🔒 Need help, not making progress

[median shoal]

I've been making no progress for the past hours, the description of the task is in this post.

[midnight thorn]

@median shoal

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[median shoal]

Contents: Sorting, printing method (str).

In our cells, amino acids form a fundamental component where certain sequences of thousands of these form peptides. More specifically, there are three consecutive "steps" on the DNA spiral (actually RNA Links to an external site.) that code for an amino acid where each step can be one of the nitrogen bases CGAT Links to an external site. This forms a number system with the base 4 and with three "digits" (steps) we get 43 = 64 combinations, however, not all of these are used and we have 20 unique amino acids. Your task is to write a program that loads these from a text file (which is located under Files/Labs and is called "aminosyror.txt") and then stored as a list of objects where each object has the properties (= the instance variables):

designation (e.g. K)
name (e.g. Lysine)
group (e.g. alkaline)
molecular weight (e.g. 146.19)

You will also need a list of sequence objects where each such object has the properties:

sequence (e.g. ACCA)
Weight (e.g. 342.59)

A run might look like this (red text is the application's output and green is the user's input):

reading aminoacids...
...done.
Choose one of the following:
1 – List all amino acids
2 - Save a sequence of amino acids (peptide)
3 – List all sequences sorter in order of weight
4 - Exit

1 

H Histidine Alkaline 155.16 
K Lysine Alkaline 146.19 
R Arginine Alkaline 174.2 
C Cysteine hydrophilic 121.16 
N Asparagine hydrophilic 132.12 
Q Glutamine hydrophilic 146.15 
S Serine hydrophilic 105.09 
T threonine hydrophilic 119.12 
Y Tyrosine hydrophilic 181.19 
A Alanine hydrophobic 89.09 
F Phenylalanine hydrophobic 165.19 
G Glycine hydrophobic 75.07
I Isoleucine hydrophobic 131.17 
L Leucine hydrophobic 131.17 
M Methionine hydrophobic 149.21 
P Proline hydrophobic 115.13 
V Selected hydrophobic 117.15 
W Tryptophan hydrophobic 204.23 
D Aspartic Acid 133.1 
E Glutamic Acid 147.13

Choose one of the following:
1 – List all amino acids
2 - Save a sequence of amino acids (peptide)
3 – List all sequences sorter in order of weight
4 - Exit

2 

Specify a sequence: CAAC

Choose one of the following: 
1 – List all amino acids 
2 - Save a sequence of amino acids (peptide) 
3 – List all sequences sorter in order of weight 
4 - Exit 

2

Specify a sequence: CA
Choose one of the following: 
1 – List all amino acids 
2 - Save a sequence of amino acids (peptide) 
3 – List all sequences sorter in order of weight 
4 - Exit 

3

CAAC:420.5 APPROX:210.25

[thorny lagoon]

what does the content of the text file look like?

[median shoal]

one second

[thorny lagoon]

are those tabs after each , ?

[median shoal]

not sure but I dont think that matters too much

I've managed to make a menu that prints this list

[thorny lagoon]

it might but anyways. What do you have so far in your code?

[median shoal]

I can share the code

[thorny lagoon]

!pastebin if its too long

[midnight thorn]

Pasting large amounts of code

If your code is too long to fit in a codeblock in Discord, you can paste your code here:
https://paste.pythondiscord.com/

After pasting your code, save it by clicking the Paste! button in the bottom left, or by pressing CTRL + S. After doing that, you will be navigated to the new paste's page. Copy the URL and post it here so others can see it.

[median shoal]

https://paste.pythondiscord.com/4PYA

here you go

something got messed up at line 48-49 with the copy and paste

[thorny lagoon]

I hope you've fixed that indentation

So I'll assume you've done menu options 1 and 4. Can you do 2 and 3?

[median shoal]

yeah. I've done 1 and 4 but cant do 2 and 3

if I input a sequence with input

it has no weight value from the textfile

and dont know why I would have my sequence as its own class

[thorny lagoon]

the weight value is the last column

designation (e.g. K)
name (e.g. Lysine)
group (e.g. alkaline)
molecular weight (e.g. 146.19)

[median shoal]

right thats for the class Aminoacid

but menu option 2 asks for user input

and that input is only a string if im not mistaken

[thorny lagoon]

The user input for e.g. is CAAC

If you break that down, you have C, A, A, and C

[median shoal]

yeah

[thorny lagoon]

C x 2, A x 2

You take the values of each

What is C?

