diff --git a/.planemo.sh b/.planemo.sh
index 96303e47a..1ded1cdf8 100755
--- a/.planemo.sh
+++ b/.planemo.sh
@@ -28,5 +28,5 @@ else
fi
planemo lint ${wrappers}
-planemo test --no_dependency_resolution --galaxy_branch release_18.05 --install_galaxy ${wrappers} 2>&1 | grep -v -e "^galaxy" | grep -v -e "^requests"
+planemo test --no_dependency_resolution --galaxy_branch release_20.09 --install_galaxy ${wrappers} 2>&1 | grep -v -e "^galaxy" | grep -v -e "^requests"
test ${PIPESTATUS[0]} -eq 0
diff --git a/CHANGES.txt b/CHANGES.txt
index bc55fc624..369375e70 100755
--- a/CHANGES.txt
+++ b/CHANGES.txt
@@ -1,3 +1,14 @@
+3.5.1
+* cmp usage is updated to fit the recent mpl updates.
+* The requirements.txt is updated.
+* "NA" occurences in plotFingerprint.py have been replaced by numpy.NAN (PR #1002)
+* computeMatrixOperations.xml is fixed (brought up in #1003)
+* plotly error is fixed. (issue #1013)
+* relase version is updated in planemo.sh
+* fixed galaxy tests
+* A bug is taken care of in computeMatrixOperations.py / dataRange
+* in plotProfile.py legen location is changed from auto to best (issue #1042)
+
3.5.0
* Fixed a small issue in computeGCBias (issue #969)
diff --git a/README.md b/README.md
index 394353d21..cf0521747 100644
--- a/README.md
+++ b/README.md
@@ -2,7 +2,6 @@
[](https://dev.azure.com/dpryan79/dpryan79/_build/latest?definitionId=1&branchName=master)
[](http://deeptools.readthedocs.org/) [](https://pypi.org/project/deepTools/)
[](http://bioconda.github.io/recipes/deeptools/README.html)
-[](https://usegalaxy.eu/root?tool_id=deeptools_multi_bam_summary)
## User-friendly tools for exploring deep-sequencing data
diff --git a/deeptools/_version.py b/deeptools/_version.py
index a39b0da3c..2c9603d53 100755
--- a/deeptools/_version.py
+++ b/deeptools/_version.py
@@ -2,4 +2,4 @@
# This file is originally generated from Git information by running 'setup.py
# version'. Distribution tarballs contain a pre-generated copy of this file.
-__version__ = '3.5.0'
+__version__ = '3.5.1'
diff --git a/deeptools/bamPEFragmentSize.py b/deeptools/bamPEFragmentSize.py
old mode 100644
new mode 100755
index b72af8b90..646b51cae
--- a/deeptools/bamPEFragmentSize.py
+++ b/deeptools/bamPEFragmentSize.py
@@ -341,7 +341,7 @@ def main(args=None):
if args.plotFileFormat == 'plotly':
fig = go.Figure()
- fig['data'] = data
+ fig.add_traces(data)
fig['layout']['yaxis1'].update(title='Frequency')
fig['layout']['xaxis1'].update(title='Fragment Length')
fig['layout'].update(title=args.plotTitle)
diff --git a/deeptools/computeGCBias.py b/deeptools/computeGCBias.py
old mode 100644
new mode 100755
index d5d9a326d..0e2309161
--- a/deeptools/computeGCBias.py
+++ b/deeptools/computeGCBias.py
@@ -571,7 +571,7 @@ def plotlyGCbias(file_name, frequencies, reads_per_gc, region_size):
x = np.linspace(0, 1, frequencies.shape[0])
trace = go.Scatter(x=x, y=np.log2(frequencies[:, 2]), xaxis='x2', yaxis='y2', showlegend=False, line=dict(color='rgb(107,174,214)'))
data.append(trace)
- fig['data'] = data
+ fig.add_traces(data)
fig['layout']['annotations'] = annos
py.plot(fig, filename=file_name, auto_open=False)
diff --git a/deeptools/computeMatrixOperations.py b/deeptools/computeMatrixOperations.py
