Related
I am trying to download a csv file to python. For some reason I can not do it. I suppose I need to add an additional argument to read_csv?
import pandas as pd
url = "https://raw.githubusercontent.com/UofGAnalyticsData/"\
"DPIP/main/assesment_datasets/assessment3/starwars.csv"
df = pd.read_csv(url)
The code you attempt is downloading the content from the url and pasting it in the data frame named 'df'.
You need to save the output csv by using the following line. You will find the output file in the same directory where the python script is saved.
import pandas as pd
url = "https://raw.githubusercontent.com/UofGAnalyticsData/"\
"DPIP/main/assesment_datasets/assessment3/starwars.csv"
df = pd.read_csv(url)
df.to_csv('output.csv')
I want a solution for reading the csv file and redirect the link present inside csv file
I want solution in any programming language.
Firstly csv file should be read which consists of links
Then it should be able to redirect to the links
Using python, we can use the pandas and urllib to get your requirement working.
Example:
import pandas as pd
from urllib.request import urlopen
df = pd.read_csv("<your_filename>", index_col=None)
for index, row in df.iterrows():
urlopen(row["<column_name_containing_links>"])
I want to read in an .dta file as a pandas data frame.
I've tried using code from https://www.fragilefamilieschallenge.org/using-dta-files-in-python/ but it gives me an error.
Thanks for any help!
import pandas as pd
df_path = "https://zenodo.org/record/3635384/files/B-PROACT1V%20Year%204%20%26%206%20child%20BP%2C%20BMI%20and%20PA%20dataset.dta?download=1"
df = None
with open(df_path, "r") as f:
df = pd.read_stata(f)
print df.head()
open can be used when you have a file saved locally on your machine. With pd.read_stata this is not necessary however, as you can specify the file path directly as a parameter.
In this case you want to read in a .dta file from a url so this does not apply. The solution is simple though, as pd.read_stata can read in files from urls directly.
import pandas as pd
url = 'https://zenodo.org/record/3635384/files/B-PROACT1V%20Year%204%20%26%206%20child%20BP%2C%20BMI%20and%20PA%20dataset.dta?download=1'
df = pd.read_stata(url)
My code:
import xlrd
wb = xlrd.open_workbook("Z:\\Data\\Locates\\3.8 locates.xls")
sh = wb.sheet_by_index(0)
print sh.cell(0,0).value
The error:
Traceback (most recent call last):
File "Z:\Wilson\tradedStockStatus.py", line 18, in <module>
wb = xlrd.open_workbook("Z:\\Data\\Locates\\3.8 locates.xls")
File "C:\Python27\lib\site-packages\xlrd\__init__.py", line 429, in open_workbook
biff_version = bk.getbof(XL_WORKBOOK_GLOBALS)
File "C:\Python27\lib\site-packages\xlrd\__init__.py", line 1545, in getbof
bof_error('Expected BOF record; found %r' % self.mem[savpos:savpos+8])
File "C:\Python27\lib\site-packages\xlrd\__init__.py", line 1539, in bof_error
raise XLRDError('Unsupported format, or corrupt file: ' + msg)
xlrd.biffh.XLRDError: Unsupported format, or corrupt file: Expected BOF record;
found '<table r'"
The file doesn't seem to be corrupted or of a different format.
Anything to help find the source of the issue would be great.
Try to open it as an HTML with pandas:
import pandas as pd
data = pd.read_html('filename.xls')
Or try any other html python parser.
That's not a proper excel file, but an html readable with excel.
You say:
The file doesn't seem to be corrupted or of a different format.
However as the error message says, the first 8 bytes of the file are '<table r' ... that is definitely not Excel .xls format. Open it with a text editor (e.g. Notepad) that won't take any notice of the (incorrect) .xls extension and see for yourself.
This will happen to some files while also open in Excel.
I had a similar problem and it was related to the version. In a python terminal check:
>> import xlrd
>> xlrd.__VERSION__
If you have '0.9.0' you can open almost all files. If you have '0.6.0' which was what I found on Ubuntu, you may have problems with newest Excel files. You can download the latest version of xlrd using the Distutils standard.
I found the similar problem when downloading .xls file and opened it using xlrd library. Then I tried out the solution of converting .xls into .xlsx as detailed here: how to convert xls to xlsx
It works like a charm and rather than opening .xls, I am working with .xlsx file now using openpyxl library.
Hope it helps to solve your issue.
