bump v1.2.2

CHANGELOG.txt

@@ -4,6 +4,11 @@ NanoVar Changelog
 Release Summary:
 
 
+Version 1.2.2 - Nov 25, 2019
+    * Updated dependency versions
+    * Changed spline in nv_cov_upper to make_interp_spline due to scipy update
+
+
 Version 1.2.1 - Nov 24, 2019
     * Added running progress spinner
     * Added bedtools as a pre-requisite for pybedtools

nanovar/nv_cov_upper.py

@@ -26,7 +26,7 @@
 matplotlib.use('Agg')
 import matplotlib.pyplot as plt
 from pybedtools import BedTool
-from scipy.interpolate import spline
+from scipy.interpolate import make_interp_spline, BSpline
 
 
 # Generate upper overlap limit, depth of coverage, and coverage curve plot
@@ -112,13 +112,14 @@ def curve(data, n, upper_limit, wk_dir):
     for i in c:
         p.append(data.count(i))
     p.append(n - sum(p))
-    y = [(float(z)/n) for z in p]
+    y = np.array([(float(z)/n) for z in p])
     # theoretical = [0.0915, 0.0441, 0.1032, 0.1498, 0.1739, 0.1626,
     # 0.1132, 0.0808, 0.0412, 0.0247, 0.0097, 0.0028, 0.0015,
     # 0.0006, 0.0002, 0.0002, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
-    c = range(int(upper_limit)+1)
-    xnew = np.linspace(0, int(upper_limit), 100)
-    smooth = spline(c, y, xnew)
+    c = np.array(range(int(upper_limit)+1))
+    xnew = np.linspace(c.min(), c.max(), 100)
+    spl = make_interp_spline(c, y)
+    smooth = spl(xnew)
     params = {'axes.labelsize': 14, 'axes.titlesize': 17, 'legend.fontsize': 10, 'xtick.labelsize': 12, 'ytick.labelsize': 12,
               'font.family': 'Arial, Helvetica, sans-serif'}
     matplotlib.rcParams.update(params)

nanovar/nv_input.py

@@ -58,7 +58,7 @@ def restrict_float(f):
                         help="BED file with genomic regions to be excluded. \
                              (e.g. telomeres and centromeres). \
                              Either specify name of in-built reference genome filter \
-                             (i.e. hg38, hg19, mm10, mm9) or provide FULL path to \
+                             (i.e. hg38, hg19, mm10) or provide FULL path to \
                              own BED file. [None]")
 
     parser.add_argument("-l", "--minlen", type=int,

nanovar/version.py

@@ -1 +1 @@
-__version__ = "1.2.1"
+__version__ = "1.2.2"

setup.py

@@ -21,12 +21,12 @@
     license='gpl-3.0',
     author='Tham Cheng Yong',
     author_email='chengyong.tham@u.nus.edu',
-    description='Structural variant caller using low-depth long reads.',
+    description='Structural variant caller using low-depth long reads',
     keywords=['nanovar', 'structural variant caller', 'sv', 'nanopore', 'long read', 'low coverage', 'low depth'],
     long_description=long_description,
     long_description_content_type="text/markdown",
-    install_requires=['numpy==1.17.3', 'scipy==1.2.1', 'biopython==1.74', 'pybedtools==0.8.0', 'matplotlib==2.2.3',
-                      'tensorflow==1.13.1', 'keras==2.3.1', 'natsort==6.2.0', 'progress==1.3'],
+    install_requires=['numpy>=1.17.3', 'scipy>=1.2.1', 'biopython>=1.74', 'pybedtools>=0.8.0', 'matplotlib>=2.2.3',
+                      'tensorflow>=1.13.1', 'keras>=2.2.4', 'natsort>=6.2.0', 'progress>=1.4'],
     python_requires='>=3.5',
     classifiers=[
         "Operating System :: POSIX :: Linux",