What is A?

[median shoal]

ofc ofc but how would you do that with programming language

[thorny lagoon]

Thats the point with the AminoAcid class. When you search up which class instance contain the designation, A or C, you get its weight value

[median shoal]

for row in listaAmino: # the list with all the aminoacids and its information
  print(row)

is this how youd get the weight?

[thorny lagoon]

no

You already got the weight in your for loop but you're not using the class to store them

And then later reference them in option 2 and 3

[median shoal]

oh right right

but arent those locally available only?

[thorny lagoon]

yea

thats fine

since all of the data is already in the text file

so its "locally available"

[median shoal]

i dont quite understand how youd get the values then

but lets take it from the start

[thorny lagoon]

Do you understand your Aminoacid class object?

And how to use it?

[median shoal]

kind of

init stores all the properties right

[thorny lagoon]

right. Now how do you access one of those properties?

[median shoal]

you type your class and end it with a .

then you can what property you want to pick form

[thorny lagoon]

show me an example

[median shoal]

amino1 = Aminoacid()

print(amino1.name)

[thorny lagoon]

ok you almost got it

Aminoacid() on its own won't work because you've defined __init__ and it expects values in the ()

[thorny lagoon]

So since you have the "name", how do you get its "weight"?

[median shoal]

dont know, is the name even connected to the weight at all?

[thorny lagoon]

it is

its in one class instance

[median shoal]

yeah but form the text file its just text in rows and columns right

and ive seperated the text file into rows

[thorny lagoon]

no. You already extracted from the text file and into a list of Aminoacid class instance. So you can forget the text file

[median shoal]

okey so I opened the file, used readlines() and got it into a list

that is sorted in this way:
A Blah blah
B Blah blah

is this correct?

for row in data:
        data = row.split(',')

[thorny lagoon]

kinda but also... hmm

[median shoal]

and by doing this I made each element in a row its own index

[thorny lagoon]

thats right

[median shoal]

okey good, then Im on track

[thorny lagoon]

Keep going

What happens from line 42 to 53?

[median shoal]

then for each row, it now has indexes 0-3 (4 items which are designation, name, group and weight)

but im not sure if each row is a list now

anyway, each of these indexes are assigned to one of the properties for the class AminoAcid

and then each row is appended to a new list called listaAmino

[thorny lagoon]

good so far

[median shoal]

what about this?

[thorny lagoon]

It is a list per row

Not sure if your line 48 to 51 is a typo

Is that supposed to be there?

[median shoal]

thats a typo

from when I copied to the website

[thorny lagoon]

alright so the next thing is you can either loop over your listaAmino or change it to a dictionary of aAmino and use the Amino Acid's name as the key

[median shoal]

not sure if we are allowed to use dictionary in this task

[thorny lagoon]

can you ask?

[median shoal]

the last task was also about classes and objects and we were supposed to use lits with objects only

its probably the same for this task aswell

[thorny lagoon]

alright then continue with list

[median shoal]

there are some req that I just saw

Requirements for the solution:

You should use the main() method to eliminate the risk of using global variables locally.

If the "aminosyror.txt" file does not exist, an error message should be written (the program can then be terminated, but not crashed). To exit a Python program, you can import the module "sys" and then type "sys.exit()"

[thorny lagoon]

ok

[median shoal]

okey so for the list

I should create a list that can store all the sequences as in the example

and append every input

[thorny lagoon]

No there's already a list created. Use the same list. And loop over it to find the matching name as per the user input

[median shoal]

right the listaAmino

[thorny lagoon]

What you need to create is a total weight value (I assume that's what it is). So it totals to 420.5 for example

[median shoal]

yeah, lets see if I can code the first step

also can I erase the second class Sequence?

[thorny lagoon]

I don't know but I don't think so

Because the assignment did say

3 – List all sequences sorter in order of weight

[median shoal]

okok

should you break down the string first?

e.g CAAC

[thorny lagoon]

why? its already iterable

[median shoal]

to see if each character matches with listaAmino

[thorny lagoon]

yea but you don't need to break it down

[median shoal]

you should use a for loop then

?

