[Tutor] Extract Field from List

[Stephen P. Molnar]

Python v-3.7.3

The Script returns a one element list:

0 str 99 CaffeicAcid    Cannflavin-A    Cannflavin-B Cannflavin-C    
Diosmetin    Echinacoside    Hesperetin L-CichoricAcid

In the next step I want to iteratively insert each name in the list in:

for i in range(1,11):
     name_in = name+.i'.log'
     data+.i = np.genfromtxt(name_in, skip_header=28, skip_footer=1)
     data+.i = data+.i[0, 1]

Most likely, it would probably be simpler to put these lines of code 
into a function.

Now I'm not certain about formatting the insertion the value of i. 
Coming out of the loop I want to have a series of files, data1 to data10 
to use as arguments for np.vstack(...

I would be most grateful for assistance in solving this problem.

Thanks in advance.

On 08/08/2021 10:36 AM, David wrote:
> On Sun, 8 Aug 2021 at 23:49, Stephen P. Molnar <s.molnar at sbcglobal.net> wrote:
>> I have hit a roadblock in a Python script I have been developing to
>> process a large number of text files of fixed format.
>>
>> I have a list of names of chemicals, which I can read into a list.csv:
>>
>> CaffeicAcid,Cannflavin-A,Cannflavin-B,Cannflavin-C,Diosmetin,Echinacoside,Hesperetin,L-CichoricAcid
>>
>> My code is;
>>
>> import csv
>>
>> with open("Ligand.list_r.txt", newline='') as csvfile:
>>       rows = csv.reader(csvfile, delimiter = ',')
>>       data = []
>>       for rows in rows:
>>           data.append(rows)
>>
>> print(data)
>>
>> This results in:
>>
>> [['CaffeicAcid\tCannflavin-A\tCannflavin-B\tCannflavin-C\tDiosmetin\tEchinacoside\tHesperetin\tL-CichoricAcid']]
>>
>> when run.
>>
>> What I need to do is iterate through the list and generate names of the
>> format of chemicalname+'.i.log'.
>>
>> This is where I can seem to hit a show stopper. How do I extract fields
>> form the list generated by the script that works? What am I missing?
> There's several reasons why your code does not give the result you want.
>
> You also don't give any clue which version of Python you are using.
> Python behaviour does differ between versions, so it is always
> important to mention that. Just run 'python --version' if you are on Linux.
>
> Debugging this code might be tricky for you because
> modern csv.reader() returns a generator object, not a list.
>
> So, I suggest as a learning exercise you replace the line:
>    rows = csv.reader(csvfile, delimiter = ',')
> with
>    rows = list(csv.reader(csvfile, delimiter = ','))
> That means that rows will become a list object, which is what older
> versions of Python used to do, and doing that will make it much
> easier for you to see what is happening in your code.
>
> After that, you can debug your code by sprinkling a few print statements
> around it so that you can see the data in the variables.
> For example:
>    print("data = ", data)
> Then, you will be able to see what the code is doing. And you might be
> able to debug it yourself. Let us know how it goes.
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-- 
Stephen P. Molnar, Ph.D.
614.312.7528 (c)
Skype:  smolnar1