Develop Reference

Adding notes to a data file (csv) in python

I am trying to capture data from an oscilloscope using a python script. The script saves it as in csv format. I need to add few lines of text describing the data at the beginning.
I looked at existing threads to see if there was a possible solution. I just started learning Python. I am using code that came with the instrument.
This is part of the script that saves the data as csv.
NewD = (np.insert(Wav_Data, 0, DataTime, axis = 0)).T
filename = BASE_DIRECTORY + BASE_FILE_NAME + ".csv"
now = time.time() # Only to show how long it takes to save
with open(filename, 'w') as filehandle:
np.savetxt(filename, NewD, delimiter = ',', header = column_titles)
I tried to use the section below from another code but am not sure how to append this to the csv file.
with open("notes.txt") as f:
NOTES = f.readlines()
NOTES = "".join(NOTES)
It is unable to find notes.txt which is located in the same directory as the script.
Eager to hear your feedback. Thanks in advance.
Updated to:
# Save data
NewD = (np.insert(Wav_Data, 0, DataTime, axis = 0)).T
filename = BASE_DIRECTORY + BASE_FILE_NAME + ".csv"
with open("notes.txt") as f:
NOTES = f.readlines()
NOTES = "".join(NOTES)
with open(filename, "a") as fh:
fh.write(NOTES)
now = time.time() # Only to show how long it takes to save
with open(filename, 'w') as filehandle:
np.savetxt(filename, NewD, delimiter = ',', header = column_titles)

Just open the file for appending or write
If you want to write CSV first then notes:
with open("notes.txt") as f:
NOTES = f.readlines()
NOTES = "".join(NOTES)
with open(filename, "w") as fh:
fh.write(NOTES)
# this time we give np the opened filehandle, not the filename
np.savetxt(fh, NewD, delimiter = ',', header = column_titles)

Converting JSON to CSV, CSV is empty

I'm attempting to convert yelps data set that is in JSON to a csv format. The new csv file that is created is empty.
I've tried different ways to iterate through the JSON but they all give me a zero bytes file.
The json file looks like this:
{"business_id":"1SWheh84yJXfytovILXOAQ","name":"Arizona Biltmore Golf Club","address":"2818 E Camino Acequia Drive","city":"Phoenix","state":"AZ","postal_code":"85016","latitude":33.5221425,"longitude":-112.0184807,"stars":3.0,"review_count":5,"is_open":0,"attributes":{"GoodForKids":"False"},"categories":"Golf, Active Life","hours":null}
import json
import csv
infile = open("business.json","r")
outfile = open("business2.csv","w")
data = json.load(infile)
infile.close()
out = csv.writer(outfile)
out.writerow(data[0].keys())
for row in data:
out.writerow(row.values())
I get an "extra data" message when the code runs. The new business2 csv file is empty and the size is zero bytes.

if you JSON has only one row.. then try this
infile = open("business.json","r")
outfile = open("business2.csv","w")
data = json.load(infile)
infile.close()
out = csv.writer(outfile)
#print(data.keys())
out.writerow(data.keys())
out.writerow(data.values())

Hi Please try the below code, by using with command the file access will automatically get closed when the control moves out of scope of with
infile = open("business.json","r")
outfile = open("business2.csv","w")
data = json.load(infile)
infile.close()
headers = list(data.keys())
values = list(data.values())
with open("business2.csv","w") as outfile:
out = csv.writer(outfile)
out.writerow(headers)
out.writerow(values)

You need to use with to close file.
import json
import csv
infile = open("business.json","r")
data = json.load(infile)
infile.close()
with open("business2.csv","w") as outfile:
out = csv.writer(outfile)
out.writerow(list(data.keys()))
out.writerow(list(data.values()))

Having problems writing to text files. Text files being overwritten/cut

I would like to write new data to the beginning of my text file, with the previous data shifting down 1 line each time new data is imported, I would like everything to be organized, but every time I import something gets deleted.
Code:
import requests
from bs4 import BeautifulSoup
from datetime import datetime
response = requests.get('https://www.lotteryusa.com/michigan/lucky-4-life/')
soup = BeautifulSoup(response.text, 'html.parser')
date = soup.find(class_='date')
results = soup.find(class_='draw-result list-unstyled list-inline')
d = datetime.strptime(date.time['datetime'], '%Y-%m-%d')
Lucky = (d.strftime("%m%d%Y")+(',')+results.get_text()[:-20].strip().replace('\n',','))
print(Lucky)
with open("webscraper2noteppad++", "r+") as f:
file = f.readlines()
f.seek(0,0)
f.write(Lucky)
Also tried doing this
with open("webscraper2noteppad++", "r+") as f:
file = f.read()
f.seek(0,0)
f.write(Lucky + '\n')
but I have to put 10 lines between the already existing data, and the new data. So it can be can be imported on top without deleting.

You can first read the content of your file, the append it to the new data and then write everything to the file:
with open("webscraper2noteppad++", "r") as f:
data = f.read()
with open("webscraper2noteppad++", "w") as f:
f.write('{}{}{}'.format(lucky, '\n' if data else '', data))

Editing a downloaded CSV in memory before writing

Forewarning: I am very new to Python and programming in general. I am trying to use Python 3 to get some CSV data and making some changes to it before writing it to a file. My problem lies in accessing the CSV data from a variable, like so:
import csv
import requests
csvfile = session.get(url)
reader = csv.reader(csvfile.content)
for row in reader:
do(something)
This returns:
_csv.Error: iterator should return strings, not int (did you open the file in text mode?)
Googling revealed that I should be feeding the reader text instead of bytes, so I also attempted:
reader = csv.reader(csvfile.text)
This also does not work as the loop works through it letter by letter instead of line by line. I also experimented with TextIOWrapper and similar options with no success. The only way I have managed to get this to work is by writing the data to a file, reading it, and then making changes, like so:
csvfile = session.get(url)
with open("temp.txt", 'wb') as f:
f.write(csvfile.content)
with open("temp.txt", 'rU', encoding="utf8") as data:
reader = csv.reader(data)
for row in reader:
do(something)
I feel like this is far from the most optimal way of doing this, even if it works. What is the proper way to read and edit the CSV data directly from memory, without having to save it to a temporary file?

