I would like to read several csv files from a directory into pandas and concatenate them into one big DataFrame. I have not been able to figure it out though. Here is what I have so far:

import glob
import pandas as pd

# get data file names
path =r'C:\DRO\DCL_rawdata_files'
filenames = glob.glob(path + "/*.csv")

dfs = []
for filename in filenames:
    dfs.append(pd.read_csv(filename))

# Concatenate all data into one DataFrame
big_frame = pd.concat(dfs, ignore_index=True)

I guess I need some help within the for loop???

Solution 1

See pandas: IO tools for all of the available .read_ methods.

If you have same columns in all your csv files then you can try the code below. I have added header=0 so that after reading csv first row can be assigned as the column names.

import pandas as pd
import glob
import os

path = r'C:\DRO\DCL_rawdata_files' # use your path
all_files = glob.glob(os.path.join(path , "/*.csv"))

li = []

for filename in all_files:
    df = pd.read_csv(filename, index_col=None, header=0)
    li.append(df)

frame = pd.concat(li, axis=0, ignore_index=True)

or, with attribution to a comment from Sid

all_files = glob.glob(os.path.join(path, "*.csv"))

df = pd.concat((pd.read_csv(f) for f in all_files), ignore_index=True)

  • It's often necessary to identify each sample of data, which can be accomplished by adding a new column to the dataframe.
  • pathlib from the standard library will be used for this example. It treats paths as objects with methods, instead of strings to be sliced.

Imports and Setup

from pathlib import Path
import pandas as pd
import numpy as np

path = r'C:\DRO\DCL_rawdata_files'  # or unix / linux / mac path

# get the files from the path provided in the OP
files = Path(path).glob('*.csv')  # .rglob to get subdirectories

Option 1:

  • Add a new column with the file name
dfs = list()
for f in files:
    data = pd.read_csv(f)
    # .stem is method for pathlib objects to get the filename w/o the extension
    data['file'] = f.stem
    dfs.append(data)
    
df = pd.concat(dfs, ignore_index=True)

Option 2:

  • Add a new column with a generic name using enumerate
dfs = list()
for i, f in enumerate(files):
    data = pd.read_csv(f)
    data['file'] = f'File {i}'
    dfs.append(data)
    
df = pd.concat(dfs, ignore_index=True)

Option 3:

  • Create the dataframes with a list comprehension, and then use np.repeat to add a new column.
    • [f'S{i}' for i in range(len(dfs))] creates a list of strings to name each dataframe.
    • [len(df) for df in dfs] creates a list of lengths
  • Attribution for this option goes to this plotting answer.
# read the files into dataframes
dfs = [pd.read_csv(f) for f in files]

# combine the list of dataframes
df = pd.concat(dfs, ignore_index=True)

# add a new column
df['Source'] = np.repeat([f'S{i}' for i in range(len(dfs))], [len(df) for df in dfs])

Option 4:

  • One liners using .assign to create the new column, with attribution to a comment from C8H10N4O2
df = pd.concat((pd.read_csv(f).assign(filename=f.stem) for f in files), ignore_index=True)

or

df = pd.concat((pd.read_csv(f).assign(Source=f'S{i}') for i, f in enumerate(files)), ignore_index=True)

Solution 2

An alternative to darindaCoder's answer:

path = r'C:\DRO\DCL_rawdata_files'                     # use your path
all_files = glob.glob(os.path.join(path, "*.csv"))     # advisable to use os.path.join as this makes concatenation OS independent

df_from_each_file = (pd.read_csv(f) for f in all_files)
concatenated_df   = pd.concat(df_from_each_file, ignore_index=True)
# doesn't create a list, nor does it append to one

Solution 3

import glob
import os
import pandas as pd   
df = pd.concat(map(pd.read_csv, glob.glob(os.path.join('', "my_files*.csv"))))

Solution 4

Almost all of the answers here are either unnecessarily complex (glob pattern matching) or rely on additional 3rd party libraries. You can do this in 2 lines using everything Pandas and python (all versions) already have built in.

For a few files - 1 liner

df = pd.concat(map(pd.read_csv, ['d1.csv', 'd2.csv','d3.csv']))

For many files

import os

filepaths = [f for f in os.listdir(".") if f.endswith('.csv')]
df = pd.concat(map(pd.read_csv, filepaths))

For No Headers

If you have specific things you want to change with pd.read_csv (i.e. no headers) you can make a separate function and call that with your map:

def f(i):
    return pd.read_csv(i, header=None)

df = pd.concat(map(f, filepaths))

This pandas line which sets the df utilizes 3 things:

  1. Python's map (function, iterable) sends to the function (the pd.read_csv()) the iterable (our list) which is every csv element in filepaths).
  2. Panda's read_csv() function reads in each CSV file as normal.
  3. Panda's concat() brings all these under one df variable.