I had faced the same xlrd.biffh.XLRDError: Unsupported format, or corrupt file: Expected BOF record; error and solved it by writing an XML to XLSX converter. The reason is that actually, xlrd does not support XML Spreadsheet (*.xml) i.e. NOT in XLS or XLSX format.
import pandas as pd
from bs4 import BeautifulSoup
def convert_to_xlsx():
with open('sample.xls') as xml_file:
soup = BeautifulSoup(xml_file.read(), 'xml')
writer = pd.ExcelWriter('sample.xlsx')
for sheet in soup.findAll('Worksheet'):
sheet_as_list = []
for row in sheet.findAll('Row'):
sheet_as_list.append([cell.Data.text if cell.Data else '' for cell in row.findAll('Cell')])
pd.DataFrame(sheet_as_list).to_excel(writer, sheet_name=sheet.attrs['ss:Name'], index=False, header=False)
writer.save()
In my case, after opening the file with a text editor as #john-machin suggested, I realized the file is not encrypted as an Excel file is supposed to but it's in the CSV format and was saved as an Excel file. What I did was renamed the file and its extension and used read_csv function instead:
os.rename('sample_file.xls', 'sample_file.csv')
csv = pd.read_csv("sample_file.csv", error_bad_lines=False)
It may be an old excel file format. It can be read as html in pandas via
import pandas as pd
df = pd.read_html('file.xls')
Eventually, this gives a list of dataframes (if you check the type is a list). https://pandas.pydata.org/pandas-docs/version/0.17.1/io.html#io-read-html
You need to extract them, for instance with df[0]
I met this problem too.I opened this file by excel and saved it as other formats such as excel 97-2003 and finally I solved this problem
I had the same issue. Those old files are formatted like a tab-delimited file. I've been able to open my problem files with read_table; ie df = pd.read_table('trouble_maker.xls').
I got this error when I tried to read some XLSX files from a folder and that one of the files was opened. I closed the XLSX file and this error did not show up.
Try this It worked for me.
import pandas as pd
data = pd.read_csv('filename.xls')
I just downloaded xlrd, created an excel document (excel 2007) for testing and got the same error (message says 'found PK\x03\x04\x14\x00\x06\x00'). Extension is a xlsx. Tried saving it to an older .xls format and error disappears .....
I meet the same problem.
it lies in the .xls file itself - it looks like an Excel file however it isn't. (see if there's a pop up when you plainly open the .xls from Excel)
sjmachin commented on Jan 19, 2013 from https://github.com/python-excel/xlrd/issues/26 helps.
Worked on the same issue , finally done this is top for the question so just putting what i did.
Observation -
1 -The file was not actually XLS i renamed to txt and noticed HTML text in file.
2 - Renamed the file to html and tried reading pd.read_html, Failed.
3- Added as it was not there in txt file, removed style to ensure that table is displaying in browser from local, and WORKED.
Below is the code may help someone..
import pandas as pd
import os
import shutil
import html5lib
import requests
from bs4 import BeautifulSoup
import re
import time
shutil.copy('your.xls','file.html')
shutil.copy('file.html','file.txt')
time.sleep(2)
txt = open('file.txt','r').read()
# Modify the text to ensure the data display in html page, delete style
txt = str(txt).replace('<style> .text { mso-number-format:\#; } </script>','')
# Add head and body if it is not there in HTML text
txt_with_head = '<html><head></head><body>'+txt+'</body></html>'
# Save the file as HTML
html_file = open('output.html','w')
html_file.write(txt_with_head)
# Use beautiful soup to read
url = r"C:\Users\hitesh kumar\PycharmProjects\OEM ML\output.html"
page = open(url)
soup = BeautifulSoup(page.read(), features="lxml")
my_table = soup.find("table",attrs={'border': '1'})
frame = pd.read_html(str(my_table))[0]
print(frame.head())
frame.to_excel('testoutput.xlsx',sheet_name='sheet1', index=False)
Open in google sheets and then download from sheets as CSV and then reupload to drive. Then you can Open CSV file from python.
2 ways I know of is to just download the xls file once again and if you are doing in google colab, just load the file once again from your computer and run the pd.read_excel("filename,xlsx") once again . It should work.
