I have a .txt file of amino acids separated by ">node" like this:
Filename.txt :
>NODE_1
MSETLVLTRPDDWHVHLRDGAALQSVVPYTARQFARAIAMPNLKPPITTAEQAQAYRERI
KFFLGTDSAPHASVMKENSVCGAGCFTALSALELYAEAFEAAGALDKLEAFASFHGADFY
GLPRNTTQVTLRKTEWTLPESVPFGEAAQLKPLRGGEALRWKLD*
>NODE_2
MSTWHKVQGRPKAQARRPGRKSKDDFVTRVEHDAKNDALLQLVRAEWAMLRSDIATFRGD
MVERFGKVEGEITGIKGQIDGLKGEMQGVKGEVEGLRGSLTTTQWVVGTAMALLAVVTQV
PSIISAYRFPPAGSSAFPAPGSLPTVPGSPASAASAP*
I want to separate this file into two (or as many as there are nodes) files;
Filename1.txt :
>NODE
MSETLVLTRPDDWHVHLRDGAALQSVVPYTARQFARAIAMPNLKPPITTAEQAQAYRERI
KFFLGTDSAPHASVMKENSVCGAGCFTALSALELYAEAFEAAGALDKLEAFASFHGADFY
GLPRNTTQVTLRKTEWTLPESVPFGEAAQLKPLRGGEALRWKLD*
Filename2.txt :
>NODE
MSTWHKVQGRPKAQARRPGRKSKDDFVTRVEHDAKNDALLQLVRAEWAMLRSDIATFRGD
MVERFGKVEGEITGIKGQIDGLKGEMQGVKGEVEGLRGSLTTTQWVVGTAMALLAVVTQV
PSIISAYRFPPAGSSAFPAPGSLPTVPGSPASAASAP*
With a number after the filename
This code works, however it deletes the ">NODE" line and does not create a file for the last node (the one without a '>' afterwards).
with open('FilePathway') as fo:
op = ''
start = 0
cntr = 1
for x in fo.read().split("\n"):
if x.startswith('>'):
if start == 1:
with open (str(cntr) + '.fasta','w') as opf:
opf.write(op)
opf.close()
op = ''
cntr += 1
else:
start = 1
else:
if op == '':
op = x
else:
op = op + '\n' + x
fo.close()
I can´t seem to find the mistake. Would be thankful if you could point it out to me.
Thank you for your help!
Hi again! Thank you for all the comments. With your help, I managed to get it to work perfectly. For anyone with similar problems, this is my final code:
import os
import glob
folder_path = 'FilePathway'
for filename in glob.glob(os.path.join(folder_path, '*.fasta')):
with open(filename) as fo:
for line in fo.readlines():
if line.startswith('>'):
original = line
content = [original]
fileno = 1
filename = filename
y = filename.replace(".fasta","_")
def writefasta():
global content, fileno
if len(content) > 1:
with open(f'{y}{fileno}.fasta', 'w') as fout:
fout.write(''.join(content))
content = [line]
fileno += 1
with open('FilePathway') as fin:
for line in fin:
if line.startswith('>NODE'):
writefasta()
else:
content.append(line)
writefasta()
You could do it like this:
def writefasta(d):
if len(d['content']) > 1:
with open(f'Filename{d["fileno"]}.fasta', 'w') as fout:
fout.write(''.join(d['content']))
d['content'] = ['>NODE\n']
d['fileno'] += 1
with open('test.fasta') as fin:
D = {'content': ['>NODE\n'], 'fileno': 1}
for line in fin:
if line.startswith('>NODE'):
writefasta(D)
else:
D['content'].append(line)
writefasta(D)
This would be better way. It is going to write only on odd iterations. So that, ">NODE" will be skipped and files will be created only for the real content.
with open('filename.txt') as fo:
cntr=1
for i,content in enumerate(fo.read().split("\n")):
if i%2 == 1:
with open (str(cntr) + '.txt','w') as opf:
opf.write(content)
cntr += 1
By the way, since you are using context manager, you dont need to close the file.