Solution 5

Easy and Fast

Import two or more csv's without having to make a list of names.

import glob
import pandas as pd

df = pd.concat(map(pd.read_csv, glob.glob('data/*.csv')))

Solution 6

The Dask library can read a dataframe from multiple files:

>>> import dask.dataframe as dd
>>> df = dd.read_csv('data*.csv')

(Source: https://examples.dask.org/dataframes/01-data-access.html#Read-CSV-files)

The Dask dataframes implement a subset of the Pandas dataframe API. If all the data fits into memory, you can call df.compute() to convert the dataframe into a Pandas dataframe.

Solution 7

Edit: I googled my way into https://stackoverflow.com/a/21232849/186078. However of late I am finding it faster to do any manipulation using numpy and then assigning it once to dataframe rather than manipulating the dataframe itself on an iterative basis and it seems to work in this solution too.

I do sincerely want anyone hitting this page to consider this approach, but don't want to attach this huge piece of code as a comment and making it less readable.

You can leverage numpy to really speed up the dataframe concatenation.

import os
import glob
import pandas as pd
import numpy as np

path = "my_dir_full_path"
allFiles = glob.glob(os.path.join(path,"*.csv"))


np_array_list = []
for file_ in allFiles:
    df = pd.read_csv(file_,index_col=None, header=0)
    np_array_list.append(df.as_matrix())

comb_np_array = np.vstack(np_array_list)
big_frame = pd.DataFrame(comb_np_array)

big_frame.columns = ["col1","col2"....]

Timing stats:

total files :192
avg lines per file :8492
--approach 1 without numpy -- 8.248656988143921 seconds ---
total records old :1630571
--approach 2 with numpy -- 2.289292573928833 seconds ---

Solution 8

one liner using map, but if you'd like to specify additional args, you could do:

import pandas as pd
import glob
import functools

df = pd.concat(map(functools.partial(pd.read_csv, sep='|', compression=None), 
                    glob.glob("data/*.csv")))

Note: map by itself does not let you supply additional args.

Solution 9

If you want to search recursively (Python 3.5 or above), you can do the following:

from glob import iglob
import pandas as pd

path = r'C:\user\your\path\**\*.csv'

all_rec = iglob(path, recursive=True)     
dataframes = (pd.read_csv(f) for f in all_rec)
big_dataframe = pd.concat(dataframes, ignore_index=True)

Note that the three last lines can be expressed in one single line:

df = pd.concat((pd.read_csv(f) for f in iglob(path, recursive=True)), ignore_index=True)

You can find the documentation of ** here. Also, I used iglobinstead of glob, as it returns an iterator instead of a list.



EDIT: Multiplatform recursive function:

You can wrap the above into a multiplatform function (Linux, Windows, Mac), so you can do:

df = read_df_rec('C:\user\your\path', *.csv)

Here is the function:

from glob import iglob
from os.path import join
import pandas as pd

def read_df_rec(path, fn_regex=r'*.csv'):
    return pd.concat((pd.read_csv(f) for f in iglob(
        join(path, '**', fn_regex), recursive=True)), ignore_index=True)

Solution 10

Inspired from MrFun's answer:

import glob
import pandas as pd

list_of_csv_files = glob.glob(directory_path + '/*.csv')
list_of_csv_files.sort()

df = pd.concat(map(pd.read_csv, list_of_csv_files), ignore_index=True)

Notes:

  1. By default, the list of files generated through glob.glob is not sorted. On the other hand, in many scenarios, it's required to be sorted e.g. one may want to analyze number of sensor-frame-drops v/s timestamp.

  2. In pd.concat command, if ignore_index=True is not specified then it reserves the original indices from each dataframes (i.e. each individual CSV file in the list) and the main dataframe looks like

        timestamp    id    valid_frame
    0
    1
    2
    .
    .
    .
    0
    1
    2
    .
    .
    .
    

    With ignore_index=True, it looks like:

        timestamp    id    valid_frame
    0
    1
    2
    .
    .
    .
    108
    109
    .
    .
    .
    

    IMO, this is helpful when one may want to manually create a histogram of number of frame drops v/s one minutes (or any other duration) bins and want to base the calculation on very first timestamp e.g. begin_timestamp = df['timestamp'][0]

    Without, ignore_index=True, df['timestamp'][0] generates the series containing very first timestamp from all the individual dataframes, it does not give just a value.

Solution 11

Another on-liner with list comprehension which allows to use arguments with read_csv.

df = pd.concat([pd.read_csv(f'dir/{f}') for f in os.listdir('dir') if f.endswith('.csv')])

Solution 12

If the multiple csv files are zipped, you may use zipfile to read all and concatenate as below:

import zipfile
import pandas as pd

ziptrain = zipfile.ZipFile('yourpath/yourfile.zip')

train = []

train = [ pd.read_csv(ziptrain.open(f)) for f in ziptrain.namelist() ]

df = pd.concat(train)

    

Solution 13

Alternative using the pathlib library (often preferred over os.path).