[thorny lagoon]

you access each character by their index

[median shoal]

mhm

for i in userinput:

[thorny lagoon]

!e

userInput = "CAAC"
print(userInput[0])
print(userInput[1])

[midnight thorn]

:white_check_mark: Your 3.12 eval job has completed with return code 0.

001 | C
002 | A

[thorny lagoon]

but yes, you use a for loop

and you loop over the length of the user input

[median shoal]

def matchInputWithAminoAcids():
    userInput = str(input())

    for i in range(len(userInput)):

[thorny lagoon]

you don't need to str() over the input(). It is by default a string

[median shoal]

but this doesnt tell me to check each character in userInput right?

[median shoal]

alright

[thorny lagoon]

It doesn't. You do that inside the for loop

[median shoal]

lets see

def matchInputWithAminoAcids():
    userInput = input()

    for i in range(len(userInput)):
        if userInput[0] in listaAmin:

[thorny lagoon]

almost

[median shoal]

I need to have listaAmin in matchInputWithAminoAcids():

[thorny lagoon]

yea but your if statement is wrong

userInput[0] would mean that on each iteration of the loop, it will always check the first index of userInput

you have 2 ways to fix this

1. change your for loop so it loops over the userinput and use the variable from the for loop to check in the if condition

2. change the if condition to use the running index from the loop

[median shoal]

for the second option

do you change 0 to i

[thorny lagoon]

yea

[median shoal]

alright nice

[thorny lagoon]

!e

fruit = "Apple"
for letter in fruit:
  print(letter)

If you're curious about option 1

[midnight thorn]

:white_check_mark: Your 3.12 eval job has completed with return code 0.

001 | A
002 | p
003 | p
004 | l
005 | e

[median shoal]

instead of letter, we have row which is one aminoacid

is the next step to use a for loop again?

no it doesnt sound right

[thorny lagoon]

you'd be surprised

Yes, you have to use another for loop

[median shoal]

[thorny lagoon]

Its why I suggested using a dictionary

[median shoal]

yeah would be easier

def matchInputWithAminoAcids(listaAmino):
    userInput = input()

    for i in range(len(userInput)):
        if userInput[i] in listaAmino:
            for aminoacid in listAmino:

starting to get confusing

[thorny lagoon]

what does listaAmino show when you print it?

I assume a list of class objects, no?

[median shoal]

basically the text file

[thorny lagoon]

Is it?

[median shoal]

one sec

[thorny lagoon]

I'm also guessing (and hoping) that this assignment also wants you to document your functions, so we (especially for you) know what the function expects in the parameter.

[thorny lagoon]

This is from printing listaAmino?

[median shoal]

thats from printing each row in listaAmin

or each aminoacid

[median shoal]

write down what each function does?

[thorny lagoon]

What I mean by document, I also mean docstrings like

def yourfunction(x, y):
  """
  @param x is an integer
  @param y is an integer
  @return an integer 
  """

[median shoal]

havent been told to document my functions

[thorny lagoon]

Right. Because you set up __str__ method. So its effectively a list of that class.

[median shoal]

but if you ask for the radius for something, you can just assume that its a float or int

[thorny lagoon]

Its good practice to do. That's up to you if it doesn't say its required

[thorny lagoon]

Thats the point of a documentation. So it destroys ambiguity like that

[median shoal]

yeah, imma implement it in the future

[median shoal]

back to the code, is this correct?

[thorny lagoon]

Anyways, to check if the user input character in a list of class objects, may not work but you'll have to test it and find out.

[median shoal]

dont know why im checking all the aminoacids in the for loop

[thorny lagoon]

How do you access the "name" property of an amino acid class object?

[median shoal]

myvariable.name

[thorny lagoon]

ok and in this context, how do you actually get it if its not myvariable?

[median shoal]

test every aminoacid till userInput matches the name of the aminoacid

[thorny lagoon]

how do you do that?