index 2212dd1f8..deb62076c 100755
--- a/deeptools/computeMatrixOperations.py
+++ b/deeptools/computeMatrixOperations.py
@@ -73,7 +73,7 @@ def parse_arguments():
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
parents=[infoArgs(), relabelArgs()],
help="Change sample and/or group label information",
- usage='An example usage is:\n computeMatrixOperations relabel -m input.mat.gz -o output.mat.gz --samples "sample 1" "sample 2"\n\n')
+ usage='An example usage is:\n computeMatrixOperations relabel -m input.mat.gz -o output.mat.gz --sampleLabels "sample 1" "sample 2"\n\n')
# subset
subparsers.add_parser(
@@ -795,10 +795,9 @@ def main(args=None):
hm = heatmapper.heatmapper()
if not isinstance(args.matrixFile, list):
hm.read_matrix_file(args.matrixFile)
-
if args.command == 'info':
printInfo(hm)
- if args.command == 'dataRange':
+ elif args.command == 'dataRange':
printDataRange(hm)
elif args.command == 'subset':
sIdx = getSampleBounds(args, hm)
diff --git a/deeptools/correlation.py b/deeptools/correlation.py
old mode 100644
new mode 100755
index 8b27323c2..18fdbfcfd
--- a/deeptools/correlation.py
+++ b/deeptools/correlation.py
@@ -1,5 +1,6 @@
import sys
import itertools
+import copy
import numpy as np
import scipy.cluster.hierarchy as sch
import scipy.stats
@@ -291,7 +292,7 @@ def plot_correlation(self, plot_filename, plot_title='', vmax=None,
link_color_func=lambda k: 'darkred')
axdendro.set_xticks([])
axdendro.set_yticks([])
- cmap = plt.get_cmap(colormap)
+ cmap = copy.copy(plt.get_cmap(colormap))
# this line simply makes a new cmap, based on the original
# colormap that goes from 0.0 to 0.9
@@ -421,7 +422,7 @@ def plotly_scatter(self, plot_filename, corr_matrix, plot_title='', minXVal=None
data[-1]['colorbar'].update(title="log10(instances per bin)", titleside="right")
data[-1].update(showscale=True)
- fig['data'] = data
+ fig.add_traces(data)
fig['layout'].update(title=plot_title, showlegend=False, annotations=annos)
offline.plot(fig, filename=plot_filename, auto_open=False)
@@ -588,7 +589,7 @@ def plotly_pca(self, plotFile, Wt, pvar, PCs, eigenvalues, cols, plotTitle):
annos.append({'yanchor': 'bottom', 'xref': 'paper', 'xanchor': 'center', 'yref': 'paper', 'text': 'PCA', 'y': 1.0, 'x': 0.25, 'font': {'size': 16}, 'showarrow': False})
annos.append({'yanchor': 'bottom', 'xref': 'paper', 'xanchor': 'center', 'yref': 'paper', 'text': 'Scree plot', 'y': 1.0, 'x': 0.75, 'font': {'size': 16}, 'showarrow': False})
- fig['data'] = data
+ fig.add_traces(data)
fig['layout']['annotations'] = annos
offline.plot(fig, filename=plotFile, auto_open=False)
diff --git a/deeptools/correlation_heatmap.py b/deeptools/correlation_heatmap.py
index 69d7506f2..58dbdfbc0 100644
--- a/deeptools/correlation_heatmap.py
+++ b/deeptools/correlation_heatmap.py
@@ -6,6 +6,7 @@
import scipy.cluster.hierarchy as sch
from matplotlib import rcParams
import matplotlib.colors as pltcolors
+import copy
rcParams['pdf.fonttype'] = 42
rcParams['svg.fonttype'] = 'none'
@@ -43,7 +44,7 @@ def plot_correlation(corr_matrix, labels, plotFileName, vmax=None,
link_color_func=lambda k: 'darkred')
axdendro.set_xticks([])
axdendro.set_yticks([])
- cmap = plt.get_cmap(colormap)
+ cmap = copy.copy(plt.get_cmap(colormap))