Context managers allow you to allocate and release resources precisely
when you want to. It opens the file, writes some data to it and then
closes it.
Please check: https://book.pythontips.com/en/latest/context_managers.html
with open('FileName') as fo:
cntr = 1
for line in fo.readlines():
with open (f'{str(cntr)}.fasta','w') as opf:
opf.write(line)
opf.close()
op = ''
cntr += 1
fo.close()
I have a csv file of about 5000 rows in python i want to split it into five files.
I wrote a code for it but it is not working
import codecs
import csv
NO_OF_LINES_PER_FILE = 1000
def again(count_file_header,count):
f3 = open('write_'+count_file_header+'.csv', 'at')
with open('import_1458922827.csv', 'rb') as csvfile:
candidate_info_reader = csv.reader(csvfile, delimiter=',', quoting=csv.QUOTE_ALL)
co = 0
for row in candidate_info_reader:
co = co + 1
count = count + 1
if count <= count:
pass
elif count >= NO_OF_LINES_PER_FILE:
count_file_header = count + NO_OF_LINES_PER_FILE
again(count_file_header,count)
else:
writer = csv.writer(f3,delimiter = ',', lineterminator='\n',quoting=csv.QUOTE_ALL)
writer.writerow(row)
def read_write():
f3 = open('write_'+NO_OF_LINES_PER_FILE+'.csv', 'at')
with open('import_1458922827.csv', 'rb') as csvfile:
candidate_info_reader = csv.reader(csvfile, delimiter=',', quoting=csv.QUOTE_ALL)
count = 0
for row in candidate_info_reader:
count = count + 1
if count >= NO_OF_LINES_PER_FILE:
count_file_header = count + NO_OF_LINES_PER_FILE
again(count_file_header,count)
else:
writer = csv.writer(f3,delimiter = ',', lineterminator='\n',quoting=csv.QUOTE_ALL)
writer.writerow(row)
read_write()
The above code creates many fileswith empty content.
How to split one files into five csv files?
In Python
Use readlines() and writelines() to do that, here is an example:
>>> csvfile = open('import_1458922827.csv', 'r').readlines()
>>> filename = 1
>>> for i in range(len(csvfile)):
... if i % 1000 == 0:
... open(str(filename) + '.csv', 'w+').writelines(csvfile[i:i+1000])
... filename += 1
the output file names will be numbered 1.csv, 2.csv, ... etc.
From terminal
FYI, you can do this from the command line using split as follows:
$ split -l 1000 import_1458922827.csv
I suggest you not inventing a wheel. There is existing solution. Source here
import os
def split(filehandler, delimiter=',', row_limit=1000,
output_name_template='output_%s.csv', output_path='.', keep_headers=True):
import csv
reader = csv.reader(filehandler, delimiter=delimiter)
current_piece = 1
current_out_path = os.path.join(
output_path,
output_name_template % current_piece
)
current_out_writer = csv.writer(open(current_out_path, 'w'), delimiter=delimiter)
current_limit = row_limit
if keep_headers:
headers = reader.next()
current_out_writer.writerow(headers)
for i, row in enumerate(reader):
if i + 1 > current_limit:
current_piece += 1
current_limit = row_limit * current_piece
current_out_path = os.path.join(
output_path,
output_name_template % current_piece
)
current_out_writer = csv.writer(open(current_out_path, 'w'), delimiter=delimiter)
if keep_headers:
current_out_writer.writerow(headers)
current_out_writer.writerow(row)
Use it like:
split(open('/your/pat/input.csv', 'r'));
A python3-friendly solution:
def split_csv(source_filepath, dest_folder, split_file_prefix,
records_per_file):
"""
Split a source csv into multiple csvs of equal numbers of records,
except the last file.
Includes the initial header row in each split file.
