Skip to content
Snippets Groups Projects
Commit ccd96b4c authored by Kedi Cao's avatar Kedi Cao
Browse files

clear notebook output

parent 0b5ebc9d
No related merge requests found
Hide whitespace changes
Inline Side-by-side
snakemodules/notebooks/read_numbers_in_bar_graph.py.ipynb
+ 2
− 71
View file @ ccd96b4c
%% Cell type:code id:e346a6bb-0831-404d-9a4c-b7e8fa48c426 tags:
``` python
pip show ipython
```
%% Output
Name: ipython
Version: 9.0.0
Summary: IPython: Productive Interactive Computing
Home-page: https://ipython.org
Author: The IPython Development Team
Author-email: ipython-dev@python.org
License: BSD-3-Clause
Location: /home/kedic/workflow_dev/popinSnake/.snakemake/conda/69c6e6c50cd0e118bb8c803e51bd5c48_/lib/python3.12/site-packages
Requires: decorator, ipython-pygments-lexers, jedi, matplotlib-inline, pexpect, prompt_toolkit, pygments, stack_data, traitlets
Required-by: ipykernel, ipywidgets, jupyter-console
Note: you may need to restart the kernel to use updated packages.
%% Cell type:code id:8f2c7f1e tags:
``` python
%load_ext autoreload
%autoreload 2
```
%% Output
---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call last)
File ~/workflow_dev/popinSnake/.snakemake/conda/69c6e6c50cd0e118bb8c803e51bd5c48_/lib/python3.12/site-packages/IPython/core/extensions.py:62, in ExtensionManager.load_extension(self, module_str)
61 try:
---> 62 return self._load_extension(module_str)
63 except ModuleNotFoundError:
File ~/workflow_dev/popinSnake/.snakemake/conda/69c6e6c50cd0e118bb8c803e51bd5c48_/lib/python3.12/site-packages/IPython/core/extensions.py:77, in ExtensionManager._load_extension(self, module_str)
76 if module_str not in sys.modules:
---> 77 mod = import_module(module_str)
78 mod = sys.modules[module_str]
File ~/workflow_dev/popinSnake/.snakemake/conda/69c6e6c50cd0e118bb8c803e51bd5c48_/lib/python3.12/importlib/__init__.py:90, in import_module(name, package)
89 level += 1
---> 90 return _bootstrap._gcd_import(name[level:], package, level)
File <frozen importlib._bootstrap>:1387, in _gcd_import(name, package, level)
File <frozen importlib._bootstrap>:1360, in _find_and_load(name, import_)
File <frozen importlib._bootstrap>:1324, in _find_and_load_unlocked(name, import_)
ModuleNotFoundError: No module named 'autoreload'
During handling of the above exception, another exception occurred:
ModuleNotFoundError Traceback (most recent call last)
Cell In[6], line 1
----> 1 get_ipython().run_line_magic('load_ext', 'autoreload')
2 get_ipython().run_line_magic('autoreload', '2')
File ~/workflow_dev/popinSnake/.snakemake/conda/69c6e6c50cd0e118bb8c803e51bd5c48_/lib/python3.12/site-packages/IPython/core/interactiveshell.py:2478, in InteractiveShell.run_line_magic(self, magic_name, line, _stack_depth)
2476 kwargs['local_ns'] = self.get_local_scope(stack_depth)
2477 with self.builtin_trap:
-> 2478 result = fn(*args, **kwargs)
2480 # The code below prevents the output from being displayed
2481 # when using magics with decorator @output_can_be_silenced
2482 # when the last Python token in the expression is a ';'.
2483 if getattr(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, False):
File ~/workflow_dev/popinSnake/.snakemake/conda/69c6e6c50cd0e118bb8c803e51bd5c48_/lib/python3.12/site-packages/IPython/core/magics/extension.py:33, in ExtensionMagics.load_ext(self, module_str)
31 if not module_str:
32 raise UsageError('Missing module name.')
