I am trying to read a gzip file using pandas.read_csv like so:
import pandas as pd
df = pd.read_csv("data.ZIP.gz", usecols=[*range(0, 39)], encoding="latin1", skipinitialspace=True)
But it throws this error:
ValueError: Passed header names mismatches usecols
However, if I manually extract the zip file from gz file, then read_csv if able to read the data without errors:
df = pd.read_csv("data.ZIP", usecols=[*range(0, 39)], encoding="latin1", skipinitialspace=True)
Since I have to read a lot of these files I don't want to manually extract them. So, how can I fix this error?
You have two levels of compression - gzip and zip - but pandas know how to work with only one level of compression.
You can use module gzip and zipfile with io.BytesIO to extract it to file-like object in memory.
Here minimal working code
It can be useful if zip has many files and you want to select which one to extract
import pandas as pd
import gzip
import zipfile
import io
with gzip.open('data.csv.zip.gz') as f1:
data = f1.read()
file_like_object_1 = io.BytesIO(data)
with zipfile.ZipFile(file_like_object_1) as f2:
#print([x.filename for x in f2.filelist]) # list all filenames
#data = f2.read('data.csv') # extract selected filename
#data = f2.read(f2.filelist[0]) # extract first file
data = f2.read(f2.filelist[0].filename) # extract first file
file_like_object_2 = io.BytesIO(data)
df = pd.read_csv(file_like_object_2)
print(df)
But if zip has only one file then you can use read_csv to extract it - it needs to add option compression='zip' because file-like object has no filename and read_csv can't use filename's extension to recognize compressed file.
import pandas as pd
import gzip
import io
with gzip.open('data.csv.zip.gz') as f1:
data = f1.read()
file_like_object_1 = io.BytesIO(data)
df = pd.read_csv(file_like_object_1, compression='zip')
print(df)
use the gzip module to unzip all your files somethings like this
for file in list_file_names:
file_name=file.replace(".gz","")
with gzip.open(file, 'rb') as f:
file_content = f.read()
with open(file_name,"wb") as r:
r.write(file_content)
You can use zipfile module, such as :
import zipfile
with zipfile.ZipFile(path_to_zip_file, 'r') as zip_ref:
zip_ref.extractall(directory_to_extract_to)
I have am writing a script that reads a folder of .pdfs and extracts their fillable fields to a pandas df. I had success extracting one .pdf with the following code:
import numpy as np
import pandas as pd
import PyPDF2
import glob, os
pwd = os.getcwd()
pdfFileObj = open('pdf_filename', 'rb')
pdfReader = PyPDF2.PdfFileReader(pdfFileObj)
fields_dict = pdfReader.getFormTextFields()
series = pd.Series(fields_dict).to_frame()
df = pd.DataFrame(pd.Series(fields_dict)).T
I want to build a function that runs this script for all pdfs in the directory. My first idea was to use a function in glob that collects all pdfs. Here is what I have so far:
import numpy as np
import pandas as pd
import PyPDF2
import glob, os
pwd = os.getcwd()
def readfiles():
os.chdir(pwd)
pdfs = []
for file in glob.glob("*.pdf"):
print(file)
pdfs.append(file)
pdfFileObj = open(readfiles, 'rb')
pdfReader = PyPDF2.PdfFileReader(pdfFileObj)
fields_dict = pdfReader.getFormTextFields()
series = pd.Series(fields_dict).to_frame()
df = pd.DataFrame(pd.Series(fields_dict)).T
Unfortunately, this doesn't work because I cannot put a function in the pdfFileReader. Does anyone have suggestions on a better way to do this? Thanks!
I can't comment, new account. But you could try making your readFiles function return the array pdfs.
Then in code execution below just:
listofPDF=readfiles()
arrayofDF=list()
for file in listofPDF:
pdfFileObj = open(file , 'rb')
pdfReader = PyPDF2.PdfFileReader(pdfFileObj)
##execute your code to obtain a single dataframe from a pdf here
fields_dict = pdfReader.getFormTextFields()
series = pd.Series(fields_dict).to_frame()
df = pd.DataFrame(pd.Series(fields_dict)).T
arrayofDF.append(df)
You would end up having a list of dataframes, each one corresponding to one of the pdf files, if the first part of the code ( in which you get the dataframe from the singular pdf file) works.
