I have an obnoxious .txt file that is output from a late 1990's program for an Agilent instrument. I am trying to comma-separate and organize the single column of the text file into multiple columns in a pd dataframe. After some organization, the txt file currently looks like the following: See link here:
Organized Text File
Each row is indexed in a pd dataframe. The code used to reorganize the file and attempt to split into multiple columns follows:
quantData = pd.read_csv(epaTemp, header = None)
trimmed_File = quantData.iloc[16:,]
trimmed_File = trimmed_File.drop([17,18,70,71,72], axis = 0)
print (trimmed_File)
###
splitFile = trimmed_File.apply( lambda x: pd.Series(str(x).split(',')))
print (splitFile)
The split function above did not get applied to all rows present in the txt file. It only split(',')the first row rather than all of them:
0 16 Compound R... 1
dtype: object
I would like this split functionality to apply to all rows in my txt file so I can further organize my data. Thank you for the help.
Related
I am working with CSV files that are each hundreds of megabytes (800k+ rows), use pipe delimiters, and have 90 columns. What I need to do is compare two files at a time, generating a CSV file of any differences (i.e. rows in File2 that do not exist in File1 as well as rows in File1 that do not exist in File2) but performing the comparison Only using a single column.
For instance, a highly simplified version would be:
File1
claim_date|status|first_name|last_name|phone|claim_number
20200501|active|John|Doe|5555551212|ABC123
20200505|active|Jane|Doe|5555551212|ABC321
File2
claim_date|status|first_name|last_name|phone|claim_number
20200501|active|Someone|New|5555551212|ABC123
20200510|active|Another|Person|5555551212|ABC000
In this example, the output file should look like this:
claim_date|status|first_name|last_name|phone|claim_number
20200505|active|Jane|Doe|5555551212|ABC321
20200510|active|Another|Person|5555551212|ABC000
As this example shows, both input files contained the row with claim_number ABC123 and although the fields first_name and last_name changed between the files I do not care as the claim_number was the same in both files. The other rows contained unique claim_number values and so both were included in the output file.
I have been told that Pandas is the way to do this, so I have set up a Jupyter environment and am able to load the files correctly but am banging my head against the wall at this point. Any suggestions are Highly appreciated!
My code so far:
import os
import pandas as pd
df1 = pd.read_table("/Users/X/Claims_20210607.txt", sep='|', low_memory=False)
df2 = pd.read_table("/Users/X/Claims_20210618.txt", sep='|', low_memory=False)
Everything else I've written is basically irrelevant at this point as it's just copypasta from the web that doesn't execute for one reason or another.
EDIT: Solution!
import os
import pandas as pd
df1 = pd.read_table("Claims_20210607.txt", sep='|', low_memory=False)
df2 = pd.read_table("Claims_20210618.txt", sep='|', low_memory=False)
df1.astype({'claim_number':'str'})
df2.astype({'claim_number':'str'})
df = pd.concat([df1,df2])
(
df.drop_duplicates(
subset=['claim_number'],
keep = False,
ignore_index=True)
.to_csv('diff.csv')
)
I still need to figure out how to kill off the first / added column before writing the file but this is fantastic! Thanks!
IIUC, you can try:
If you wanna drop duplicates based on all columns except ['first_name', 'last_name']:
df = pd.concat([df1, df2])
(
df.drop_duplicates(
subset=df.columns.difference(['first_name', 'last_name']),
keep=False)
.to_csv('file3.csv')
)
If you wanna drop duplicates based on duplicate claim_number column only:
df = pd.concat([df1,df2])
(
df.drop_duplicates(
subset=['claim_number'],
keep = False)
.to_csv('file3.csv')
)
I have a very large data frame that I want to split ALL of the columns except first two based on a comma delimiter. So I need to logically reference column names in a loop or some other way to split all the columns in one swoop.
In my testing of the split method:
I have been able to explicitly refer to ( i.e. HARD CODE) a single column name (rs145629793) as one of the required parameters and the result was 2 new columns as I wanted.
See python code below
HARDCODED COLUMN NAME --
df[['rs1','rs2']] = df.rs145629793.str.split(",", expand = True)
The problem:
It is not feasible to refer to the actual column names and repeat code.
I then replaced the actual column name rs145629793 with columns[2] in the split method parameter list.
It results in an ERROR
'str has ni str attribute'
You can index columns by position rather than name using iloc. For example, to get the third column:
df.iloc[:, 2]
Thus you can easily loop over the columns you need.
