Questions tagged [dna]

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230 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
619 views

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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1answer
41 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 ...
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0answers
112 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
43 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
96 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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1answer
245 views

Why can't I print the entire string from the read file?

For the DNA assignment in pset6, I'm trying to print out the output of slicing the string that was read from one of the DNA sequence text files, which reads as follows: ...
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1answer
72 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 ...
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2answers
341 views

PSET6(DNA)- How do I access the STR's from the list (first line of csv file) dna

so I basically finished the code but the problem is I can't access the first line of the csv file. What I did was this with open(sys.argv[1], newline='') as database: reader = csv.reader(database) ...
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1answer
501 views

DNA doesn't work with large database

My program gives valid output with small databases, but with large I always get "No match". Do you have any idea what may be the cause ? Belowe is my code, It may seem a little messy so if you find it ...
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1answer
32 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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1answer
38 views

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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1answer
57 views

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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1answer
148 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 ...
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1answer
92 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 ...
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1answer
121 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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1answer
246 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
189 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
55 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
413 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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1answer
188 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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1answer
125 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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1answer
365 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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1answer
33 views

Stroring the header row from a csv file

Trying to store the header row of csv file, i.e. it's first row in a list after reading the file using reader(). Tried using next() and filednames() but none worked. Could anyone guide me how to ...
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1answer
852 views

Problem Set 6 - DNA (Using the DictReader function)

Currently my code functions in so far that I get the appropriate results for the maximum STR counts when I pass a certain sequence. However, I have no clue as to what I should do to progress; I tried ...
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1answer
1k views

PSET6 DNA How to read each value in the CSV file?

In PSET6 DNA, I have to read the CSV file. I use with open("P:\Code\Python\dna\databases\small.csv") as csvfile: #open on my PC dna_db = csv.DictReader(csvfile) for row in dna_db: ...
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1answer
2k views

PSET 6 - DNA - How to pass only value in python

~~~python import csv import sys import copy dbPath = sys.argv[1] seqPath = sys.argv[2] if len(sys.argv) > 3: print("error") exit() str_list = [] DB = open(dbPath, 'r') DBreader = csv....
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2answers
674 views

PSET 6 - DNA.py faiils checks 2 out of 21 text files. (8.txt and 9.txt.)

My code works fine for 19 out of 21 SRT Counts but fails check on 8.txt and 9.txt files. I am not sure what I am doing wrong. Have tried many different approaches but to no change of luck. please if ...
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0answers
31 views

There is something wrong with the DNA file

I am doing Problem Set 6 DNA. And it looks like the data given to me in the large file is incorrect. When I am running my code with small file it works fine. But when I run with large file it is not ...
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0answers
22 views

How to get the index of iteration from the 'for' loop?

I've been trying to solve pset6 (DNA in specific). I finished all of its parts but stuck on the part of comparing two lists. A list of lists containing the STR repetitions of each person (sth like ...
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0answers
22 views

My DNA program is showing me this error repeatedly

The error is written below: Traceback (most recent call last): File "/home/ubuntu/pset/pset6/dna/dna.py", line 54, in <module> main() File "/home/ubuntu/pset/pset6/dna/dna....
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0answers
31 views

Code Pset6 - DNA fails: no result at all

Can anyone please give me a hint? I've been working on my code for days now and I don't have a clue how to fix it. My code is included below. import csv from sys import argv, exit #initialize ...
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1answer
70 views

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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1answer
65 views

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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1answer
79 views

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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1answer
78 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 ...
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1answer
93 views

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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1answer
66 views

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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1answer
72 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) ...
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1answer
21 views

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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0answers
88 views

pset6 dna question regarding searching string for substring, two types of code give different output

I am currently following along ayoutube tutorial for pset 6 DNA, and have a small question regarding a specific function. In this function, it basically takes a substring and a string, and counts the ...
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1answer
95 views

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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1answer
53 views

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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1answer
46 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 ...
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0answers
22 views

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
138 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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1answer
235 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
69 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
263 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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1answer
212 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. ...