# this line simply makes a new cmap, based on the original
# colormap that goes from 0.0 to 0.9
diff --git a/deeptools/plotCoverage.py b/deeptools/plotCoverage.py
old mode 100644
new mode 100755
index de6f7cdcb..02ce25dad
--- a/deeptools/plotCoverage.py
+++ b/deeptools/plotCoverage.py
@@ -320,7 +320,7 @@ def main(args=None):
# Don't clip plots
y_max = max(y_max)
if args.plotFileFormat == "plotly":
- fig['data'] = data
+ fig.add_traces(data)
fig['layout']['yaxis1'].update(range=[0.0, min(1, y_max + (y_max * 0.10))])
fig['layout']['yaxis2'].update(range=[0.0, 1.0])
py.plot(fig, filename=args.plotFile, auto_open=False)
diff --git a/deeptools/plotEnrichment.py b/deeptools/plotEnrichment.py
old mode 100644
new mode 100755
index b6baab8d7..7ef474eff
--- a/deeptools/plotEnrichment.py
+++ b/deeptools/plotEnrichment.py
@@ -440,7 +440,7 @@ def plotEnrichment(args, featureCounts, totalCounts, features):
ax.set_ylim(0.0, 100.0)
if args.plotFileFormat == 'plotly':
- fig['data'] = data
+ fig.add_traces(data)
py.plot(fig, filename=args.plotFile, auto_open=False)
# colors
else:
diff --git a/deeptools/plotFingerprint.py b/deeptools/plotFingerprint.py
old mode 100644
new mode 100755
index f1f118fa4..4aee5b470
--- a/deeptools/plotFingerprint.py
+++ b/deeptools/plotFingerprint.py
@@ -202,10 +202,10 @@ def getCHANCE(args, idx, mat):
"""
# Get the index of the reference sample
if args.JSDsample not in args.bamfiles:
- return ["NA", "NA", "NA"]
+ return [np.NAN, np.NAN, np.NAN]
refIdx = args.bamfiles.index(args.JSDsample)
if refIdx == idx:
- return ["NA", "NA", "NA"]
+ return [np.NAN, np.NAN, np.NAN]
subMatrix = np.copy(mat[:, [idx, refIdx]])
subMatrix[np.isnan(subMatrix)] = 0
@@ -271,10 +271,10 @@ def getJSD(args, idx, mat):
# Get the index of the reference sample
if args.JSDsample not in args.bamfiles:
- return "NA"
+ return np.NAN
refIdx = args.bamfiles.index(args.JSDsample)
if refIdx == idx:
- return "NA"
+ return np.NAN
# These will hold the coverage histograms
chip = np.zeros(MAXLEN, dtype=np.int)
@@ -338,7 +338,7 @@ def signalAndBinDist(x):
if abs(sum(PMFinput) - 1) > 0.01 or abs(sum(PMFchip) - 1) > 0.01:
sys.stderr.write("Warning: At least one PMF integral is significantly different from 1! The JSD will not be returned")
- return "NA"
+ return np.NAN
# Compute the JSD from the PMFs
M = (PMFinput + PMFchip) / 2.0
@@ -430,7 +430,7 @@ def main(args=None):
if args.plotFileFormat == 'plotly':
fig = go.Figure()
- fig['data'] = data
+ fig.add_traces(data)
fig['layout'].update(title=args.plotTitle)
fig['layout']['xaxis1'].update(title="rank")
fig['layout']['yaxis1'].update(title="fraction w.r.t bin with highest coverage")
diff --git a/deeptools/plotHeatmap.py b/deeptools/plotHeatmap.py
old mode 100644
new mode 100755
index aee0a6280..bc4bbcc2a
--- a/deeptools/plotHeatmap.py
+++ b/deeptools/plotHeatmap.py
@@ -9,17 +9,17 @@
matplotlib.use('Agg')
matplotlib.rcParams['pdf.fonttype'] = 42
matplotlib.rcParams['svg.fonttype'] = 'none'
-from deeptools import cm # noqa: F401
import matplotlib.pyplot as plt
from matplotlib.font_manager import FontProperties
import matplotlib.gridspec as gridspec
from matplotlib import ticker
-
+import copy
import sys
import plotly.offline as py
import plotly.graph_objs as go