I know what you are asking, but it's still helpful to provide some input data and expected output data. I have included random input data in my code below, so you can just copy and paste this to run, and try to apply it to your dataframe:
import pandas as pd
your_dataframe=pd.DataFrame({'a':['1,2,3', '9,8,7'],
'b':['4,5,6', '6,5,4'],
'c':['7,8,9', '3,2,1']})
import copy
def split_cols(df):
dict_of_df = {}
cols=df.columns.to_list()
for col in cols:
key_name = 'df'+str(col)
dict_of_df[key_name] = copy.deepcopy(df)
var=df[col].str.split(',', expand=True).add_prefix(col)
df=pd.merge(df, var, how='left', left_index=True, right_index=True).drop(col, axis=1)
return df
split_cols(your_dataframe)
Essentially, in this solution you create a list of the columns that you want to loop through. Then you loop through that list and create new dataframes for each column where you run the split() function. Then you merge everything back together on the index. I also:
included a prefix of the column name, so the column names did not have duplicate names and could be more easily identifiable
dropped the old column that we did the split on.
Just import copy and use the split_cols() function that I have created and pass the name of your dataframe.
I have a list of csv files that I am trying to concatenate using Pandas.
Given below is sample view of the csv file:
Note: Column 4 - stores the latitude
Column 5 - store the longitude
store-001,store_name,building_no_060,23.4324,43.3532,2018-10-01 10:00:00,city_1,state_1
store-002,store_name,building_no_532,12.4345,45.6743,2018-10-01 12:00:00,city_2,state_1
store-003,store_name,building_no_536,54.3453,23.3444,2018-07-01 04:00:00,city_3,state_1
store-004,store_name,building_no_004,22.4643,56.3322,2018-04-01 07:00:00,city_2,state_3
store-005,store_name,building_no_453,76.3434,55.4345,2018-10-02 16:00:00,city_4,state_2
store-006,store_name,building_no_456,35.3455,54.3334,2018-10-05 10:00:00,city_6,state_2
When I try to concat multiple csv files in the above format, I see the columns having latitude and longitude are first saved in the first row from A2 - A30 and they are followed by the other columns all in the row 1.
Given below is the way I am performing the concat:
masterlist = glob.glob('path') <<- This is the path where all the csv files are stored.
df_v1 = [pd.read_csv(fp, sep=',', error_bad_lines=False).assign(FileName=os.path.basename(fp)) for fp in masterlist] <<-- This also includes the file name in the csv file
df = pd.concat(df_v1, ignore_index=True)
df.to_csv('path'), index=False) <<-- This stores the final concatenated csv file
Could anyone guide me why is the concatenation not working properly. Thanks
My code plan is as follows:
1) find csv files in folder using glob and create a list of files
2) covert each csv file into dataframe
3) extract data from a column location and convert into a separate dataframe
4) append the new data into a separate summary csv file
code is as follows:
Result = []
def result(filepath):
files = glob.glob(filepath)
print files
dataframes = [pd.DataFrame.from_csv(f, index_col=None) for f in files]
new_dfb = pd.DataFrame()
for i, df in enumerate(dataframes):
colname = 'Run {}'.format(i+1)
selected_data = df['3'].ix[0:4]
new_dfb[colname] = selected_data
Result.append(new_dfb)
folder = r"C:/Users/Joey/Desktop/tcd/summary.csv"
new_dfb.to_csv(folder)
result("C:/Users/Joey/Desktop/tcd/*.csv")
print Result
The code error is shown below. The issue seems to be with line 36 .. which corresponds to the selected_data = df['3'].ix[0:4].
I show one of my csv files below:
I'm not sure what the problem is with the dataframe constructor?
You're csv snippet is a bit unclear. But as suggested in the comments, read_csv (from_csv in this case) automatically taken the first row as a list of headers. The behaviour you appear to want is the columns to be labelled as 1,2,3 etc. To achieve this you need to have
[pd.DataFrame.from_csv(f, index_col=None,header=None) for f in files]
I wrote a function that outputs selected data from a parsing function. I am trying to put this information into a DataFrame using pandas.DataFrame but I am having trouble.
The headers are listed below as well as the function.head() data output
QUESTION
How will I be able to place the function output within the pandas DataFrame so the headers are linked to the output
HEADERS
--TICK---------NI----------CAPEXP----------GW---------------OE---------------RE-------
OUTPUT
['MMM', ['4,956,000'], ['(1,493,000)'], ['7,050,000'], ['13,109,000'], ['34,317,000']]
['ABT', ['2,284,000'], ['(1,077,000)'], ['10,067,000'], ['21,526,000'], ['22,874,000']]
['ABBV', ['1,774,000'], ['(612,000)'], ['5,862,000'], ['1,742,000'], ['535,000']]
-Loop through each item (I'm assuming data is a list with each element being one of the lists shown above)
-Take the first element as the ticker and convert the rest into numbers using translate to undo the string formatting
-Make a DataFrame per row and then concat all at the end, then transpose
-Set the columns by parsing the header string (I've called it headers)
dflist = list()
for x in data:
h = x[0]
rest = [float(z[0].translate(str.maketrans('(','-','),'))) for z in x[1:]]
dflist.append(pd.DataFrame([h]+rest))
df = pd.concat(dflist, 1).T
df.columns = [x for x in headers.split('-') if len(x) > 0]
But this might be a bit slow - would be easier if you could get your input into a more consistent format.