Questions tagged [dna]
The dna tag has no usage guidance.
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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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My code looks and works correctly but check50 fails
import csv
import sys
def main():
x = 0
# Check for command-line usage
if len(sys.argv) != 3:
sys.exit("Usage: python dna.py data.csv sequence.txt")
# TODO: Read ...
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1
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PSET 6 - DNA - Checking the equality of STRs
This is my loop to check the equality of STR counts, csv list is a list storing data of the csv file and STRlist is a list storing all the STRs. It prints the wrong name, I guess it has something to ...
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Index to integer
How do i convert an index to an integer?
I tried int(index), that didnt work.
For example;
S = [a,b,c,d]
For index in S:
n = int(index)
print (n)
break
print ()
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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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2
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121
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cs50 pset6 takes too long to run
I am trying to improve my code for pset6, it works but currently takes a few minutes for the larges files. Can I get some help as to how to improve performance?
from sys import argv, exit
import csv
...
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My DNA code works with the small database but not the large one
My code works perfectly fine with the small database but gives "No Match" for the large one and I can't figure out why. Any help would be appreciated!
import csv
from sys import argv, exit
def main()...
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DNA: Excluding a column from my dict iteration
Logic: I'm trying to do this in such a way that I check the database first, then I check the DNA sequence to see if that information corresponds to any of the information in my database.
I want to ...
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PSET 6 DNA.py wrong output [spoiler]
I am a beginner in cs50 and I have a problem with the DNA problem that gives the wrong result for most of the queries. I wonder if anyone could point where is the mistake.
ie. python dna.py databases/...
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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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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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314
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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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cs50 pset 6 DNA. How to compare my results with the databse to print out the answer?
I got to a point in this problem where my code was working alright for the small csv, but it was clumsy and repetitive, so I tried to make it more elegant by making more complicated nested loops to ...
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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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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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Print keys of CSV files in DNA pset6
I want to see what the keys of the reader dictionary are so I use the print(key) function. The result is all the lines of the dictionary. Why is that?
import csv
from sys import argv, exit
# Check if ...
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CS50 DNA prints "No match"
My pset has some issues,can you please tell me what do i have to change in the main function in order to print name of longest DNA matched person.
import csv
import sys
def main():
# TODO: Check for ...
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2
answers
124
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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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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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pset6 DNA. My code passes all tests but this one: python dna.py databases/large.csv sequences/18.txt
from sys import argv, exit
import pandas as pd
# Checks if the number of files is correct
if len(argv) != 3:
print("Usage: python dna.py data.csv sequence.txt")
exit(1)
# Reads the text file
...
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1
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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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cs50 pset6 dna error while reading two file 8.txt and 9.txt
import sys
import csv
AATG, GATA, TATC, TCTG, AGATC, GAAA, TCTAG = 1, 1, 1, 1, 1, 1, 1
TTTTTTCT = 1
temp = 0
if int(len(sys.argv)) > 3 or int(len(sys.argv)) < 3:
print("Usage: python dna.py ...
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pset6 DNA: check50 ran into an error while running checks! at checking 'dna.py exists!'
The code runs for all 20 sequences on the terminal but during submit50/check50, it runs into an error with the following log:
the code is attached for reference.
import csv
import sys
if __name__ ==...
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PSET6: DNA check50 expecting no match on txt18 ,but my program returns harry
my code works for all the other tests on check50 besides the one for txt18. I checked the Large.csv file and the return value of longest_match function (both provided by cs50) and they match up yet ...
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PSET6 DNA storing STR subsequences in a dictionary
I am working on one of the TODOs where the longest match of each short tandem repeat (STR) needs to be found from the DNA sequence read—written as just "sequence" in this code. To check ...
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pset6 - DNA - works for small.csv but not large.csv
import csv
import sys
with open(sys.argv[1], 'r') as file:
# stores data from small.csv in both dict and list form
dna_names_dict = csv.DictReader(file)
...
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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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259
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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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PSET6 DNA Sumbit50 not matching with usual output
Hello,
After a lots of effort I was finally able to implement DNA and it works correctly ! but Submit50 shows correct output for text file (1-5) but incorrect for rest
The text file which have ...
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PSET 6 - DNA - Is there something wrong with my if statement?
