I want to show the graph using the python code below, but I am getting a syntax error as seen on the image. Please help to correct this error. I am using Python 3
import os
import sys
import fnss
import networkx as nx
import fnss
import cvxopt
import numpy as np
import codecs
import random
import matplotlib.pyplot as plt
topo_str = 'topo_peter.xml'
topology = fnss.read_topology(topo_str)
topology_directed = topology.to_directed(topology)
print nx.info(topology_directed)
nx.draw(topology_directed)
plt.show()
and this is the am getting
File "<ipython-input-1-fa7157dd7268>", line 14
print nx.info(topology_directed)
^
SyntaxError: invalid syntax
Based on the information provided:
Python version: 3
Error message: invalid syntax on line 14 -> print nx.info(topology_directed)
It is clearly a simple syntax error for people using Python 3 to execute a Python 2 statement.
print "something" # is valid for Python 2, but not Python 3
For Python 3, use
print("something", "and more", "even more")
So changing print nx.info(topology_directed) to print(nx.info(topology_directed)) solves the problem.
Related
I am getting an error when I am going to read a VCF file using scikit-allel library inside a docker image and os ubuntu 18.04. It shows that
raise RuntimeError('VCF file is missing mandatory header line ("#CHROM...")')
RuntimeError: VCF file is missing mandatory header line ("#CHROM...")
But in the VCF file is well-formatted.
Here is my code of how I applied :
import pandas as pd
import os
import numpy as np
import allel
import tkinter as tk
from tkinter import filedialog
import matplotlib.pyplot as plt
from scipy.stats import norm
GenomeVariantsInput = allel.read_vcf('quartet_variants_annotated.vcf', samples=['ISDBM322015'],fields=[ 'variants/CHROM', 'variants/ID', 'variants/REF',
'variants/ALT','calldata/GT'])
version what Installed :
Python 3.6.9
Numpy 1.19.5
pandas 1.1.5
scikit-allel 1.3.5
You need to add a line like this in the first:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
but it's not static for all of the files, you have to make a Header like above for your file. (I suggest try this header first and if it's got error then customize it)
I saw there is a way to directly read XML files using pandas. I followed and used this package. However, I keep getting errors.
https://pypi.org/project/pandas-read-xml/
import pandas as pd
import pandas_read_xml as pdx
from pandas.io.json import json_normalize
The error was generated by last line and the error is
ImportError: cannot import name 'json_normalize'
I am using kernel python 3, can anyone tell me what was wrong with it?
import plotly.express as px
import matplotlib
import matplotlib.pyplot as plt
import seaborn as sns
%matplotlib inline
I imported these libraries and used %matplotlib inline . The code runs fine but the terminal in vs code shows the error :
Syntax Error: invalid syntax
I found an answer to use %matplotlibinline in VS Code
# Suppress matplotlib user warnings
# Necessary for newer version of matplotlib
import warnings
warnings.filterwarnings("ignore", category = UserWarning, module = "matplotlib")
#
# Display inline matplotlib plots with IPython
from IPython import get_ipython
get_ipython().run_line_magic('matplotlib', 'inline')
%matplotlib inline is not a valid python command. This has a specific meaning when used in ipython/jupyter.
I am getting an error:
"OptionError: 'You can only set the value of existing options'"
after using the below code, please can someone help?
### Data Analaysis
import numpy as np
import pandas as pd
### Data Visualization
import matplotlib.pyplot as plt
import seaborn as sns
import plotly.graph_objs as go
import plotly.express as px
from plotly.subplots import make_subplots
from scipy.interpolate import make_interp_spline, BSpline
%matplotlib inline
import warnings
warnings.simplefilter(action='ignore', category=Warning)
pd.set_option('display.max_columns', None)
pd.options.plotting.backend = "plotly"
The option error "you can only set the value of existing options" are coming because of your last line of script
pd.options.plotting.backend = "plotly"
where you are trying to update your pandas backend plotting method.
Please update your pandas and plotly packages. Because it only works with pandas version>=0.25 and plotly version>=4.8.
So update both the packages, restart your kernel, if you are working on Jupyter notebook. For upgrading the packages
pip install -U pandas
pip install -U plotly
Whenever I try to run the following code I get an error message
import matplotlib
import pandas as pd
import _pickle as pickle
import numpy as np
print(matplotlib.version)
AttributeError: module 'matplotlib' has no attribute 'version'
I get the same error if i try this: matplotlib.style.use('bmh')
I'm using PyCharm
The errors are stating those attributes do not exist. It is not a problem of the installation.
To get the version:
print(matplotlib.__version__)
Regarding the style:
You do not "apply" that in matplotlib. You may want to use the module pyplot:
import matplotlib.pyplot as plt
plt.style.use("bmh")