[median shoal]

is it another if statement?

if x in userinput == listaAmino.name

[thorny lagoon]

you just need 1 if statement

[median shoal]

alright

if userInput[i] in listaAmino:

this line only checks if its the list

good if it passes

then

okey if you have the user input CAAC

it takes the first index "C"

checks if its in the list, one row or aminoacid has a C in it

then it moves on to the second for loop

and then for every aminoacid in listaAmin

[median shoal]

see, this step isnt connected to the "C" I just mentioned above

it just goes on and does its own quest

will be back, I have another task that I have to present

[median shoal]

alright I'm back @thorny lagoon

[thorny lagoon]

OK. so don't use in

you really have to check on each AminoAcid class's name against the User Input's index

[median shoal]

alright

lets see what I can do

I think I lost the progress

bruh

got it back, at least most of it

[median shoal]

which of them, the first or the second

[thorny lagoon]

There's 2?

[median shoal]

 for i in range(len(userInput)):
        if userInput[i] in listaAmino:
            for aminoacid in 

[thorny lagoon]

I was talking about the in in if statement

You obviously need the in for the for loop

[median shoal]

def matchInputWithAminoAcids(listaAmino):
    userInput = input()

    for i in range(len(userInput)):
        if userInput[i] == aminoacid.name:
            for aminoacid in 

if the character you get from the userinput is the same as aminoacid.name then go on

or should it be aminoacid.name in listaAmino

[thorny lagoon]

Think about it. Where does aminoacid come from in your if statement?

[median shoal]

it comes from no where really

but what eles should you write

[thorny lagoon]

You can get it from your for loop

for whatevervariableyouwanthere in whateverlistyouhave

The whatevervariableyouwanthere is anything you want to refer to each element/item/index of that list

Like how I did for letter in fruit

That basically assigns the value of each index to the variable letter

And the value changes after each iteration/loop

Does that make sense?

[median shoal]

but that for loop comes after the if statment?

[thorny lagoon]

Move it up

[median shoal]

alright

[thorny lagoon]

So it's for loop, for loop, then if

[median shoal]

got it

what do I want to do after

take the .weight of that aminoacid

[thorny lagoon]

Yes

[median shoal]

but I still dont know the accurate name of the aminoacid

[thorny lagoon]

Wdym?

[median shoal]

but python does

if the == statement goes through

it means that a match has been made

nvm I can just look at the input and see what character passed if statement

[thorny lagoon]

Right

So you still need to total the weights, right?

[median shoal]

yeah

do I append all the new weights to a new list

[thorny lagoon]

You don't have to

Just add them as you find them

totalweight = totalweight + aminoacid.weight

Don't forget to save the sequence

[median shoal]

and for that I need to save it into a list

def matchInputWithAminoAcids(listaAmino):
    userInput = input()
    
    for i in range(len(userInput)):
        for aminoacid in listaAmino:
            if userInput[i] == aminoacid.name:
                totalWeight = totalWeight + aminoacid.moleculeWeight       

    return totalWeight

so far it looks like this

[thorny lagoon]

I can see a problem. See if you can spot it

[median shoal]

aminoacid.moleculeWeight

this one?

[thorny lagoon]

That's one

[median shoal]

nice

maybe its better to append totalweight to a list directly

or why would I do that

maybe I should use the class Sequence

because now I got the sequence (order) and the weight

a dictionary would be good rn

also it seems like I cant print totalWeight

[thorny lagoon]

And why is that?

[median shoal]

UnboundLocalError: cannot access local variable 'totalWeight' where it is not associated with a value

thats when I used print in elif choice 2

 while True:
        # menu 
        print('1 -')
        print('2 -')
        print('3 -')
        print('4 -')

        choice = int(input())
        
        if choice == 1:
            showListOfAminoacids(listaAmino)

        elif choice == 2:
            matchInputWithAminoAcids(listaAmino)
            print(totalWeight)
           
        elif choice == 3:
            pass

        elif choice == 4:
            sys.exit()

        else:
            print('\nGive a correct alternative\n')

[thorny lagoon]

You can't access totalWeight outside of the function scope

unless you return it

[median shoal]

I do return it here

[thorny lagoon]

!return-gif will explain it better

[midnight thorn]

Print and return

Here's a handy animation demonstrating how print and return differ in behavior.