The individual conditions are satisfied as checked by print statement, but when I consolidate all conditions in my if statement, the does'nt seem to print the name. Any ideas?, is there something ...
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pset6 DNA - help creating and referencing dictionaries
This may be a strange question - my code actually worked, but I feel like I got to a solution by brute force, rather than something more elegant.
I'm still not sure how to create and reference ...
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PSET6 DNA Almost done - matching not working correctly
I have been stuck with last part of the code that is supposed to match the DNA sequence from sequence.txt with the one in database.csv.
It passes most of the tests in check50 and fails only in ...
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DNA - String Compare
I have a question about DNA, specifically this while statement:
while dna_string[char: char + length_str] == dna_string[char - length_str: char]:
I'm not getting dna_string[char - length_str: char] ...
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pset6 I just don't understand what I have to do
import csv
import sys
counter = 0
def main():
if len(sys.argv) != 3:
sys.exit("Usage: python dna.py data.csv sequence.txt")
# Open csv file and read it's contents into memory
...
0
votes
1
answer
93
views
PSET6 DNA Why is my (count consecutive substrings in string) function always returns 0's?
I tried writing different function variations but my count_dna function keeps returning zeroes (despite having consecutive sequences of STRs in the dna sequences)--can anyone please tell me why?
Note: ...
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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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74
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What does "consecutively" mean in pset6 DNA?
I am working on pset6 DNA and I'm not sure I understand the terms of the problem.
The objective is to write a program that matches a DNA sequence to a person in a DNA database based on the largest ...
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Pset6 - DNA - Strange Error
I'm in the [ Testing ] section and my program works fine with [ small.csv ], but the expected data is not the same as the real data:
For example:
If I run this: python dna.py databases/large.csv ...
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DNA pset6 My code works fine in small csv, but not large (Spoiler)
The problem happens with the count when i try to count STRs, it counts some str right and some wrong, which is strange for me, and when i deal with small csv all works fine.
can someone help me in ...
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DNA Max Sequence Bug | Working on small.csv but not on large.csv
This is the complete code:
"""
- open csv file and sequence , read contents
- for each str, compute longest chain
- compare str counts aganist ech row in csv file
"""...
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Minor change in pset6/dna required, need some help or hint
I am really really close to completing pset/dna.
But there seems to be some problem in the 'if statement'. Somebody please guide.
Before the line of underscores in the terminal, I have printed the ...
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Pset 6 - Dna - My outputs are slightly incorrect. Could someone help me figure out what might be the problem here?
I've been stuck on this question for a week. After countless hours of debugs, I decided to post it here. Please refer to images and code snippets below and kindly explain to me what might be the ...
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pset6 DNA // having problem comparing elements from the database and the sequence file
Hi there I am having an issue comparing the data I have extracted from the sequence and the database files for now I am doing a sort of in efficient way but later I will fix it I am not sure really ...
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PSET6 DNA Think I'm getting an infinite loop which is apparent when testing with every txt file after 4.txt
Hi all I'm having trouble for PSET6 DNA. My code works fine for everything up until and including 4.txt but whenever I go to check the large.csv file and thus 5.txt, 6.txt, 7.txt and so on I seem to ...
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pset6 DNA works with small database but not with the large one
For some reason, when counting the times a substring repeats within a string (a STR in a DNA), my code fails with the large database. It is not a matter of overlapping sequences, because the numbers ...
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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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DNA code doesn't work sometimes
OK, so I`ve got a strange bug in my DNA code.
Basically, it works fine, but somehow it gives incorrect output at samples 6, 8, 9, 19.
When I looked more carefully through my STR check results, it ...
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Getting ONE error on check50 for DNA - ValueError: max() arg is an empty sequence - Where is the bug?
I'm so close the finish line, but I get error on one out of the 21 CS50 tests.
The test that is generating the error is number #2, which is:
python dna.py databases/small.csv sequences/2.txt
And I ...
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DNA - Getting the highest key value from a defaultdict
I have come a bit on DNA and have managed to write an algorithm for adding the number of matches in the sequence to a defaultdict. But I'm having problems with how to get the maximum value from the ...
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PSET 6 DNA - Computing STRs
I am trying to compute the most repeated STR for each sequence in a dictionary called str_dict.
# compute STRs
i = 0
# stablish length of the sequence
length_seq = len(sequence)
# iterate through all ...
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