---> 33 res = self.shell.extension_manager.load_extension(module_str)
35 if res == 'already loaded':
36 print("The %s extension is already loaded. To reload it, use:" % module_str)
File ~/workflow_dev/popinSnake/.snakemake/conda/69c6e6c50cd0e118bb8c803e51bd5c48_/lib/python3.12/site-packages/IPython/core/extensions.py:66, in ExtensionManager.load_extension(self, module_str)
64 if module_str in BUILTINS_EXTS:
65 BUILTINS_EXTS[module_str] = True
---> 66 return self._load_extension("IPython.extensions." + module_str)
67 raise
File ~/workflow_dev/popinSnake/.snakemake/conda/69c6e6c50cd0e118bb8c803e51bd5c48_/lib/python3.12/site-packages/IPython/core/extensions.py:77, in ExtensionManager._load_extension(self, module_str)
75 with self.shell.builtin_trap:
76 if module_str not in sys.modules:
---> 77 mod = import_module(module_str)
78 mod = sys.modules[module_str]
79 if self._call_load_ipython_extension(mod):
File ~/workflow_dev/popinSnake/.snakemake/conda/69c6e6c50cd0e118bb8c803e51bd5c48_/lib/python3.12/importlib/__init__.py:90, in import_module(name, package)
88 break
89 level += 1
---> 90 return _bootstrap._gcd_import(name[level:], package, level)
File <frozen importlib._bootstrap>:1387, in _gcd_import(name, package, level)
File <frozen importlib._bootstrap>:1360, in _find_and_load(name, import_)
File <frozen importlib._bootstrap>:1331, in _find_and_load_unlocked(name, import_)
File <frozen importlib._bootstrap>:935, in _load_unlocked(spec)
File <frozen importlib._bootstrap_external>:999, in exec_module(self, module)
File <frozen importlib._bootstrap>:488, in _call_with_frames_removed(f, *args, **kwds)
File ~/workflow_dev/popinSnake/.snakemake/conda/69c6e6c50cd0e118bb8c803e51bd5c48_/lib/python3.12/site-packages/IPython/extensions/autoreload.py:110
108 from IPython.core import magic_arguments
109 from IPython.core.magic import Magics, magics_class, line_magic
--> 110 from IPython.extensions.deduperreload.deduperreload import DeduperReloader
112 __skip_doctest__ = True
114 # -----------------------------------------------------------------------------
115 # Copyright (C) 2000 Thomas Heller
116 # Copyright (C) 2008 Pauli Virtanen <pav@iki.fi>
(...) 127 # Imports
128 # -----------------------------------------------------------------------------
ModuleNotFoundError: No module named 'IPython.extensions.deduperreload'
%% Cell type:code id:5ebc1c0a-0d55-430e-988f-ea6521abcfdb tags:
``` python
```
%% Cell type:code id:e9cb92ab-fc91-4311-a745-3a03e0fbde3c tags:
``` python
import os
import sys
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
```
%% Cell type:code id:f9489982 tags:
``` python
# If executing with snakemake, use the path below
sys.path.append(snakemake.config["WORKFLOW_PATH"]+'/snakemodules/notebooks/src/')
# If executing directly with jupyter notebook from the commandline, use the path below
# sys.path.append(os.getcwd()+'/src/')
from stat_func import calculator
from stat_func import visualization
%matplotlib inline
```
%% Cell type:code id:6d70671b tags:
``` python
fastq1 = snakemake.input.paired1
#fastq2 = snakemake.input.paired2
single = snakemake.input.single
```
%% Cell type:code id:48567039 tags:
``` python
read_paired_fq,sample_names = visualization.fastq_read_num(fastq1)
read_single_fq,sample_names = visualization.fastq_read_num(single)
```
%% Cell type:code id:93a00353-0770-4e90-8cd5-a916b9d08625 tags:
``` python
```
%% Cell type:code id:2dc4651c tags:
``` python
df = pd.DataFrame()
df['samples']=sample_names
df['read_number_paired']=calculator.double(read_paired_fq)
df['read_number_single']=read_single_fq
df['total'] = df['read_number_paired']+df['read_number_single']
read_data = df.sort_values(by=['samples'])
```
%% Cell type:code id:d9b63e80 tags:
``` python
```
%% Cell type:code id:80f28248 tags:
``` python
sns.set_theme(style="whitegrid")
# Initialize the matplotlib figure
f, ax = plt.subplots(figsize=(3, 6))
# Plot the total reads
sns.set_color_codes("pastel")
sns.barplot(x="samples", y="total", data=read_data,
label="paired reads", color="b")
# Plot the total single reads
sns.set_color_codes("muted")
sns.barplot(x="samples", y="read_number_single", data=read_data,
label="single reads", color="b")
sns.set(font_scale = 1)
# Add a legend and informative axis label
ax.legend(bbox_to_anchor=(1.02, 1),loc="upper left", borderaxespad=0)
plt.xticks(rotation=90)
ax.set(ylabel="read numbers",
xlabel="genomes")
sns.despine(left=True, bottom=True)
plt.savefig(snakemake.output[0], dpi=300, format="pdf", bbox_inches = 'tight')
read_data.to_csv(snakemake.output[1], sep='\t', index=False)
# plt.show()
```
%% Cell type:code id:d18c4eaa tags:
``` python
```
%% Cell type:code id:4913e41e tags:
``` python
```
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment