sep 17 00:00:00 2001
From: Thomas Faraut <Thomas Faraut>
Date: Wed, 5 Dec 2018 11:17:21 +0100
Subject: [PATCH] removing izip and pysamstats import
---
snakecnv/bin/detect_regions_to_exclude.py | 14 ++++++--------
1 file changed, 6 insertions(+), 8 deletions(-)
diff --git a/snakecnv/bin/detect_regions_to_exclude.py b/snakecnv/bin/detect_regions_to_exclude.py
index d46f5a3..d0c90f5 100755
--- a/snakecnv/bin/detect_regions_to_exclude.py
+++ b/snakecnv/bin/detect_regions_to_exclude.py
@@ -4,7 +4,6 @@ import argparse
import os
from tempfile import NamedTemporaryFile, mkdtemp
from shutil import rmtree
-from itertools import izip
import multiprocessing
from functools import partial
@@ -12,7 +11,6 @@ from functools import partial
import numpy as np
import pysam
-import pysamstats
import pybedtools
from svrunner_utils import eprint
@@ -62,12 +60,12 @@ def get_bamcoverage(bamfile, fafile, chrom, window_size=500,
return a
-def get_pysamstatsbamcoverage(bamfile, fafile, chrom, window_size=500):
- mybam = pysam.AlignmentFile(bamfile)
- a = pysamstats.load_binned("coverage", mybam,
- fafile=fafile,
- chrom=chrom,
- window_size=window_size)
+# def get_pysamstatsbamcoverage(bamfile, fafile, chrom, window_size=500):
+# mybam = pysam.AlignmentFile(bamfile)
+# a = pysamstats.load_binned("coverage", mybam,
+# fafile=fafile,
+# chrom=chrom,
+# window_size=window_size)
return a
--
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