you don't have to write to a temp file, here is what I would do, using the "csv" and "requests" modules:
import csv
import requests
__csvfilepathname__ = r'c:\test\test.csv'
__url__ = 'https://server.domain.com/test.csv'
def csv_reader(filename, enc = 'utf_8'):
with open(filename, 'r', encoding = enc) as openfileobject:
reader = csv.reader(openfileobject)
for row in reader:
#do something
print(row)
return
def csv_from_url(url):
line = ''
datalist = []
s = requests.Session()
r = s.get(url)
for x in r.text.replace('\r',''):
if not x[0] == '\n':
line = line + str(x[0])
else:
datalist.append(line)
line = ''
datalist.append(line)
# at this point you already have a data list 'datalist'
# no need really to use the csv.reader object, but here goes:
reader = csv.reader(datalist)
for row in reader:
#do something
print(row)
return
def main():
csv_reader(__csvfilepathname__)
csv_from_url(__url__)
return
if __name__ == '__main__':
main ()
not very pretty, and probably not very good in regards to memory/performance, depending on how "big" your csv/data is
HTH, Edwin.

extracting data from CSV file using a reference

I have a csv file with several hundred organism IDs and a second csv file with several thousand organism IDs and additional characteristics (taxonomic information, abundances per sample, etc)
I am trying to write a code that will extract the information from the larger csv using the smaller csv file as a reference. Meaning it will look at both smaller and larger files, and if the IDs are in both files, it will extract all the information form the larger file and write that in a new file (basically write the entire row for that ID).
so far I have written the following, and while the code does not error out on me, I get a blank file in the end and I don't exactly know why. I am a graduate student that knows some simple coding but I'm still very much a novice,
thank you
import sys
import csv
import os.path
SparCCnames=open(sys.argv[1],"rU")
OTU_table=open(sys.argv[2],"rU")
new_file=open(sys.argv[3],"w")
Sparcc_OTUs=csv.writer(new_file)
d=csv.DictReader(SparCCnames)
ids=csv.DictReader(OTU_table)
for record in ids:
idstopull=record["OTUid"]
if idstopull[0]=="OTUid":
continue
if idstopull[0] in d:
new_id.writerow[idstopull[0]]
SparCCnames.close()
OTU_table.close()
new_file.close()

I'm not sure what you're trying to do in your code but you can try this:
def csv_to_dict(csv_file_path):
csv_file = open(csv_file_path, 'rb')
csv_file.seek(0)
sniffdialect = csv.Sniffer().sniff(csv_file.read(10000), delimiters='\t,;')
csv_file.seek(0)
dict_reader = csv.DictReader(csv_file, dialect=sniffdialect)
csv_file.seek(0)
dict_data = []
for record in dict_reader:
dict_data.append(record)
csv_file.close()
return dict_data
def dict_to_csv(csv_file_path, dict_data):
csv_file = open(csv_file_path, 'wb')
writer = csv.writer(csv_file, dialect='excel')
headers = dict_data[0].keys()
writer.writerow(headers)
# headers must be the same with dat.keys()
for dat in dict_data:
line = []
for field in headers:
line.append(dat[field])
writer.writerow(line)
csv_file.close()
if __name__ == "__main__":
big_csv = csv_to_dict('/path/to/big_csv_file.csv')
small_csv = csv_to_dict('/path/to/small_csv_file.csv')
output = []
for s in small_csv:
for b in big_csv:
if s['id'] == b['id']:
output.append(b)
if output:
dict_to_csv('/path/to/output.csv', output)
else:
print "Nothing."
Hope that will help.

You need to read the data into a data structure, assuming OTUid is unique you can store this into a dictionary for fast lookup:
with open(sys.argv[1],"rU") as SparCCnames:
d = csv.DictReader(SparCCnames)
fieldnames = d.fieldnames
data = {i['OTUid']: i for i in d}
with open(sys.argv[2],"rU") as OTU_table, open(sys.argv[3],"w") as new_file:
Sparcc_OTUs = csv.DictWriter(new_file, fieldnames)
ids = csv.DictReader(OTU_table)
for record in ids:
if record['OTUid'] in data:
Sparcc_OTUs.writerow(data[record['OTUid']])

Thank you everyone for your help. I played with things and consulted with an advisor, and finally got a working script. I am posting it in case it helps someone else in the future.
Thanks!
import sys
import csv
input_file = csv.DictReader(open(sys.argv[1], "rU")) #has all info
ref_list = csv.DictReader(open(sys.argv[2], "rU")) #reference list
output_file = csv.DictWriter(
open(sys.argv[3], "w"), input_file.fieldnames) #to write output file with headers
output_file.writeheader() #write headers in output file
white_list={} #create empty dictionary
for record in ref_list: #for every line in my reference list
white_list[record["Sample_ID"]] = None #store into the dictionary the ID's as keys
for record in input_file: #for every line in my input file
record_id = record["Sample_ID"] #store ID's into variable record_id
if (record_id in white_list): #if the ID is in the reference list
output_file.writerow(record) #write the entire row into a new file
else: #if it is not in my reference list
continue #ignore it and continue iterating through the file