Additionally, you could make a dictionary like {filename:file , dataframe: df} and then append that to your list, so you can later recover the dataframe based of the name of the file. It all depends on what you plan to do with the dataframes later.
So an update, I found my compile issue was that I needed to change my notebook to a py file and choosing save as doesn't do that. So I had to run a different script turn my notebook to a py file. And part of my exe issue was I was using the fopen command that apparently isn't useable when compiled into a exe. So I redid the code to what is above. But now I get a write error when trying to run the script. I can not find anything on write functions with os is there somewhere else I should look?
Original code:
import requests
import json
import pandas as pd
import csv
from pathlib import Path
response = requests.get('url', headers={'CERT': 'cert'}, stream=True).json()
json2 = json.dumps(response)
f = open('data.json', 'r+')
f.write(json2)
f.close()
Path altered code:
import requests
import json
import pandas as pd
import csv
from pathlib import Path
response = requests.get('url', headers={'CERT': 'cert'}, stream=True).json()
json2 = json.dumps(response)
filename = 'data.json'
if '_MEIPASS2' in os.environ:
filename = os.path.join(os.environ['_MEIPASS2'], filename)
fd = open(filename, 'r+')
fd.write(json2)
fd.close()
The changes to the code allowed me to get past the fopen issue but created a write issue. Any ideas?
If you want to write to a file, you have to open it as writable.
fd = open(filename, 'wb')
Although I don't know why you're opening it in binary if you're writing text.
I am using win32.client in python for converting my .xlsx and .xls file into a .csv. When I execute this code it's giving an error. My code is:
def convertXLS2CSV(aFile):
'''converts a MS Excel file to csv w/ the same name in the same directory'''
print "------ beginning to convert XLS to CSV ------"
try:
import win32com.client, os
from win32com.client import constants as c
excel = win32com.client.Dispatch('Excel.Application')
fileDir, fileName = os.path.split(aFile)
nameOnly = os.path.splitext(fileName)
newName = nameOnly[0] + ".csv"
outCSV = os.path.join(fileDir, newName)
workbook = excel.Workbooks.Open(aFile)
workbook.SaveAs(outCSV, c.xlCSVMSDOS) # 24 represents xlCSVMSDOS
workbook.Close(False)
excel.Quit()
del excel
print "...Converted " + nameOnly + " to CSV"
except:
print ">>>>>>> FAILED to convert " + aFile + " to CSV!"
convertXLS2CSV("G:\\hello.xlsx")
I am not able to find the error in this code. Please help.
I would use xlrd - it's faster, cross platform and works directly with the file.
As of version 0.8.0, xlrd reads both XLS and XLSX files.
But as of version 2.0.0, support was reduced back to only XLS.
import xlrd
import csv
def csv_from_excel():
wb = xlrd.open_workbook('your_workbook.xls')
sh = wb.sheet_by_name('Sheet1')
your_csv_file = open('your_csv_file.csv', 'wb')
wr = csv.writer(your_csv_file, quoting=csv.QUOTE_ALL)
for rownum in xrange(sh.nrows):
wr.writerow(sh.row_values(rownum))
your_csv_file.close()
I would use pandas. The computationally heavy parts are written in cython or c-extensions to speed up the process and the syntax is very clean. For example, if you want to turn "Sheet1" from the file "your_workbook.xls" into the file "your_csv.csv", you just use the top-level function read_excel and the method to_csv from the DataFrame class as follows:
import pandas as pd
data_xls = pd.read_excel('your_workbook.xls', 'Sheet1', index_col=None)
data_xls.to_csv('your_csv.csv', encoding='utf-8')
Setting encoding='utf-8' alleviates the UnicodeEncodeError mentioned in other answers.
Maybe someone find this ready-to-use piece of code useful. It allows to create CSVs from all spreadsheets in Excel's workbook.
