Questions tagged [dna]
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77
questions
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DNA code can't count
My program always return 'no match' and it's because it can't count the occurence of a substring. I have spent a lot of time trying to figure it out, so I hope someone can help me.
here's the function....
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1answer
36 views
pset6 count STR in the DNA sequence issues
so i m a bit confused...i have been testing my code using the small database and what i have so far produced what i expected ....
more specifically the STRcounts (i marked that part #?????). it is ...
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39 views
Can't figure out how to fix my code, any help please?
# open the CSV file and read its contents into memory
with open(argv[1], newline = '') as csvfile:
readCSV = list(csv.reader(csvfile))
for raw in readCSV:
pass
# Your program should ...
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49 views
pset6 DNA only getting “no match” SPOILER
I'm new to programming and have been stuck on the pset6 DNA assignment for a long time. The code outputs "no match" for everything, even though the output numbers from calculating the STR ...
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50 views
I'm stack with dna (pset6). can you please help me?
I have divided my code into three main pieces:
1- open the CSV file and read its contents into memory and open the DNA sequence and read its contents into memory
2- compute the longest run of ...
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1answer
105 views
PSET 6 DNA: How to get number of repeats for each value of STR's? [SPOILER: Full code]
I have written a code to count the highest number of consecutive repeats of specific DNA substring sequences in a long string of DNA...or so I thought. While my code can correctly count the longest ...
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1answer
43 views
DNA: Errors in sequences.3 and 18.txt
I have worked hard on writing codes for DNA. Everything works except for sequences/18.txt, which returns "Harry" instead of "No match". The problem still exists in spite of several ...
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21 views
DNA.py error: 'TypeError: unsupported operand type(s) for *: 'NoneType' and 'int''. It passes all but 2 of the tests
DNA.py is nearly finished, but it is failing the tests with sequence/15.txt and 16.txt. This is the error message:
~/pset6/dna/ $ python dna.py databases/large.csv sequences/16.txt
Traceback (most ...
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1answer
50 views
Issue with recording STRs in memory (PSET6 - DNA)
I'm trying to record the number of repetitions of each str in the sequence. I created a dictionary as below and another empty dict because i couldn't update a dict while iterating through it. But for ...
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1answer
153 views
Struggling with PSET6 DNA
I've been doing this for quite some time now, but I'm struggling to get the appropriate output. In the below code (which is incomplete as of now, but the main pieces are all on the board), I'm not ...
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66 views
PSET 6 DNA ~ some STR count is above the correct value by 1?
I'm almost done with pset6 hopefully
but I have one problem with my code
When i run it with for example python dna.py databases/small.csv sequences/4.txt python dna.py databases/large.csv sequences/10....
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1answer
103 views
Pset6 DNA Not matching to names in the database
The print statements seem to turn out what I hoped for up until trying to compare the STR counts to the database STR counts.
I would just appreciate any pointers of where I'm going wrong thanks.
...
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1answer
39 views
Unexpected error in homemade string search function
I am playing around with Python on the DNA problem. I realize there are some string methods that might make this problem easier but my gut instinct was to try and make an "search function" ...
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0answers
41 views
DNA Pset6 Can't run my program
I cant even run my program it keeps saying "list index out of range". I don't know whats wrong... Does anyone have any idea?
import sys
import csv
def repeats(seq, part):
rep = [0] * ...
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1answer
127 views
Pset6 DNA help - trouble calculating STR repeats with long database
I have really tried to just solve this one myself but after a few weeks this seems futile without guidance. I am having trouble getting a for loop to calculate the maximum consecutive occurrences of ...
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0answers
96 views
PSET6 DNA [SPOILER] Refactor
I have solved the problem however is there anyway to optimize this further? Also, how do I judge the time-space complexity of the same?
import csv
from sys import argv, exit
from csv import reader, ...
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0answers
80 views
Confused about DNA in pset6
I've just started DNA, and I've got what seems to be a working algorithm to see if the count of the STRs in the database and sequence are the same, but it does not seem to be working. I've been a bit ...