This method avoids iterative use of pandas concat()/apped().

From the pandas documentation:
It is worth noting that concat() (and therefore append()) makes a full copy of the data, and that constantly reusing this function can create a significant performance hit. If you need to use the operation over several datasets, use a list comprehension.

import pandas as pd
from pathlib import Path

dir = Path("../relevant_directory")

df = (pd.read_csv(f) for f in dir.glob("*.csv"))
df = pd.concat(df)

Solution 14

Based on @Sid's good answer.

To identify issues of missing or unaligned columns

Before concatenating, you can load csv files into an intermediate dictionary which gives access to each data set based on the file name (in the form dict_of_df['filename.csv']). Such a dictionary can help you identify issues with heterogeneous data formats, when column names are not aligned for example.

Import modules and locate file paths:

import os
import glob
import pandas
from collections import OrderedDict
path =r'C:\DRO\DCL_rawdata_files'
filenames = glob.glob(path + "/*.csv")

Note: OrderedDict is not necessary, but it'll keep the order of files which might be useful for analysis.

Load csv files into a dictionary. Then concatenate:

dict_of_df = OrderedDict((f, pandas.read_csv(f)) for f in filenames)
pandas.concat(dict_of_df, sort=True)

Keys are file names f and values are the data frame content of csv files. Instead of using f as a dictionary key, you can also use os.path.basename(f) or other os.path methods to reduce the size of the key in the dictionary to only the smaller part that is relevant.

Solution 15

import os

os.system("awk '(NR == 1) || (FNR > 1)' file*.csv > merged.csv")

Where NR and FNR represent the number of the line being processed.

FNR is the current line within each file.

NR == 1 includes the first line of the first file (the header), while FNR > 1 skips the first line of each subsequent file.

Solution 16

In case anyone is facing Unnamed column issue, can use this code for merging multiple csv files along x-axis.

import glob
import os
import pandas as pd

merged_df = pd.concat([pd.read_csv(csv_file, index_col=0, header=0) for csv_file in glob.glob(
        os.path.join("data/", "*.csv"))], axis=0, ignore_index=True)
    
merged_df.to_csv("merged.csv")

Solution 17

You can do it this way also:

import pandas as pd
import os

new_df = pd.DataFrame()
for r, d, f in os.walk(csv_folder_path):
    for file in f:
        complete_file_path = csv_folder_path+file
        read_file = pd.read_csv(complete_file_path)
        new_df = new_df.append(read_file, ignore_index=True)


new_df.shape

Solution 18

Consider using convtools library, which provides lots of data processing primitives and generates simple ad hoc code under the hood. It is not supposed to be faster than pandas/polars, but sometimes it can be.

e.g. you could concat csv files into one for further reuse - here's the code:

import glob

from convtools import conversion as c
from convtools.contrib.tables import Table
import pandas as pd


def test_pandas():
    df = pd.concat(
        (
            pd.read_csv(filename, index_col=None, header=0)
            for filename in glob.glob("tmp/*.csv")
        ),
        axis=0,
        ignore_index=True,
    )
    df.to_csv("out.csv", index=False)
# took 20.9 s


def test_convtools():
    table = None
    for filename in glob.glob("tmp/*.csv"):
        table_ = Table.from_csv(filename, header=False)
        if table is None:
            table = table_
        else:
            table = table.chain(table_)

    table.into_csv("out_convtools.csv", include_header=False)
# took 15.8 s

Of course if you just want to obtain a dataframe without writing a concatenated file, it will take 4.63 s and 10.9 s correspondingly (pandas is faster here because it doesn't need to zip columns for writing it back).

Solution 19

import pandas as pd
import glob

path = r'C:\DRO\DCL_rawdata_files' # use your path
file_path_list = glob.glob(path + "/*.csv")

file_iter = iter(file_path_list)

list_df_csv = []
list_df_csv.append(pd.read_csv(next(file_iter)))

for file in file_iter:
    lsit_df_csv.append(pd.read_csv(file, header=0))
df = pd.concat(lsit_df_csv, ignore_index=True)

Solution 20

This is how you can do using Colab on Google Drive

import pandas as pd
import glob

path = r'/content/drive/My Drive/data/actual/comments_only' # use your path
all_files = glob.glob(path + "/*.csv")

li = []

for filename in all_files:
    df = pd.read_csv(filename, index_col=None, header=0)
    li.append(df)

frame = pd.concat(li, axis=0, ignore_index=True,sort=True)
frame.to_csv('/content/drive/onefile.csv')