As they already wrote it is actually html, to see the first table you can use
df= pd.read_html(file)
df[0]
To see how many tables there are you can use
print('Tables found:', len(df))
This work for me, using encoding="utf-8" from this post
UnicodeDecodeError: 'charmap' codec can't decode byte 0x90 in position 100: character maps to <undefined>
def convert_to_xlsx():
with open('sample.xls', encoding="utf-8") as xml_file:
soup = BeautifulSoup(xml_file.read(), 'xml')
writer = pd.ExcelWriter('sample.xlsx')
for sheet in soup.findAll('Worksheet'):
sheet_as_list = []
for row in sheet.findAll('Row'):
sheet_as_list.append([cell.Data.text if cell.Data else '' for cell in row.findAll('Cell')])
pd.DataFrame(sheet_as_list).to_excel(writer, sheet_name=sheet.attrs['ss:Name'], index=False,
header=False)
writer.save()
melike's answer works for me, while the last output sentence did't work, so if anyone has the same issue with me and wants to output the xlsx file into local location, can just easily modify the last three lines.
import pandas as pd
from bs4 import BeautifulSoup
def convert_to_xlsx():
with open('sample.xls') as xml_file:
soup = BeautifulSoup(xml_file.read(), 'xml')
writer = pd.ExcelWriter('sample.xlsx')
for sheet in soup.findAll('Worksheet'):
sheet_as_list = []
for row in sheet.findAll('Row'):
sheet_as_list.append([cell.Data.text if cell.Data else '' for cell in row.findAll('Cell')])
output_df = pd.DateFrame(sheet_as_list)
output_df.to_excel(writer, sheet_name='sheet1',index=False, header=False)
writer.close()
import os
import pandas as pd
# Rename the file if it's not already a .csv file
if not os.path.exists('3.8 locates.csv'):
os.rename('3.8 locates.xls', '3.8 locates.csv')
# Load the data into a pandas dataframe
df = pd.read_csv("3.8 locates.csv", sep='\t|\n', engine='python')
# Show the first 5 rows of the dataframe
print(df.head())
The code imports the os and pandas modules and then uses them to perform the following operations:
Check if the file '3.8 locates.csv' exists.
If it does not exist, it renames the file '3.8 locates.xls' to '3.8 locates.csv'.
Load the contents of the file '3.8 locates.csv' into a Pandas dataframe using the pd.read_csv method. The sep argument is set to '\t|\n' and the engine argument is set to 'python' to handle the file's separators correctly.
Print the first 5 rows of the dataframe using the df.head() method.
Note: The code may not work as expected if the file is not a valid tab-separated or newline-separated file.
there's nothing wrong with your file. xlrd does not yet support xlsx (excel 2007+) files although it's purported to have supported this for some time.
Simplistix github
2-days ago they committed a pre-alpha version to their git which integrates xlsx support. Other forums suggest that you use a DOM parser for xlsx files since the xlsx file type is just a zip archive containing XML. I have not tried this. there is another package with similar functionality as xlrd and this is called openpyxl which you can get from easy_install or pip. I have not tried this either, however, its API is supposed to be similar to xlrd.
I know there should be a proper way to solve it
but just to save time
I uploaded my xlsx sheet to Google Sheets and then again downloaded it from Google Sheets
it working now
If you don't have time to solve the problem, you can try this
Sometimes help to add ?raw=true at the end of a file path. For example:
wb = xlrd.open_workbook("Z:\\Data\\Locates\\3.8 locates.xls?raw=true")
My code:
import xlrd
wb = xlrd.open_workbook("Z:\\Data\\Locates\\3.8 locates.xls")
sh = wb.sheet_by_index(0)
print sh.cell(0,0).value
The error:
Traceback (most recent call last):
File "Z:\Wilson\tradedStockStatus.py", line 18, in <module>
wb = xlrd.open_workbook("Z:\\Data\\Locates\\3.8 locates.xls")
File "C:\Python27\lib\site-packages\xlrd\__init__.py", line 429, in open_workbook
biff_version = bk.getbof(XL_WORKBOOK_GLOBALS)
File "C:\Python27\lib\site-packages\xlrd\__init__.py", line 1545, in getbof
bof_error('Expected BOF record; found %r' % self.mem[savpos:savpos+8])
File "C:\Python27\lib\site-packages\xlrd\__init__.py", line 1539, in bof_error
raise XLRDError('Unsupported format, or corrupt file: ' + msg)
xlrd.biffh.XLRDError: Unsupported format, or corrupt file: Expected BOF record;
found '<table r'"
The file doesn't seem to be corrupted or of a different format.