Split files follow a zero-index sequential naming convention like so:
`{split_file_prefix}_0.csv`
"""
if records_per_file <= 0:
raise Exception('records_per_file must be > 0')
with open(source_filepath, 'r') as source:
reader = csv.reader(source)
headers = next(reader)
file_idx = 0
records_exist = True
while records_exist:
i = 0
target_filename = f'{split_file_prefix}_{file_idx}.csv'
target_filepath = os.path.join(dest_folder, target_filename)
with open(target_filepath, 'w') as target:
writer = csv.writer(target)
while i < records_per_file:
if i == 0:
writer.writerow(headers)
try:
writer.writerow(next(reader))
i += 1
except StopIteration:
records_exist = False
break
if i == 0:
# we only wrote the header, so delete that file
os.remove(target_filepath)
file_idx += 1
I have modified the accepted answer a little bit to make it simpler
Edited: Added the import statement, modified the print statement for printing the exception. #Alex F code snippet was written for python2, for python3 you also need to use header_row = rows.__next__() instead header_row = rows.next(). Thanks for pointing out.
import os
import csv
def split_csv_into_chunks(file_location, out_dir, file_size=2):
count = 0
current_piece = 1
# file_to_split_name.csv
file_name = file_location.split("/")[-1].split(".")[0]
split_file_name_template = file_name + "__%s.csv"
splited_files_path = []
if not os.path.exists(out_dir):
os.makedirs(out_dir)
try:
with open(file_location, "rb") as csv_file:
rows = csv.reader(csv_file, delimiter=",")
headers_row = rows.next()
for row in rows:
if count % file_size == 0:
current_out_path = os.path.join(out_dir,
split_file_name_template%str(current_piece))
current_out_writer = None
current_out_writer = csv.writer(open(current_out_path, 'w'), delimiter=",")
current_out_writer.writerow(headers_row)
splited_files_path.append(current_out_path)
current_piece += 1
current_out_writer.writerow(row)
count += 1
return True, splited_files_path
except Exception as e:
print("Exception occurred as {}".format(e))
return False, splited_files_path
#Ryan, Python3 code worked for me. I used newline='' as below to avoid the blank line issue:
with open(target_filepath, 'w', newline='') as target:
Another pandas solution (each 1000 rows), similar to Aziz Alto solution:
suffix = 1
for i in range(len(df)):
if i % 1000 == 0:
df[i:i+1000].to_csv(f"processed/{filename}_{suffix}.csv", sep ='|', index=False, index_label=False)
suffix += 1
where df is the csv loaded as pandas.DataFrame; filename is the original filename, the pipe is a separator; index and index_label false is to skip the autoincremented index columns
A simple Python 3 solution with Pandas that doesn't cut off the last batch
def to_csv_batch(src_csv, dst_dir, size=30000, index=False):
import pandas as pd
import math
# Read source csv
df = pd.read_csv(src_csv)
# Initial values
low = 0
high = size
# Loop through batches
for i in range(math.ceil(len(df) / size)):
fname = dst_dir+'/Batch_' + str(i+1) + '.csv'
df[low:high].to_csv(fname, index=index)
# Update selection
low = high
if (high + size < len(df)):
high = high + size
else:
high = len(df)
Usage example
to_csv_batch('Batch_All.csv', 'Batches')
if count <= count:
pass
This condition is always true so you pass everytime
Otherwise you can look at this post: Splitting a CSV file into equal parts?
I suggest you leverage the possibilities offered by pandas. Here are functions you could use to do that :
def csv_count_rows(file):
"""
Counts the number of rows in a file.
:param file: path to the file.
:return: number of lines in the designated file.
"""
with open(file) as f:
nb_lines = sum(1 for line in f)
return nb_lines
def split_csv(file, sep=",", output_path=".", nrows=None, chunksize=None, low_memory=True, usecols=None):
"""
Split a csv into several files.
:param file: path to the original csv.
:param sep: View pandas.read_csv doc.
:param output_path: path in which to output the resulting parts of the splitting.
:param nrows: Number of rows to split the original csv by, also view pandas.read_csv doc.
:param chunksize: View pandas.read_csv doc.
:param low_memory: View pandas.read_csv doc.
:param usecols: View pandas.read_csv doc.
