tgc | A Tiny Garbage Collector for C | Interpreter library
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A Tiny Garbage Collector for C
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QUESTION
Im currently working on a study project where I am to make a python program where I can enter a DNA sequence, get all the possible reading frames from it and then find any open reading frame. I can't use Biopython as we are to do this ourselves.
From the code I have written, I will get an output in the style of:
["TGC", "ATG", "ATA", "TGG", "AGG", "AGG", "CCG", TAA", "TAG", "TGA"]
What I want to do now is to define the start codon as "ATG" and get its index as well as define stop codons as ["TAA", "TAG", "TGA"] and if any of these three are found, the index of the first found is reported and the rest is ignored. And if no stop codon is found to return some string.
In addition to this, i want to be able to compare the "lengts" of up to 6 different input in the style mentioned above and chone the one which is the longest.
This is my first time posting here so appologies if the question is not well phrased and thanks for any help!
...ANSWER
Answered 2021-May-17 at 18:00I am not completely sure if this is what you want, but to find the first occurrence of strings in a longer string you can do like this for example
QUESTION
I would like to loop through file1, which has two columns. Each column has a string that I would like to use to search in a dataframe file (file2) with 18 columns. I'd like to select rows from file2 that have both strings from file1 in two different columns to create a new file.
file1 (tab separated file with about 150 rows, it has no header)
...ANSWER
Answered 2021-May-12 at 15:22You may try this awk that stores all value from 1st column in region array and 2nd column in motif array while going through file1. Later we print records from file2 if $18 is found in region array and $15 is found in motif array:
QUESTION
I had no error. Always refresh cache and local memory.
Resources for Verifying Translations:
[NCBI Protein Translation Tool][1] (Validation)
[Text Compare][2] (Verification)
[Solution Inspiration][3]
300 DNA chars -> 100 protein chars.
...ANSWER
Answered 2021-Mar-31 at 09:38I think the issue is with you mixing up variable names - your translation code appends to protein but you print output_protein which I assume is actually created somewhere else in your code(?). Also, you first edit the variable dna_sequence but iterate over dna which I assume is also defined elsewhere and maybe doesn't match dna_sequence.
After editing the variable names I can use your code to get the same translation as the NCBI tool.
QUESTION
I have a list of pandas data frames that I got applying the groupby function and I want to add to them a new column with the frequency of each kmer. I did that with a loop but I got a message warning that I need to use df.loc[index, col_names]. Here it is a link to one example of the csv file: https://drive.google.com/file/d/17vYbIEza7l-1mFnavGGO1QjCjPdhxG7C/view?usp=sharing
...ANSWER
Answered 2021-Apr-05 at 12:28It's an error related SettingWithCopyWarning. It's important — read up on it here. Usually you can avoid it with .loc and by avoiding repeat-slicing, but in some cases where you have to slice repeatedly you can get around it by ending .copy() to the end of the expression. You can learn when and why this is important via the link. For a more precise answer for how this is emerging from you'll code, you'll need to show us an MRCE of your code.
QUESTION
I’m working on a variation of the Motif Search Problem and have hit a block on the logic of one of the subparts.
The problem is:
You have the alphabet — ['A', 'C', 'G', 'T']
Now, you are given an array of strings made of these alphabets with length L and are given a hamming distance D.
For example, if we take L=3, d=2 and are given the array ["ACT","TGC","GTA"].
For each string in the array, we must generate strings of the same length (3 in this case) using the alphabet which have a hamming distance of d. The hamming distance d means that the final string will only have d edits (two if d = 2) as compared to the original string.
So if we take the example of ACT from the array, we must generate GTT, AAG, CGT and so on. And I want to store these generated strings in a list.
A recursive function that breaks down the string seems like the most efficient way to do it but I’m having trouble implementing it. Any ideas for the logic explained with code/pseudocode? I need to be able to extend this problem to L = 15 and d = 5.
Example of Hamming distance d = 1.
...ANSWER
Answered 2021-Mar-09 at 01:02This can get you started. It doesn't handle creating strings of different length than the source. Perhaps you could add that.