Anything to help find the source of the issue would be great.
Try to open it as an HTML with pandas:
import pandas as pd
data = pd.read_html('filename.xls')
Or try any other html python parser.
That's not a proper excel file, but an html readable with excel.
You say:
The file doesn't seem to be corrupted or of a different format.
However as the error message says, the first 8 bytes of the file are '<table r' ... that is definitely not Excel .xls format. Open it with a text editor (e.g. Notepad) that won't take any notice of the (incorrect) .xls extension and see for yourself.
This will happen to some files while also open in Excel.
I had a similar problem and it was related to the version. In a python terminal check:
>> import xlrd
>> xlrd.__VERSION__
If you have '0.9.0' you can open almost all files. If you have '0.6.0' which was what I found on Ubuntu, you may have problems with newest Excel files. You can download the latest version of xlrd using the Distutils standard.
I found the similar problem when downloading .xls file and opened it using xlrd library. Then I tried out the solution of converting .xls into .xlsx as detailed here: how to convert xls to xlsx
It works like a charm and rather than opening .xls, I am working with .xlsx file now using openpyxl library.
Hope it helps to solve your issue.
I had faced the same xlrd.biffh.XLRDError: Unsupported format, or corrupt file: Expected BOF record; error and solved it by writing an XML to XLSX converter. The reason is that actually, xlrd does not support XML Spreadsheet (*.xml) i.e. NOT in XLS or XLSX format.
import pandas as pd
from bs4 import BeautifulSoup
def convert_to_xlsx():
with open('sample.xls') as xml_file:
soup = BeautifulSoup(xml_file.read(), 'xml')
writer = pd.ExcelWriter('sample.xlsx')
for sheet in soup.findAll('Worksheet'):
sheet_as_list = []
for row in sheet.findAll('Row'):
sheet_as_list.append([cell.Data.text if cell.Data else '' for cell in row.findAll('Cell')])
pd.DataFrame(sheet_as_list).to_excel(writer, sheet_name=sheet.attrs['ss:Name'], index=False, header=False)
writer.save()
In my case, after opening the file with a text editor as #john-machin suggested, I realized the file is not encrypted as an Excel file is supposed to but it's in the CSV format and was saved as an Excel file. What I did was renamed the file and its extension and used read_csv function instead:
os.rename('sample_file.xls', 'sample_file.csv')
csv = pd.read_csv("sample_file.csv", error_bad_lines=False)
It may be an old excel file format. It can be read as html in pandas via
import pandas as pd
df = pd.read_html('file.xls')
Eventually, this gives a list of dataframes (if you check the type is a list). https://pandas.pydata.org/pandas-docs/version/0.17.1/io.html#io-read-html
You need to extract them, for instance with df[0]
I met this problem too.I opened this file by excel and saved it as other formats such as excel 97-2003 and finally I solved this problem
I had the same issue. Those old files are formatted like a tab-delimited file. I've been able to open my problem files with read_table; ie df = pd.read_table('trouble_maker.xls').
I got this error when I tried to read some XLSX files from a folder and that one of the files was opened. I closed the XLSX file and this error did not show up.
Try this It worked for me.
import pandas as pd
data = pd.read_csv('filename.xls')
I just downloaded xlrd, created an excel document (excel 2007) for testing and got the same error (message says 'found PK\x03\x04\x14\x00\x06\x00'). Extension is a xlsx. Tried saving it to an older .xls format and error disappears .....
I meet the same problem.
it lies in the .xls file itself - it looks like an Excel file however it isn't. (see if there's a pop up when you plainly open the .xls from Excel)
sjmachin commented on Jan 19, 2013 from https://github.com/python-excel/xlrd/issues/26 helps.
Worked on the same issue , finally done this is top for the question so just putting what i did.
Observation -
1 -The file was not actually XLS i renamed to txt and noticed HTML text in file.
2 - Renamed the file to html and tried reading pd.read_html, Failed.
3- Added as it was not there in txt file, removed style to ensure that table is displaying in browser from local, and WORKED.
