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Melt a big data frame without pandas

I have a 3GB dataset with 40k rows and 60k columns which Pandas is unable to read and I would like to melt the file based on the current index.
The current file looks like this:
The first column is an index and I would like to melt all the file based on this index.
I tried pandas and dask, but all of them crush when reading the big file.
Do you have any suggestions?
thanks

You need to use the chunksize property of pandas. See for example How to read a 6 GB csv file with pandas.
You will process N rows at one time, without loading the whole dataframe. N will depend on your computer: if N is low, it will cost less memory but it will increase the run time and will cost more IO load.
# create an object reading your file 100 rows at a time
reader = pd.read_csv( 'bigfile.tsv', sep='\t', header=None, chunksize=100 )
# process each chunk at a time
for chunk in file:
result = chunk.melt()
# export the results into a new file
result.to_csv( 'bigfile_melted.tsv', header=None, sep='\t', mode='a' )
Furthermore, you can use the argument dtype=np.int32 for read_csv if you have integer or dtype=np.float32 to process data faster if you do not need precision.
NB: here you have examples of memory usage: Using Chunksize in Pandas.

Fixed Width File manipulation in Pandas

I have a fixed-width file with the following format:
5678223313570888271712000000024XAXX0101010006461801325345088800.0784001501.25abc#yahoo.com
5678223324686600271712000000070XAXX0101010006461801325390998280.0784001501.25abcde.12345#gmail.com 5678123422992299
Here's what i tried :
import pandas as pd
ColSpecs = [(0,16),(16,31),(31,44),(44,62),(62,70),(70,73),(73,77),(77,127),(127,143)]
df = pd.read_fwf("~/filename.txt",colspecs=ColSpecs,Header=True)
Now this surely helps me to convert cleanly in Pandas format. However, the blank(or fixed white spaces) get trimmed off. For Eg: the Email field(#8) has 50 characters set fixed. They get truncated as soon as they're imported to Pandas dataframe.
For the data manipulation, I am creating 3 new fields that are extracted from the values of the previously imported fields.
Final Output file structure:
[(0,16),(16,31),(31,44),(44,62),(62,70),(70,73),(73,77),(77,127),(127,143),(143,153),(153,163),(164,165)]
Since, I haven't found any to_fwf method on dataframes or any other alternative for Pandas -> Flat File (keeping original lengths intact) , I would really appreciate if anyone has a better solution.
P.S. : I read that awk/sed in Unix works better, but still would like to know for Python

Loading large csv file in pandas

I am trying to load csv files in pandas dataframe. However, Python is taking very large amount of memory while loading the files. For example, the size of csv file is 289 MB but the memory usage goes to around 1700 MB while I am trying to load the file. And at that point, the system shows memory error. I have also tried chunk size but the problem persists. Can anyone please show me a way forward?

OK, first things first, do not confuse disk size and memory size. A csv, in it's core is a plain text file, whereas a pandas dataframe is a complex object loaded in memory. That said, I can't give a statement about your particular case, considering that I don't know what you have in your csv. So instead I'll give you an example with a csv on my computer that has a similar size:
-rw-rw-r-- 1 alex users 341M Jan 12 2017 cpromo_2017_01_12_rec.csv
Now reading the CSV:
>>> import pandas as pd
>>> df = pd.read_csv('cpromo_2017_01_12_rec.csv')
>>> sys:1: DtypeWarning: Columns (9) have mixed types. Specify dtype option on import or set low_memory=False.
>>> df.memory_usage(deep=True).sum() / 1024**2
1474.4243307113647
Pandas will attempt to optimize it as much as it can, but it won't be able to do the impossible. If you are low on memory, this answer is a good place to start. Alternatively you could try dask but I think that's too much work for a small csv.

You can use the library "dask" e.g:
# Dataframes implement the Pandas API
import dask.dataframe as dd`<br>
df = dd.read_csv('s3://.../2018-*-*.csv')

try like this - 1) load with dask and then 2) convert to pandas
import pandas as pd
import dask.dataframe as dd
import time
t=time.clock()
df_train = dd.read_csv('../data/train.csv', usecols=[col1, col2])
df_train=df_train.compute()
print("load train: " , time.clock()-t)

Pandas read_csv large file Performance improvement

Just was wondering if there is a way to improve the performance of reading large csv files into a pandas dataframe. I have 3 large (3.5MM records each) pipe delimited file which I want to load into dataframe and perform some task on it. Currently I am using pandas.read_csv() defining the cols and there datatypes in the parameter like below. I did see some improvement by defining the datatype of the columns but it still takes more than 3 minutes to load.
import pandas as pd
df = pd.read_csv(file_, index_col=None, usecols = sourceFields, sep='|', header=0, dtype={'date':'str', 'gwTimeUtc':'str', 'asset':'|str',
'instrumentId':'|str', 'askPrice':'float64', 'bidPrice':'float64',
'askQuantity':'float64', 'bidQuantity':'float64', 'currency':'|str',
'venue':'|str', 'owner':'|str', 'status':'|str', 'priceNotation':'|str', 'nominalQuantity':'float64'})

Depending on what you wish to do with the data, a good option is dask.dataframe. This library works out-of-memory, and allows you to perform a subset of pandas operations lazily. You can then bring the results in memory as a pandas dataframe. Below is example code you can try:
import dask.dataframe as dd, pandas as pd
# point to all files beginning with "file"
dask_df = dd.read_csv('file*.csv')
# define your calculations as you would in pandas
dask_df['col2'] = dask_df['col1'] * 2
# compute results & return to pandas
df = dask_df.compute()
Crucially, nothing significant is computed until the very last line.

The .feather file is significantly faster than .csv. Pandas has built-in support for feather files.
Read the csv in using pd.read_csv(path) and then export it to a feather file: pd.to_feather(path). Now, read the feather file instead of csv.
In my case, a 950 MB csv file was compressed to a 180 MB feather file. Instead of taking 30 seconds to read, it takes about 1 second. I know I am a bit late to the party, but feather files are seriously underrated.

Extracting data from a large csv file:causes dtype warnings

I work for a company and I recently switched from using spreadsheet package to python. Since, I am very new to python there are alot of things that I have difficulty grasping.Using python, I am trying to extract data from a large csv file(37791 rows and 316 columns.) Here is a piece of code I wrote:
Solution 1
import numpy as np
import pandas as pd
df=pd.read_csv=('C:\\Users\\Maxwell\\Desktop\\Test.data.csv',skiprows=1)
data=df.loc[:,['Steps','Parameter']]
This command generates an error,i.e, it gives a DtypeWwarning:columns (0,1,2,3........81) have mixed types. Specify dtype option on import or set low memory= False
So, I found a workaround.
Solution 2
import pandas as pd
import numpy as np
df=pd.read_csv(('C:\\Users\\Maxwell\\Desktop\\Test.data.csv',skiprows=1,error_bad_lines=False, index_col=False, dtype='unicode')
data=df.loc[:,['Steps','Parameter']]
Two questions:
i)I was able to get around the error, but now the columns that I want(Steps & Parameter)have been converted to objects(probably due to the dtype='unicode' command). How can I convert Steps column into an integer type and parameter into a float.
ii) Some people say that dtype warning isn't really an error. But, I found out that when I use Solution 1 and read the csv file. The Steps column contains some floats.The original csv file doesn't have any floats in Steps column. It looks as if, some floats have been placed by python itself!! Why does this happen?
(I am not able to upload the original csv file, because my company doesn't allow it!)