# own modules
+from deeptools import cm # noqa: F401
from deeptools import parserCommon
from deeptools import heatmapper
from deeptools.heatmapper_utilities import plot_single, plotly_single
@@ -371,7 +371,7 @@ def plotlyMatrix(hm,
trace.update(zmin=zMinUse, zmax=zMaxUse, colorscale=convertCmap(cmap[0], vmin=zMinUse, vmax=zMaxUse))
dataSummary.extend(dataHeatmap)
- fig['data'] = dataSummary
+ fig.add_traces(dataSummary)
fig['layout']['annotations'] = annos
py.plot(fig, filename=outFilename, auto_open=False)
@@ -477,7 +477,8 @@ def plotMatrix(hm, outFileName,
if colorMapDict['colorMap']:
cmap = []
for color_map in colorMapDict['colorMap']:
- cmap.append(plt.get_cmap(color_map))
+ copy_cmp = copy.copy(plt.get_cmap(color_map))
+ cmap.append(copy_cmp)
cmap[-1].set_bad(colorMapDict['missingDataColor']) # nans are printed using this color
if colorMapDict['colorList'] and len(colorMapDict['colorList']) > 0:
@@ -529,7 +530,6 @@ def plotMatrix(hm, outFileName,
else:
color_list = cmap_plot(np.arange(numgroups) / numgroups)
alpha = colorMapDict['alpha']
-
if image_format == 'plotly':
return plotlyMatrix(hm,
outFileName,
@@ -735,7 +735,7 @@ def plotMatrix(hm, outFileName,
col = sample
ax = fig.add_subplot(grids[-1, col])
tick_locator = ticker.MaxNLocator(nbins=3)
- cbar = fig.colorbar(img, cax=ax, alpha=alpha, orientation='horizontal', ticks=tick_locator)
+ cbar = fig.colorbar(img, cax=ax, orientation='horizontal', ticks=tick_locator)
labels = cbar.ax.get_xticklabels()
ticks = cbar.ax.get_xticks()
if ticks[0] == 0:
@@ -759,7 +759,7 @@ def plotMatrix(hm, outFileName,
grid_start = 0
ax = fig.add_subplot(grids[grid_start:, -1])
- fig.colorbar(img, cax=ax, alpha=alpha)
+ fig.colorbar(img, cax=ax)
if box_around_heatmaps:
plt.subplots_adjust(wspace=0.10, hspace=0.025, top=0.85, bottom=0, left=0.04, right=0.96)
@@ -767,7 +767,7 @@ def plotMatrix(hm, outFileName,
# When no box is plotted the space between heatmaps is reduced
plt.subplots_adjust(wspace=0.05, hspace=0.01, top=0.85, bottom=0, left=0.04, right=0.96)
- plt.savefig(outFileName, bbox_inches='tight', pdd_inches=0, dpi=dpi, format=image_format)
+ plt.savefig(outFileName, bbox_inches='tight', pad_inches=0.1, dpi=dpi, format=image_format)
plt.close()
diff --git a/deeptools/plotProfile.py b/deeptools/plotProfile.py
index e953e4550..b46be32bb 100755
--- a/deeptools/plotProfile.py
+++ b/deeptools/plotProfile.py
@@ -99,7 +99,7 @@ def __init__(self, hm, out_file_name,
plot_type='lines',
image_format=None,
color_list=None,
- legend_location='auto',
+ legend_location='best',
plots_per_row=8,
label_rotation=0,
dpi=200):
@@ -454,7 +454,7 @@ def plotly_hexbin(self):
for trace in data:
trace.update(zmin=vmin, zmax=vmax)
- fig['data'] = data
+ fig.add_traces(data)
fig['layout']['annotations'] = annos
py.plot(fig, filename=self.out_file_name, auto_open=False)
@@ -668,7 +668,7 @@ def plotly_heatmap(self):
zmaxUse = self.y_max[i % len(self.y_max)]
trace.update(zmin=zminUse, zmax=zmaxUse)
- fig['data'] = data
+ fig.add_traces(data)
fig['layout']['annotations'] = annos
py.plot(fig, filename=self.out_file_name, auto_open=False)
@@ -828,15 +828,16 @@ def plotly_profile(self):
yMin = None
yMax = None
for i in range(self.numplots):