Below is the code may help someone..
import pandas as pd
import os
import shutil
import html5lib
import requests
from bs4 import BeautifulSoup
import re
import time
shutil.copy('your.xls','file.html')
shutil.copy('file.html','file.txt')
time.sleep(2)
txt = open('file.txt','r').read()
# Modify the text to ensure the data display in html page, delete style
txt = str(txt).replace('<style> .text { mso-number-format:\#; } </script>','')
# Add head and body if it is not there in HTML text
txt_with_head = '<html><head></head><body>'+txt+'</body></html>'
# Save the file as HTML
html_file = open('output.html','w')
html_file.write(txt_with_head)
# Use beautiful soup to read
url = r"C:\Users\hitesh kumar\PycharmProjects\OEM ML\output.html"
page = open(url)
soup = BeautifulSoup(page.read(), features="lxml")
my_table = soup.find("table",attrs={'border': '1'})
frame = pd.read_html(str(my_table))[0]
print(frame.head())
frame.to_excel('testoutput.xlsx',sheet_name='sheet1', index=False)
Open in google sheets and then download from sheets as CSV and then reupload to drive. Then you can Open CSV file from python.
2 ways I know of is to just download the xls file once again and if you are doing in google colab, just load the file once again from your computer and run the pd.read_excel("filename,xlsx") once again . It should work.
As they already wrote it is actually html, to see the first table you can use
df= pd.read_html(file)
df[0]
To see how many tables there are you can use
print('Tables found:', len(df))
This work for me, using encoding="utf-8" from this post
UnicodeDecodeError: 'charmap' codec can't decode byte 0x90 in position 100: character maps to <undefined>
def convert_to_xlsx():
with open('sample.xls', encoding="utf-8") as xml_file:
soup = BeautifulSoup(xml_file.read(), 'xml')
writer = pd.ExcelWriter('sample.xlsx')
for sheet in soup.findAll('Worksheet'):
sheet_as_list = []
for row in sheet.findAll('Row'):
sheet_as_list.append([cell.Data.text if cell.Data else '' for cell in row.findAll('Cell')])
pd.DataFrame(sheet_as_list).to_excel(writer, sheet_name=sheet.attrs['ss:Name'], index=False,
header=False)
writer.save()
melike's answer works for me, while the last output sentence did't work, so if anyone has the same issue with me and wants to output the xlsx file into local location, can just easily modify the last three lines.
import pandas as pd
from bs4 import BeautifulSoup
def convert_to_xlsx():
with open('sample.xls') as xml_file:
soup = BeautifulSoup(xml_file.read(), 'xml')
writer = pd.ExcelWriter('sample.xlsx')
for sheet in soup.findAll('Worksheet'):
sheet_as_list = []
for row in sheet.findAll('Row'):
sheet_as_list.append([cell.Data.text if cell.Data else '' for cell in row.findAll('Cell')])
output_df = pd.DateFrame(sheet_as_list)
output_df.to_excel(writer, sheet_name='sheet1',index=False, header=False)
writer.close()
import os
import pandas as pd
# Rename the file if it's not already a .csv file
if not os.path.exists('3.8 locates.csv'):
os.rename('3.8 locates.xls', '3.8 locates.csv')
# Load the data into a pandas dataframe
df = pd.read_csv("3.8 locates.csv", sep='\t|\n', engine='python')
# Show the first 5 rows of the dataframe
print(df.head())
The code imports the os and pandas modules and then uses them to perform the following operations:
Check if the file '3.8 locates.csv' exists.
If it does not exist, it renames the file '3.8 locates.xls' to '3.8 locates.csv'.
Load the contents of the file '3.8 locates.csv' into a Pandas dataframe using the pd.read_csv method. The sep argument is set to '\t|\n' and the engine argument is set to 'python' to handle the file's separators correctly.
Print the first 5 rows of the dataframe using the df.head() method.
Note: The code may not work as expected if the file is not a valid tab-separated or newline-separated file.
there's nothing wrong with your file. xlrd does not yet support xlsx (excel 2007+) files although it's purported to have supported this for some time.
Simplistix github
2-days ago they committed a pre-alpha version to their git which integrates xlsx support. Other forums suggest that you use a DOM parser for xlsx files since the xlsx file type is just a zip archive containing XML. I have not tried this. there is another package with similar functionality as xlrd and this is called openpyxl which you can get from easy_install or pip. I have not tried this either, however, its API is supposed to be similar to xlrd.
I know there should be a proper way to solve it
but just to save time
I uploaded my xlsx sheet to Google Sheets and then again downloaded it from Google Sheets
it working now
If you don't have time to solve the problem, you can try this
Sometimes help to add ?raw=true at the end of a file path. For example:
wb = xlrd.open_workbook("Z:\\Data\\Locates\\3.8 locates.xls?raw=true")