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85 views
PSET 6 DNA! Stuck for so long
so the problem I face is when computing the greatest number of STR's in a sequence. I was able to hardcode "GATA" and compute the greatest sequence for a textfile using my sequencecount ...
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96 views
cs50 pset6 DNA, minor differences in counting STRs |Spoiler entire code included|
My code counts STRs for some people correctly, but for others the difference is very small. For example for python dna.py databases/large.csv sequences/5.txt expected output is Luna, whose STR counts ...
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1answer
42 views
Desperately need help with DNA Python! please help!
Desperately need help with my DNA python code. I get the correct sequence printed out but I can't seem to find a working comparison code. Please someone take a look:
https://pastebin.com/DCdxtxMx
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1answer
35 views
Help with Python DNA!
Here is the code I have an issue with: https://i.ibb.co/0VrvCqj/code2.jpg
It works for small databases but not the big ones. Here the code works and shows Albus when it should show Lavander. As you ...
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36 views
How can I compare 2 dataframes on DNA?
obtained 2 data frames but I really don't know how can I compare them.
Do you have any ideas?
~/pset6/dna/ $ python dna.py databases/small.csv sequences/1.txt
name AGATC AATG TATC
0 0 4 1 ...
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45 views
SPOILER - CS50: Python PSET6. How do I ensure that my code does not show 1 and 2?
I am about halfway done with my python Pset6 code for DNA.
One problem I have been having is that without this particular line of code below:
lresults = [i for i in lresults if i != '1' and i != '2']
...
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1answer
120 views
PS6 - DNA (Python) Weird problem counting STRs
Which part of the problem are you working on?
I am at a very early stage of the problem, trying to scan a specific sequence for STRs, counting how many times they show up and storing this count as a ...
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1answer
161 views
PSET6 DNA only getting no match
I've been stuck on this pset for days, trying to get some help here :x
Basically my program only outputs no match no matter what I do. I tested my re.finditer separately and it prints out what I want, ...
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1answer
101 views
Else is ruining my code in dna and I don't get why
I'm trying to record the longest run of each STR I need and I'm close. Without the final "else" the code works fine with small dictionary and almost fine with long (because the count I ...
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1answer
227 views
My code is 95% correct and I can't understand why. Why, Harry? WHY?
I can't figure out why just only one is not correct. I really need to understand this. Please, help me
import sys
import csv
# Open sequence file
sequence_file = open(str(sys.argv[2]), 'r')
...
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1answer
225 views
PSET6: DNA returns “no match”
import csv
import sys
def maxrepeats(sequences, substring):
# calculate maximum consecutive frequency for each STR
repeats = [0] * (len(sequences)+1)
for i in range(len(sequences)-len(...
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1answer
73 views
pset6 DNA - range() not working as expected
DNA was a breeze until I got to the part where I have to check the dna sequences for patterns. Regardless of wich file I pass to the program it always detects only 1 repetition for every pattern.
...
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1answer
142 views
PSet 6: DNA gives correct as well as wrong ouput
Problem Set 6: DNA gives output
No Match
No Match
No Match
No Match
No Match
No Match
No Match
No Match
No Match
No Match
Lavender
No Match
No Match
No Match
No Match
No Match
No Match
No Match
No ...
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0answers
83 views
PSET6 - DNA - Code works for small database, but not large
I believe that the issue comes from my 'sequencing' function.
When I run the small database, everything works, however, when I run the large database, the counts of specific STRs are incorrect.
I'm ...
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0answers
57 views
Can you help me making my pset6's 'dna' more dynamic
I want suggestions on how to manage my so many lists in the loops.
Hello helpful soul,
I actually can't figure out how I can declare lists more dynamically, and thus using them in the loops easily.
...
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0answers
106 views
PSET6 DNA algorithm help and comparing data
I've really struggled with DNA trying to come up with a good algorithm. I have half my code written, but I have no idea how to compare the data in the Dict with the CSV file. Any thoughts would be ...
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0answers
49 views
PSET6: dna.py, updating dictionary
I'm struggling with Python, specifically adding/updating keys and values in a dictionary.
