Questions tagged [dna]
The dna tag has no usage guidance.
78
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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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70
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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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67
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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
...
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1
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65
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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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52
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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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27
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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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35
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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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55
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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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39
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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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85
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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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75
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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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45
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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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88
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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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141
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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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80
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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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239
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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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68
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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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78
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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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91
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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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1
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22
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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 ()
- 15
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1
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109
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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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66
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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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159
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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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1
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69
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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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52
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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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97
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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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23
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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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152
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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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277
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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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178
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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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75
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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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284
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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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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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221
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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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43
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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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1
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238
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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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72
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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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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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48
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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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162
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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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253
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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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107
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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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249
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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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461
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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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1
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107
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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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201
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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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0
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108
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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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205
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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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57
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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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445
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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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