Python 2:
# -*- coding: utf-8 -*-
import xlrd
import csv
from os import sys
def csv_from_excel(excel_file):
workbook = xlrd.open_workbook(excel_file)
all_worksheets = workbook.sheet_names()
for worksheet_name in all_worksheets:
worksheet = workbook.sheet_by_name(worksheet_name)
with open(u'{}.csv'.format(worksheet_name), 'wb') as your_csv_file:
wr = csv.writer(your_csv_file, quoting=csv.QUOTE_ALL)
for rownum in xrange(worksheet.nrows):
wr.writerow([unicode(entry).encode("utf-8") for entry in worksheet.row_values(rownum)])
if __name__ == "__main__":
csv_from_excel(sys.argv[1])
Python 3:
import xlrd
import csv
from os import sys
def csv_from_excel(excel_file):
workbook = xlrd.open_workbook(excel_file)
all_worksheets = workbook.sheet_names()
for worksheet_name in all_worksheets:
worksheet = workbook.sheet_by_name(worksheet_name)
with open(u'{}.csv'.format(worksheet_name), 'w', encoding="utf-8") as your_csv_file:
wr = csv.writer(your_csv_file, quoting=csv.QUOTE_ALL)
for rownum in range(worksheet.nrows):
wr.writerow(worksheet.row_values(rownum))
if __name__ == "__main__":
csv_from_excel(sys.argv[1])
I'd use csvkit, which uses xlrd (for xls) and openpyxl (for xlsx) to convert just about any tabular data to csv.
Once installed, with its dependencies, it's a matter of:
python in2csv myfile > myoutput.csv
It takes care of all the format detection issues, so you can pass it just about any tabular data source. It's cross-platform too (no win32 dependency).
First read your excel spreadsheet into pandas, below code will import your excel spreadsheet into pandas as a OrderedDict type which contain all of your worksheet as dataframes. Then simply use worksheet_name as a key to access specific worksheet as a dataframe and save only required worksheet as csv file by using df.to_csv(). Hope this will workout in your case.
import pandas as pd
df = pd.read_excel('YourExcel.xlsx', sheet_name=None)
df['worksheet_name'].to_csv('YourCsv.csv')
If your Excel file contain only one worksheet then simply use below code:
import pandas as pd
df = pd.read_excel('YourExcel.xlsx')
df.to_csv('YourCsv.csv')
If someone want to convert all the excel worksheets from single excel workbook to the different csv files, try below code:
import pandas as pd
def excelTOcsv(filename):
df = pd.read_excel(filename, sheet_name=None)
for key, value in df.items():
return df[key].to_csv('%s.csv' %key)
This function is working as a multiple Excel sheet of same excel workbook to multiple csv file converter. Where key is the sheet name and value is the content inside sheet.
#andi I tested your code, it works great, BUT
In my sheets there's a column like this
2013-03-06T04:00:00
date and time in the same cell
It gets garbled during exportation, it's like this in the exported file
41275.0416667
other columns are ok.
csvkit, on the other side, does ok with that column but only exports ONE sheet, and my files have many.
xlsx2csv is faster than pandas and xlrd.
xlsx2csv -s 0 crunchbase_monthly_.xlsx cruchbase
excel file usually comes with n sheetname.
-s is sheetname index.
then, cruchbase folder will be created, each sheet belongs to xlsx will be converted to a single csv.
p.s. csvkit is awesome too.
Quoting an answer from Scott Ming, which works with workbook containing multiple sheets:
Here is a python script getsheets.py (mirror), you should install pandas and xlrd before you use it.
Run this:
pip3 install pandas xlrd # or `pip install pandas xlrd`
How does it works?
$ python3 getsheets.py -h
Usage: getsheets.py [OPTIONS] INPUTFILE
Convert a Excel file with multiple sheets to several file with one sheet.
Examples:
getsheets filename
getsheets filename -f csv
Options:
-f, --format [xlsx|csv] Default xlsx.
-h, --help Show this message and exit.
Convert to several xlsx:
$ python3 getsheets.py goods_temp.xlsx
Sheet.xlsx Done!
Sheet1.xlsx Done!
All Done!
Convert to several csv:
$ python3 getsheets.py goods_temp.xlsx -f csv
Sheet.csv Done!
Sheet1.csv Done!
All Done!
getsheets.py:
# -*- coding: utf-8 -*-
import click
import os
import pandas as pd
def file_split(file):
s = file.split('.')
name = '.'.join(s[:-1]) # get directory name
return name
def getsheets(inputfile, fileformat):
name = file_split(inputfile)
try:
os.makedirs(name)
except:
pass
df1 = pd.ExcelFile(inputfile)
for x in df1.sheet_names:
print(x + '.' + fileformat, 'Done!')
df2 = pd.read_excel(inputfile, sheetname=x)
filename = os.path.join(name, x + '.' + fileformat)
if fileformat == 'csv':
df2.to_csv(filename, index=False)
else:
df2.to_excel(filename, index=False)
print('\nAll Done!')
