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Questions tagged [dna]

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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 ...
Michael's user avatar
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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 ...
Jae-Min's user avatar
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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 ...
Ronit Kumar Singh's user avatar
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1 answer
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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 ...
Ronit Kumar Singh's user avatar
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1 answer
173 views

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 ...
ITz_tact1cz's user avatar
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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 ...
Kh12769's user avatar
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266 views

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 ...
Cyrus's user avatar
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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] ...
Drallas's user avatar
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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 ...
Pahilajani Palak's user avatar
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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: ...
General Noob's user avatar
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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 ...
Eystein Thanisch's user avatar
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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 ...
Code Maker's user avatar
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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 """...
Agnij Moitra's user avatar
1 vote
1 answer
63 views

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 ...
user13641095's user avatar
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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 ...
Orbey Paltaci's user avatar
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1 answer
163 views

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 ...
Raghav Gupta's user avatar
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96 views

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 ...
Arsham's user avatar
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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 ...
Alexander Alexandrov's user avatar
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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 ...
M-J -Y's user avatar
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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 ...
Lucas RH's user avatar
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1 answer
117 views

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) ...
Anon's user avatar
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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 ()
Olhuwhorlhey's user avatar
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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 ...
Alexander's user avatar
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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 ...
Alexander's user avatar
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1 answer
174 views

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 ...
Jaime's user avatar
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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 ...
Mazen's user avatar
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1 answer
57 views

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 ...
nmn's user avatar
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1 answer
99 views

Computing consecutive STR is sometimes off by a little (Spoiler!)

My code works fine for the small csv file; however, when I get to the big csv file, my counts for the number of consecutive STR are less than the actual value by about 1 or 2. Here is my code: import ...
dillon__nguyen's user avatar
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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....
Thomaslusignan's user avatar
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1 answer
162 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 ...
andream's user avatar
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1 answer
311 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 ...
Leoness's user avatar
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1 answer
320 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 ...
Winnie HO's user avatar
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1 answer
79 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 ...
zeek's user avatar
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1 answer
314 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 ...
Hasan's user avatar
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1 vote
0 answers
119 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....
Yoda's user avatar
  • 11
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1 answer
259 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. ...
Ewan Willsmer's user avatar
1 vote
1 answer
45 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" ...
Rob Watt's user avatar
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1 answer
241 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 ...
GFitzP's user avatar
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1 answer
85 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
Class316's user avatar
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1 answer
66 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 ...
Class316's user avatar
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0 answers
49 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 ...
William Otero's user avatar
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1 answer
175 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 ...
Xavier Villà Aguilar's user avatar
1 vote
1 answer
298 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, ...
real trash's user avatar
0 votes
1 answer
110 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 ...
Alejandro Sánchez's user avatar
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1 answer
254 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') ...
Luana Nunes's user avatar
0 votes
1 answer
528 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(...
Siwon Lee's user avatar
0 votes
2 answers
124 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. ...
Henrique Baesa's user avatar
0 votes
1 answer
213 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 ...
Activity Uday's user avatar
1 vote
0 answers
116 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, ...
jReX's user avatar
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0 votes
1 answer
237 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:...
JackJack's user avatar