This is my code so far (I know it's probably far from perfect, this is my first time working with Python, ...
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0answers
60 views
Using csv.reader and csv.DictReader on the same file
I'm working on pset6 - DNA. My code is a work in progress, but the part I'm having trouble with is at the bottom. Right now I'm running without cmd line arguments, so I'm opening 1.txt and small.csv. ...
0
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1answer
118 views
Pset6, DNA - Convert all columns in a list to integers, skipping the first column
I'm trying to figure out how to take the csv file I opened and convert specific columns to ints since when the csv is opened and read, every element becomes an int.
Inside of the for row in csv_list:...
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1answer
44 views
Counter fails to update for DNA
My dna program always returns no match and after debugging it I've pin pointed the problem to the counter not updating correctly. My program finds the correct number of matches, which I've confirmed ...
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1answer
232 views
DNA pset6 - Unable to calculate maximum STR repeats in DNA file
Below is my code for PSET6 DNA:
from sys import argv
import csv
# "string" represents the DNA chain and "substring" represents an individual STR e.g. "ACTGC"
def maxrepeats(string, substring):
...
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0answers
91 views
DNA is good for the small database but not for the large database - CS50 Pset6
I'm currently developing the small and the large database functions separately and I wonder why in the large one it does not keep track of the STR repetitions. Here is my code from both functions:
...
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0answers
98 views
solved pset6 BUT still wondering
while reading the CSV file in these lines :
csv_file = open(sys.argv[1], "r") # reading the csv file into memoery
csv_reader = csv.DictReader(csv_file)
when i tried to make a copy of the csv_reader ...
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1answer
147 views
PSET6 DNA - I passed every test it wanted me to do, but I got 42% after submitting?
I completed the DNA problem on pset6. There is a series of tests you need to enter into the command line before you submit, and I did all of them and passed every single one (as shown below).
However, ...
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0answers
22 views
checking column for value results in wrong column being searched
I am trying to obtain obtain a column from a dataframe. I used panda to read the file.
df = pd.read_csv(sys.argv[1])
When I am trying to access the df by a specific STR, the STR is placed as the ...
0
votes
1answer
85 views
MY code works with a hardcoded string, but not a string object
I'm working on pset6 2020 dna. I'm having trouble inputting the sequence file to be compared into my search function. If I just open the file and copy paste the sequence into the code as a string, it ...
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0answers
136 views
PSET6 DNA - Counting some of the STRs incorrectly
I've spent many days working on DNA and on the verge of giving up. I was hoping to get some help with my code. It finds some of the STRs correctly but miscounts the other STRs. I'm trying to ...
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0answers
64 views
Need help with Iteration & Compare DNA - CS50
I need help building code to iterate through the DNA sequence and then compare it with Names in CSV.
Can anyone please guide me on how to proceed from the code written below with proper comment ...
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0answers
118 views
Problems with PSET6 – DNA
I don't understand why my code below isn't working. Instead of printing out the name of the person, it simply prints out No match found every time, even when there is supposed to be a match. If anyone ...
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1answer
86 views
Python pset6 - should a file be closed at the end of the program or in the middle?
I'm slowly working through DNA on pset6 and I am running into some issues with the opening/closing of CSVs. I open the CSV using
with open(database, "r") as csv_file:
csv_reader = csv.DictReader(...
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1answer
300 views
Kind of lost in pset6 dna, How to compare the max number of occurrences of the STR's with the database?
I'm kind of lost I don't know how I can compare the max number of occurrences with the database. My program here can get the max number of it stored in a list called counts to get it I used a function ...
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1answer
277 views
Difficulty comparing sequence and individual in PSET6 DNA
I have nearly completed DNA in Pset6 of CS50 but I am having difficulty on the last section.
I have managed to populate each of the max_AGATC, max_TTTTTTCT, max_AATG etc. with the correct values from ...
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77 views
Hello, why does my code only work with the small database but it's inaccurate for the large one?
i'm just working out my code for the correct cases! i know there are a few conditions I have to add when the user enters wrong input but i'll work on that later:) why does my code give me a wrong ...