- row = rows - i / self.plots_per_row - 1
+ row = np.floor(i / self.plots_per_row)
+ # row = rows - i / self.plots_per_row - 1
col = i % self.plots_per_row
xanchor = 'x{}'.format(i + 1)
yanchor = 'y{}'.format(i + 1)
base = row * (domainHeight + bufferHeight)
domain = [base, base + domainHeight]
titleY = base + domainHeight
- base = col * (domainWidth + bufferWidth)
fig['layout']['yaxis{}'.format(i + 1)] = {'domain': domain, 'title': self.y_axis_label, 'anchor': xanchor, 'autorange': False}
+ base = col * (domainWidth + bufferWidth)
domain = [base, base + domainWidth]
titleX = base + 0.5 * domainWidth
fig['layout']['xaxis{}'.format(i + 1)] = {'domain': domain, 'anchor': yanchor}
@@ -900,7 +901,7 @@ def plotly_profile(self):
yRange[1] = self.y_max[i % len(self.y_max)]
fig['layout'][yaxis].update(range=yRange)
- fig['data'] = data
+ fig.add_traces(data)
fig['layout']['annotations'] = annos
py.plot(fig, filename=self.out_file_name, auto_open=False)
diff --git a/deeptools/utilities.py b/deeptools/utilities.py
old mode 100644
new mode 100755
index b0ae27631..64cc7a75c
--- a/deeptools/utilities.py
+++ b/deeptools/utilities.py
@@ -41,7 +41,7 @@ def convertCmap(c, vmin=0, vmax=1):
h = 1.0 / 254
colorScale = []
for k in range(255):
- C = map(np.uint8, np.array(cmap(k * h)[:3]) * 255)
+ C = list(map(np.uint8, np.array(cmap(k * h)[:3]) * 255))
colorScale.append([k * h, 'rgb' + str((C[0], C[1], C[2]))])
return colorScale
diff --git a/galaxy/wrapper/computeMatrixOperations.xml b/galaxy/wrapper/computeMatrixOperations.xml
old mode 100644
new mode 100755
index 40ebbccf1..2d996e910
--- a/galaxy/wrapper/computeMatrixOperations.xml
+++ b/galaxy/wrapper/computeMatrixOperations.xml
@@ -74,6 +74,7 @@
#else if $submodule.command == "dataRange":
dataRange
-m $submodule.matrixFile
+ > $outFileTxt
#end if
]]>
@@ -159,7 +160,6 @@
-
diff --git a/galaxy/wrapper/deepTools_macros.xml b/galaxy/wrapper/deepTools_macros.xml
index 6cc2547fc..38a6f8e02 100755
--- a/galaxy/wrapper/deepTools_macros.xml
+++ b/galaxy/wrapper/deepTools_macros.xml
@@ -1,10 +1,10 @@
--numberOfProcessors "\${GALAXY_SLOTS:-4}"
- 3.5.0.0
+ 3.5.1.0
- deeptools
+ deeptools
samtools
diff --git a/galaxy/wrapper/test-data/bamPEFragmentSize_result1.txt b/galaxy/wrapper/test-data/bamPEFragmentSize_result1.txt
index 6d37c2a1b..95115e2f5 100644
--- a/galaxy/wrapper/test-data/bamPEFragmentSize_result1.txt
+++ b/galaxy/wrapper/test-data/bamPEFragmentSize_result1.txt
@@ -12,7 +12,7 @@ Median: 242.0
Max.: 251.0
Std: 4.496912521077347
MAD: 1.0
-Len. 10%: 241.20000000000002
+Len. 10%: 241.2
Len. 20%: 241.4
Len. 30%: 241.6
Len. 40%: 241.8
diff --git a/galaxy/wrapper/test-data/bamPEFragmentSize_table1.txt b/galaxy/wrapper/test-data/bamPEFragmentSize_table1.txt
index 88ffc4adf..0b0e47004 100644
--- a/galaxy/wrapper/test-data/bamPEFragmentSize_table1.txt
+++ b/galaxy/wrapper/test-data/bamPEFragmentSize_table1.txt
@@ -1,2 +1,2 @@
Frag. Sampled Frag. Len. Min. Frag. Len. 1st. Qu. Frag. Len. Mean Frag. Len. Median Frag. Len. 3rd Qu. Frag. Len. Max Frag. Len. Std. Frag. Med. Abs. Dev. Frag. Len. 10% Frag. Len. 20% Frag. Len. 30% Frag. Len. 40% Frag. Len. 60% Frag. Len. 70% Frag. Len. 80% Frag. Len. 90% Frag. Len. 99% Reads Sampled Read Len. Min. Read Len. 1st. Qu. Read Len. Mean Read Len. Median Read Len. 3rd Qu. Read Len. Max Read Len. Std. Read Med. Abs. Dev. Read Len. 10% Read Len. 20% Read Len. 30% Read Len. 40% Read Len. 60% Read Len. 70% Read Len. 80% Read Len. 90% Read Len. 99%