CONTEXT_SETTINGS = dict(help_option_names=['-h', '--help'])
#click.command(context_settings=CONTEXT_SETTINGS)
#click.argument('inputfile')
#click.option('-f', '--format', type=click.Choice([
'xlsx', 'csv']), default='xlsx', help='Default xlsx.')
def cli(inputfile, format):
'''Convert a Excel file with multiple sheets to several file with one sheet.
Examples:
\b
getsheets filename
\b
getsheets filename -f csv
'''
if format == 'csv':
getsheets(inputfile, 'csv')
else:
getsheets(inputfile, 'xlsx')
cli()
We can use Pandas lib of Python to conevert xls file to csv file
Below code will convert xls file to csv file .
import pandas as pd
Read Excel File from Local Path :
df = pd.read_excel("C:/Users/IBM_ADMIN/BU GPA Scorecard.xlsx",sheetname=1)
Trim Spaces present on columns :
df.columns = df.columns.str.strip()
Send Data frame to CSV file which will be pipe symbol delimted and without Index :
df.to_csv("C:/Users/IBM_ADMIN/BU GPA Scorecard csv.csv",sep="|",index=False)
Python is not the best tool for this task. I tried several approaches in Python but none of them work 100% (e.g. 10% converts to 0.1, or column types are messed up, etc). The right tool here is PowerShell, because it is an MS product (as is Excel) and has the best integration.
Simply download this PowerShell script, edit line 47 to enter the path for the folder containing the Excel files and run the script using PowerShell.
Using xlrd is a flawed way to do this, because you lose the Date Formats in Excel.
My use case is the following.
Take an Excel File with more than one sheet and convert each one into a file of its own.
I have done this using the xlsx2csv library and calling this using a subprocess.
import csv
import sys, os, json, re, time
import subprocess
def csv_from_excel(fname):
subprocess.Popen(["xlsx2csv " + fname + " --all -d '|' -i -p "
"'<New Sheet>' > " + 'test.csv'], shell=True)
return
lstSheets = csv_from_excel(sys.argv[1])
time.sleep(3) # system needs to wait a second to recognize the file was written
with open('[YOUR PATH]/test.csv') as f:
lines = f.readlines()
firstSheet = True
for line in lines:
if line.startswith('<New Sheet>'):
if firstSheet:
sh_2_fname = line.replace('<New Sheet>', '').strip().replace(' - ', '_').replace(' ','_')
print(sh_2_fname)
sh2f = open(sh_2_fname+".csv", "w")
firstSheet = False
else:
sh2f.close()
sh_2_fname = line.replace('<New Sheet>', '').strip().replace(' - ', '_').replace(' ','_')
print(sh_2_fname)
sh2f = open(sh_2_fname+".csv", "w")
else:
sh2f.write(line)
sh2f.close()
I've tested all anwers, but they were all too slow for me. If you have Excel installed you can use the COM.
I thought initially it would be slower since it will load everything for the actual Excel application, but it isn't for huge files. Maybe because the algorithm for opening and saving files runs a heavily optimized compiled code, Microsoft guys make a lot of money for it after all.
import sys
import os
import glob
from win32com.client import Dispatch
def main(path):
excel = Dispatch("Excel.Application")
if is_full_path(path):
process_file(excel, path)
else:
files = glob.glob(path)
for file_path in files:
process_file(excel, file_path)
excel.Quit()
def process_file(excel, path):
fullpath = os.path.abspath(path)
full_csv_path = os.path.splitext(fullpath)[0] + '.csv'
workbook = excel.Workbooks.Open(fullpath)
workbook.Worksheets(1).SaveAs(full_csv_path, 6)
workbook.Saved = 1
workbook.Close()
def is_full_path(path):
return path.find(":") > -1
if __name__ == '__main__':
main(sys.argv[1])
This is very raw code and won't check for errors, print help or anything, it will just create a csv file for each file that matches the pattern you entered in the function so you can batch process a lot of files only launching excel application once.