See also: /tag return

[median shoal]

something = matchInputWithAminoAcids(listaAmino)

tried that

but then it ruins the menu

and it asks for userinput directly

or do I have to put totalweight here

matchInputWithAminoAcids(listaAmino, totalWeight)

[thorny lagoon]

this is right. Then you print something

The totalWeight error is another thing. You have not set a default value to totalWeight before the for loops

[median shoal]

okey in the function

I set it to 0

now it returns 0

does that mean aminoacid.weight didnt work

[thorny lagoon]

share the latest code

[median shoal]

sharing the whole code

https://paste.pythondiscord.com/ZYKA

[thorny lagoon]

What did you put as your input?

[median shoal]

C only

[thorny lagoon]

That should work

print(aminoacid) before your if statement and try again

[median shoal]

the if statement in the menu?

[thorny lagoon]

no. In the matchInputWithAminoAcids

[median shoal]

doesnt work

it prints the text file basically

and returns 0

def matchInputWithAminoAcids(listaAmino):
    totalWeight = 0
    userInput = input()
    
    for i in range(len(userInput)):
        for aminoacid in listaAmino:
            print(aminoacid)
            if userInput[i] == aminoacid.name:
                totalWeight = totalWeight + aminoacid.moleculeWeight       

    return totalWeight

[thorny lagoon]

can you share a screenshot of what you see?

[thorny lagoon]

can I see before that?

[median shoal]

used CA instead C

but I get the same result if I type C only

[thorny lagoon]

ah wait. Forgot that you need to break the 2nd loop when you found a match

Also, change your print to show aminoacid.name

[median shoal]

change my print mhm

to what?

[thorny lagoon]

to aminoacid.name

Then test and show me the output of your test

[median shoal]

wait

where do you add the break

[thorny lagoon]

in your if

[median shoal]

so if else

and under else I add break

if i break directly after if

then totalWeight will be gone no?

[thorny lagoon]

you got it

so not directly after if

Where should you place it?

[median shoal]

    for i in range(len(userInput)):
        for aminoacid in listaAmino:
            aminoacid.name
            if userInput[i] == aminoacid.name:
                totalWeight = totalWeight + aminoacid.moleculeWeight
        break

[thorny lagoon]

no

[median shoal]

[thorny lagoon]

place the break in the if. but after the totalweight

[thorny lagoon]

This aminoacid.name is not inside print()

[median shoal]

yeah

no print

[thorny lagoon]

are you gonna print it still or?

[median shoal]

I wouldnt print anything right now

except the totalWeight

[thorny lagoon]

ok

[median shoal]

yeah the list works if you want to print something

but now I get no value returned from totalweight

which is good because I shouldnt

[thorny lagoon]

no value?

Not 0?

[median shoal]

no, I have no print

wait

let me

print(something)

under choice 2

yeah now I got a 0

[thorny lagoon]

Thats still there, right?

ok

So the problem we're trying to debug is, if aminoacid does contain properties like name or moleculeWeight.

Do you know how to find out?

[median shoal]

yeah we print it

and it worked for designation and name

let me try weight

[thorny lagoon]

oh wait...

is C a designation or name?

[median shoal]

designation

[thorny lagoon]

and your if statement is checking ... ?

[median shoal]

C for cystein and it checks for .name

bruh

[thorny lagoon]

ok so fix it up

[median shoal]

totalWeight = totalWeight + aminoacid.moleculeWeight
TypeError: unsupported operand type(s) for +: 'int' and 'str'

almost

which one is str

I set totalweight to = 0

[thorny lagoon]

The values for moleculeWeight is a string

[median shoal]

then we make it an int

can you go to class and int()

[thorny lagoon]

Best if you make it an int when you make them into the class instance

[median shoal]

yeah or float

[thorny lagoon]

yeah make them floats

[median shoal]

hel yeah

it works!

[thorny lagoon]

cool

[median shoal]

menu option 2 should be to save sequences

not to print the totalweight just yet

[thorny lagoon]

yup

[median shoal]

okey I just have to remove print(something)

[thorny lagoon]

you got this 🦾

[median shoal]

Thanks

[midnight thorn]

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