"""
nb_of_rows = csv_count_rows(file)
# Parsing file elements : Path, name, extension, etc...
# file_path = "/".join(file.split("/")[0:-1])
file_name = file.split("/")[-1]
# file_ext = file_name.split(".")[-1]
file_name_trunk = file_name.split(".")[0]
split_files_name_trunk = file_name_trunk + "_part_"
# Number of chunks to partition the original file into
nb_of_chunks = math.ceil(nb_of_rows / nrows)
if nrows:
log_debug_process_start = f"The file '{file_name}' contains {nb_of_rows} ROWS. " \
f"\nIt will be split into {nb_of_chunks} chunks of a max number of rows : {nrows}." \
f"\nThe resulting files will be output in '{output_path}' as '{split_files_name_trunk}0 to {nb_of_chunks - 1}'"
logging.debug(log_debug_process_start)
for i in range(nb_of_chunks):
# Number of rows to skip is determined by (the number of the chunk being processed) multiplied by (the nrows parameter).
rows_to_skip = range(1, i * nrows) if i else None
output_file = f"{output_path}/{split_files_name_trunk}{i}.csv"
log_debug_chunk_processing = f"Processing chunk {i} of the file '{file_name}'"
logging.debug(log_debug_chunk_processing)
# Fetching the original csv file and handling it with skiprows and nrows to process its data
df_chunk = pd.read_csv(filepath_or_buffer=file, sep=sep, nrows=nrows, skiprows=rows_to_skip,
chunksize=chunksize, low_memory=low_memory, usecols=usecols)
df_chunk.to_csv(path_or_buf=output_file, sep=sep)
log_info_file_output = f"Chunk {i} of file '{file_name}' created in '{output_file}'"
logging.info(log_info_file_output)
And then in your main or jupyter notebook you put :
# This is how you initiate logging in the most basic way.
logging.basicConfig(level=logging.DEBUG)
file = {#Path to your file}
split_csv(file,sep=";" ,output_path={#Path where you'd like to output it},nrows = 4000000, low_memory = False)
P.S.1 : I put nrows = 4000000 because when it's a personal preference. You can change that number if you wish.
P.S.2 : I used the logging library to display messages. When would apply such a function on big files that exist on a remote server, you really want to avoid 'simple printing' and incorporate logging capabilities. You can replace logging.info or logging.debug with print
P.S.3 : Of course, you need to replace the {# Blablabla} parts of the code with your own parameters.
A simpler script works for me.
import pandas as pd
path = "path to file" # path to file
df = pd.read_csv(path) # reading file
low = 0 # Initial Lower Limit
high = 1000 # Initial Higher Limit
while(high < len(df)):
df_new = df[low:high] # subsetting DataFrame based on index
low = high #changing lower limit
high = high + 1000 # givig uper limit with increment of 1000
df_new.to_csv("Path to output file") # output file
import pandas as pd
df = pd.read_csv('input.csv')
file_len = len(df)
filename = 'output'
n = 1
for i in range(file_len):
if i % 10 == 0:
sf = (df[i:i+10])
sf.to_csv(f'{filename}_{n}.csv', index=False)
n += 1
Building upon the top voted answer, here is a python solution that also includes the headers in each file.
file = open('file.csv', 'r')
header = file.readline()
csvfile = file.readlines()
filename = 1
batch_size = 1000
for i in range(len(csvfile)):
if i % batch_size == 0:
open(str(filename) + '.csv', 'w+').writelines(header)
open(str(filename) + '.csv', 'a+').writelines(csvfile[i:i+batch_size])
filename += 1
This will output the same file names as 1.csv, 2.csv, ... etc.
The following is a very simple solution, that does not loop over all rows, but only on the chunks - imagine if you have millions of rows.
chunk_size = 100_000
for i in range(len(df) // chunk_size + 1):
df[i*chunk_size:(i+1)*chunk_size].to_csv(f"output_{i:02d}.csv",
sep=";", index=False)
You define the chunk size and if the total number of rows is not an integer multiple of the chunk size, the last chunk will contain the rest.