As much as I hate to rely on Windows Excel proprietary software, which is not cross-platform, my testing of csvkit for .xls, which uses xlrd under the hood, failed to correctly parse dates (even when using the commandline parameters to specify strptime format).
For example, this xls file, when parsed with csvkit, will convert cell G1 of 12/31/2002 to 37621, whereas when converted to csv via excel -> save_as (using below) cell G1 will be "December 31, 2002".
import re
import os
from win32com.client import Dispatch
xlCSVMSDOS = 24
class CsvConverter(object):
def __init__(self, *, input_dir, output_dir):
self._excel = None
self.input_dir = input_dir
self.output_dir = output_dir
if not os.path.isdir(self.output_dir):
os.makedirs(self.output_dir)
def isSheetEmpty(self, sheet):
# https://archive.is/RuxR7
# WorksheetFunction.CountA(ActiveSheet.UsedRange) = 0 And ActiveSheet.Shapes.Count = 0
return \
(not self._excel.WorksheetFunction.CountA(sheet.UsedRange)) \
and \
(not sheet.Shapes.Count)
def getNonEmptySheets(self, wb, as_name=False):
return [ \
(sheet.Name if as_name else sheet) \
for sheet in wb.Sheets \
if not self.isSheetEmpty(sheet) \
]
def saveWorkbookAsCsv(self, wb, csv_path):
non_empty_sheet_names = self.getNonEmptySheets(wb, as_name=True)
assert (len(non_empty_sheet_names) == 1), \
"Expected exactly 1 sheet but found %i non-empty sheets: '%s'" \
%(
len(non_empty_sheet_names),
"', '".join(name.replace("'", r"\'") for name in non_empty_sheet_names)
)
wb.Worksheets(non_empty_sheet_names[0]).SaveAs(csv_path, xlCSVMSDOS)
wb.Saved = 1
def isXlsFilename(self, filename):
return bool(re.search(r'(?i)\.xls$', filename))
def batchConvertXlsToCsv(self):
xls_names = tuple( filename for filename in next(os.walk(self.input_dir))[2] if self.isXlsFilename(filename) )
self._excel = Dispatch('Excel.Application')
try:
for xls_name in xls_names:
csv_path = os.path.join(self.output_dir, '%s.csv' %os.path.splitext(xls_name)[0])
if not os.path.isfile(csv_path):
workbook = self._excel.Workbooks.Open(os.path.join(self.input_dir, xls_name))
try:
self.saveWorkbookAsCsv(workbook, csv_path)
finally:
workbook.Close()
finally:
if not len(self._excel.Workbooks):
self._excel.Quit()
self._excel = None
if __name__ == '__main__':
self = CsvConverter(
input_dir='C:\\data\\xls\\',
output_dir='C:\\data\\csv\\'
)
self.batchConvertXlsToCsv()
The above will take an input_dir containing .xls and output them to output_dir as .csv -- it will assert that there is exactly 1 non-empty sheet in the .xls; if you need to handle multiple sheets into multiple csv then you'll need to edit saveWorkbookAsCsv.
I was trying to use xlrd library in order to convert the format xlsx into csv, but I was getting error: xlrd.biffh.XLRDError: Excel xlsx file; not supported. That was happening because this package is no longer reading any other format unless xls, according to xlrd documentation.
Following the answer from Chris Withers I was able to change the engine for the function read_excel() from pandas, then I was able to a create a function that is converting any sheet from your Excel spreadsheet you want to successfully.
In order to work the function below, don't forget to install the openpyxl library from here.
Function:
import os
import pathlib
import pandas as pd
# Function to convert excel spreadsheet into csv format
def Excel_to_csv():
# Excel file full path
excel_file = os.path.join(os.path.sep, pathlib.Path(__file__).parent.resolve(), "Excel_Spreadsheet.xlsx")
# Excel sheets
excel_sheets = ['Sheet1', 'Sheet2', 'Sheet3']
for sheet in excel_sheets:
# Create dataframe for each sheet
df = pd.DataFrame(pd.read_excel(excel_file, sheet, index_col=None, engine='openpyxl'))
# Export to csv. i.e: sheet_name.csv
df.to_csv(os.path.join(os.path.sep, pathlib.Path(__file__).parent.resolve(), sheet + '.csv'), sep=",", encoding='utf-8', index=False, header=True)
# Runs the excel_to_csv function:
Excel_to_csv()