-bowtie2 test1.bam 3 241.0 241.5 244.66666666666666 242.0 246.5 251.0 4.496912521077347 1.0 241.20000000000002 241.4 241.6 241.8 243.8 245.6 247.4 249.2 250.82 3 251.0 251.0 251.0 251.0 251.0 251.0 0.0 0.0 251.0 251.0 251.0 251.0 251.0 251.0 251.0 251.0 251.0
+bowtie2 test1.bam 3 241.0 241.5 244.66666666666666 242.0 246.5 251.0 4.496912521077347 1.0 241.2 241.4 241.6 241.8 243.8 245.6 247.4 249.2 250.82 3 251.0 251.0 251.0 251.0 251.0 251.0 0.0 0.0 251.0 251.0 251.0 251.0 251.0 251.0 251.0 251.0 251.0
diff --git a/galaxy/wrapper/test-data/plotFingerprint_quality_metrics.tabular b/galaxy/wrapper/test-data/plotFingerprint_quality_metrics.tabular
index 1a5bb2d70..f2e160882 100644
--- a/galaxy/wrapper/test-data/plotFingerprint_quality_metrics.tabular
+++ b/galaxy/wrapper/test-data/plotFingerprint_quality_metrics.tabular
@@ -1,3 +1,3 @@
Sample AUC Synthetic AUC X-intercept Synthetic X-intercept Elbow Point Synthetic Elbow Point JS Distance Synthetic JS Distance % genome enriched diff. enrichment CHANCE divergence
-bowtie2 test1.bam 0.00493632029863651 0.481650684757865 0.984443061605476 1.1531044350267195e-24 0.9849408836341008 0.5232688298112538 NA 0.26900449806812143 NA NA NA
-bowtie2 test1.bam 0.00493632029863651 0.481650684757865 0.984443061605476 1.1531044350267195e-24 0.9849408836341008 0.5232688298112538 0.0 0.26900449806812143 0 0 0
+bowtie2 test1.bam 0.00493632029863651 0.481650684757865 0.984443061605476 1.1531044350267195e-24 0.9849408836341008 0.5232688298112538 nan 0.2690044980681214 nan nan nan
+bowtie2 test1.bam 0.00493632029863651 0.481650684757865 0.984443061605476 1.1531044350267195e-24 0.9849408836341008 0.5232688298112538 0.0 0.2690044980681214 0 0 0
diff --git a/galaxy/wrapper/test-data/plotPCA_result2.tabular b/galaxy/wrapper/test-data/plotPCA_result2.tabular
index ebdc6ff74..f2b79eed3 100644
--- a/galaxy/wrapper/test-data/plotPCA_result2.tabular
+++ b/galaxy/wrapper/test-data/plotPCA_result2.tabular
@@ -1,4 +1,4 @@
#plotPCA --outFileNameData
Component bowtie2-test1.bam bowtie2-test1.bam Eigenvalue
1 -0.7071067811865476 -0.7071067811865475 4.0
-2 -0.7071067811865475 0.7071067811865476 1.2325951644078315e-32
+2 -0.7071067811865475 0.7071067811865476 2.49319462166397e-32
diff --git a/requirements.txt b/requirements.txt
old mode 100644
new mode 100755
index 5ddfb47df..d84bd4c31
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,9 +1,9 @@
numpy>=1.9.0
scipy>=0.17.0
-matplotlib>=3.1.0
+matplotlib>=3.3.0
pysam>=0.14.0
py2bit>=0.2.0
numpydoc>=0.5
pyBigWig>=0.2.1
-plotly>=2.0.0
+plotly>=4.9
deeptoolsintervals>=0.1.8
diff --git a/setup.py b/setup.py
index 5c2fb94d7..c926ac0b3 100755
--- a/setup.py
+++ b/setup.py
@@ -84,12 +84,12 @@ def openREADME():
install_requires=[
"numpy >= 1.9.0",
"scipy >= 0.17.0",
- "matplotlib >= 3.1.0",
+ "matplotlib >= 3.3.0",
"pysam >= 0.14.0",
"numpydoc >= 0.5",
"pyBigWig >= 0.2.1",
"py2bit >= 0.2.0",
- "plotly >= 2.0.0",
+ "plotly >= 4.9",
"deeptoolsintervals >= 0.1.8"
],
zip_safe=True,