JavaScript code:
QUESTION
As I was bored and wanted to practice my python, I thought I'd write a script that took some genetic code and converted it into the amino acid sequence. It looks through the code one letter at a time and when it sees a certain sequence, starts translating triplets of genetic code into their equivalent amino acid and strings them together until it reaches a triplet of genetic code that doesn't encode an amino acid. The script then goes back to where it started this translation, and restarts iterating through the code until it finds another start sequence.
The script works, up to a point. I started off using a while loop to iterate through the triplets of genetic code after a start sequence, but when it reaches the end of the genetic code, it goes out of range:
...ANSWER
Answered 2021-Feb-24 at 20:38You keep incrementing base and incrementing l but without checking if you've exceeded the length of the rna string. Changing the condition of your while loop to
QUESTION
I'm trying to receive stock data for about 1000 stocks, to speed up the process I'm using multiprocessing, unfortunately due to the large amount of stock data I'm trying to receive python as a whole just crashes.
Is there a way to use multiprocessing without python crashing, I understand it would still take some time to do all of the 1000 stocks, but all I need is to do this process as fast as possible.
...ANSWER
Answered 2021-Jan-31 at 19:18Ok, here is one way to obtain what you want in about 2min. Some tickers are bad, that's why it crashes.
Here's the code. I use joblib for threading or multiprocess since it doesn't work in my env. But, that's the spirit.
QUESTION
Below is my code. I am trying to input "ATC" to get an output of "UAG". All it does is replace 'A' with 'U', 'T' with 'A', 'C' with 'G', and 'G' with 'C' (Just like transcription - DNA to mRNA).
The problem is... when I input ATC, AGC, TGC, or anything with 'C' at the end, the program will replace 'C' with 'G' and then proceed to replace the new 'G' with a 'C'.
.replace('C','G').replace('G','C');
How can I stop the program from replacing the 'C' back to a 'C'? My input should be AGC, and the intended output should be UCG.
...ANSWER
Answered 2021-Jan-21 at 01:06String codon = scanner.next(); /*ATGC*/
char[] codonArr = codon.toCharArray();
for (int i=0;iQUESTION
i have a protein sequence:
...ANSWER
Answered 2021-Jan-04 at 19:54import itertools
list_codons = [('ATT', 'ATC', 'ATA'),
('GAA', 'GAG'),
('GAA', 'GAG'),
('GCT', 'GCC', 'GCA', 'GCG'),
('ACT', 'ACC', 'ACA', 'ACG'),
('CAT', 'CAC'),
('ATG',),
('ACT', 'ACC', 'ACA', 'ACG'),
('CCT', 'CCC', 'CCA', 'CCG'),
('TGT', 'TGC'),
('TAT', 'TAC'),
('GAA', 'GAG'),
('TTA', 'TTG', 'CTT', 'CTC', 'CTA', 'CTG'),
('CAT', 'CAC'),
('GGT', 'GGC', 'GGA', 'GGG'),
('TTA', 'TTG', 'CTT', 'CTC', 'CTA', 'CTG'),
('CGT', 'CGC', 'CGA', 'CGG', 'AGA', 'AGG'),
('TGG',),
('GTT', 'GTC', 'GTA', 'GTG'),
('CAA', 'CAG'),
('ATT', 'ATC', 'ATA'),
('CAA', 'CAG'),
('GAT', 'GAC'),
('TAT', 'TAC'),
('GCT', 'GCC', 'GCA', 'GCG'),
('ATT', 'ATC', 'ATA'),
('AAT', 'AAC'),
('GTT', 'GTC', 'GTA', 'GTG'),
('ATG',),
('CAA', 'CAG'),
('TGT', 'TGC'),
('TTA', 'TTG', 'CTT', 'CTC', 'CTA', 'CTG')]
counter = 0; max_proc = 1000000; list_seq = []
for x in itertools.product(*list_codons):
counter += 1
if counter % max_proc == 0:
#Do your stuff by slice and clear the list
list_seq = []
list_seq.append(x)
print (counter)
print (x)
QUESTION
I'm trying to convert a DNA sequence to an amino acid sequence. I have a dictionary of codons:
...ANSWER
Answered 2020-Oct-26 at 02:52if codon_mapping[mySeq[n:n+3]] != '*':
translated += codon_mapping[mySeq[n:n+3]]
if codon_mapping[seq[n:n+3]] == '*':
break
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