Using f"output_{i:02d}.csv" the suffix will be formatted with two digits and a leading zero
If you want to have a header only for the first chunk (and no header for the other chunks), then you can use a boolean over the suffix index at i == 0, that is:
for i in range(len(df) // chunk_size + 1):
df[i*chunk_size:(i+1)*chunk_size].to_csv(f"output_{i:02d}.csv",
sep=";", index=False, header=(i == 0))
here is my code for readinng individual cell of one csv file. but want to read multiple csv file one by one from .txt file where csv file paths are located.
import csv
ifile = open ("C:\Users\BKA4ABT\Desktop\Test_Specification\RDBI.csv", "rb")
data = list(csv.reader(ifile, delimiter = ';'))
REQ = []
RES = []
n = len(data)
for i in range(n):
x = data[i][1]
y = data[i][2]
REQ.append (x)
RES.append (y)
i += 1
for j in range(2,n):
try:
if REQ[j] != '' and RES[j]!= '': # ignore blank cell
print REQ[j], ' ', RES[j]
except:
pass
j += 1
And csv file paths are stored in a .txt file like
C:\Desktop\Test_Specification\RDBI.csv
C:\Desktop\Test_Specification\ECUreset.csv
C:\Desktop\Test_Specification\RDTC.csv
and so on..
You can read stuff stored in files into variables. And you can use variables with strings in them anywhere you can use a literal string. So...
with open('mytxtfile.txt', 'r') as txt_file:
for line in txt_file:
file_name = line.strip() # or was it trim()? I keep mixing them up
ifile = open(file_name, 'rb')
# ... the rest of your code goes here
Maybe we can fix this up a little...
import csv
with open('mytxtfile.txt', 'r') as txt_file:
for line in txt_file:
file_name = line.strip()
csv_file = csv.reader(open(file_name, 'rb', delimiter=';'))
for record in csv_file[1:]: # skip header row
req = record[1]
res = record[2]
if len(req + res):
print req, ' ', res
you just need to add a while which will read your file containing your list of files & paths upon your first open statement, for example
from __future__ import with_statement
with open("myfile_which_contains_file_path.txt") as f:
for line in f:
ifile = open(line, 'rb')
# here the rest of your code
You need to use a raw string string your path contains \
import csv
file_list = r"C:\Users\BKA4ABT\Desktop\Test_Specification\RDBI.csv"
with open(file_list) as f:
for line in f:
with open(line.strip(), 'rb') as the_file:
reader = csv.reader(the_file, delimiter=';')
for row in reader:
req,res = row[1:3]
if req and res:
print('{0} {1}'.format(req, res))
I need to be able to reverse a whole file, or at least the contents of it. My code so far is:
def reverse_file(of, rf):
oldfile = open(of, 'r')
reversefile = open(rf, 'w')
filedata = oldfile.read()
rdata = str_reverse(filedata)
reversefile.write(rdata)
oldfile.close()
reversefile.close()
The problem is I need to define str_reverse and I'm not sure how to create a function that reverses everything. Any help?
If you want to reverse the entire file, you can just call write with data[::-1]
def reverse_file(of, rf):
with open(of) as oldfile:
with open(rf, "w") as reversefile:
reversefile.write(oldfile.read()[::-1])
example:
% cat testdata
line1
line2
line3
% cat reverse_file.py
def reverse_file(of, rf):
with open(of) as oldfile:
with open(rf, "w") as reversefile:
reversefile.write(oldfile.read()[::-1])
if __name__ == "__main__":
reverse_file("testdata", "newdata")
% python reverse_file.py
% cat newdata
3enil
2enil
1enil
To support files that do not fit in memory (based on #Darius Bacon's answer):
import os
from io import DEFAULT_BUFFER_SIZE
def reverse_blocks(file, blocksize=DEFAULT_BUFFER_SIZE):
"""Yield blocks from the file in reverse order."""
file.seek(0, os.SEEK_END) # move file position to the end
position = file.tell()
while position > 0:
delta = min(blocksize, position)
file.seek(position - delta, os.SEEK_SET)
yield file.read(delta)
position -= blocksize
# reverse input and write it to output
with open("input", "rb") as infile, open("output", "wb") as outfile:
for block in reverse_blocks(infile):
outfile.write(block[::-1])