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Search Results
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Thread: Replace a list or string element with a random one..
Post: RE: Replace a list or string element with a random...
| Thank you very much for your solution! I didn't put 'if is equal to N' because sometimes in chromosomes you can find also other letters like R or M. Your code is really simple and efficient! |
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pianistseb |
General Coding Help |
3 |
2,442 |
May-09-2019, 08:21 AM |
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Thread: Replace a list or string element with a random one..
Post: Replace a list or string element with a random one...
| Hello!
I have to do a very simple task, but I have problems with speed. I have a list called 'chromosome', and I want to replace each N into A,G,C or T at random. I made this code, which is very slow... |
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pianistseb |
General Coding Help |
3 |
2,442 |
May-09-2019, 08:03 AM |
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Thread: How can I make a faster search algorithm
Post: RE: How can I make a faster search algorithm
| The only problem with this function from fuzzysearch library is that it works fast only for small errors. If I put in my code max_substitutions=100, it takes approximately 1 minute to run, if I put ma... |
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pianistseb |
General Coding Help |
19 |
6,585 |
Apr-17-2019, 10:31 AM |
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Thread: How can I make a faster search algorithm
Post: RE: How can I make a faster search algorithm
| Thank you very much Larz60+ ! I think you found the solution to my problem! |
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pianistseb |
General Coding Help |
19 |
6,585 |
Apr-16-2019, 10:33 AM |
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Thread: How can I make a faster search algorithm
Post: RE: How can I make a faster search algorithm
| My goal is to detect the positions that are similar (similar means that I accept an error like 10% that I can change in the program) to Erdos sequence in DNA or chromosome and put it in a text file. I... |
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pianistseb |
General Coding Help |
19 |
6,585 |
Apr-15-2019, 07:36 PM |
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Thread: How can I make a faster search algorithm
Post: RE: How can I make a faster search algorithm
| For example! Here is the bottom part chromosome of Arabidopsis:
https://www.ebi.ac.uk/ena/data/view/AE005173
(you can reach this page if you press the right button AE005173 in the eucariotic chromosom... |
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pianistseb |
General Coding Help |
19 |
6,585 |
Apr-15-2019, 12:19 PM |
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Thread: How can I make a faster search algorithm
Post: RE: How can I make a faster search algorithm
| Thank you very much! I started learn python some months ago, but I haven't problems with speed because I didn't deal with big data. Now as my job is in dna sequences, the data structures are very big.... |
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pianistseb |
General Coding Help |
19 |
6,585 |
Apr-15-2019, 11:13 AM |
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Thread: How can I make a faster search algorithm
Post: RE: How can I make a faster search algorithm
| If for loops don't work fast in python, what work fast? Biopython have some functions, but if someone want to make something new must use for loops. I started programming in python because I thought t... |
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pianistseb |
General Coding Help |
19 |
6,585 |
Apr-15-2019, 05:49 AM |
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Thread: How can I make a faster search algorithm
Post: RE: How can I make a faster search algorithm
| There is the biopython package.
https://biopython.org/wiki/Download |
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pianistseb |
General Coding Help |
19 |
6,585 |
Apr-14-2019, 08:38 AM |
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Thread: How can I make a faster search algorithm
Post: How can I make a faster search algorithm
| I am using biopython for dna sequences. I want to make an algorithm which searches a big motif (about 1000 letters). Because it is impossible to find this 1000-letters motif, I accept also motifs whic... |
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pianistseb |
General Coding Help |
19 |
6,585 |
Apr-14-2019, 07:42 AM |
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Thread: To make an algorithm work faster
Post: RE: To make an algorithm work faster
| I finally found that a very fast way to do it is to use something like that:
for seq_record in SeqIO.parse("OMOK01.fasta", "fasta"):
new_str=str(seq_record.seq).replace("A","+");
new_str=new_... |
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pianistseb |
General Coding Help |
3 |
2,808 |
Apr-01-2019, 07:54 AM |
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Thread: To make an algorithm work faster
Post: To make an algorithm work faster
| I am using biopython for dna sequences. I am new in this python library. I have a .fasta file that has a 4-letters dna code, and I want to convert it in 2-letters purines and pyrimidines binary code. ... |
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pianistseb |
General Coding Help |
3 |
2,808 |
Mar-28-2019, 06:58 PM |
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Thread: How to change the resolution of an image and save multiple plots.
Post: How to change the resolution of an image and save ...
| This code solves a differential equation by the method of 4nd Runge-Kutta. It works fine, but I want to save the diagram for each loop with high resolution. What can I do?
from sympy.solvers import s... |
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pianistseb |
Data Science |
1 |
2,384 |
Dec-11-2018, 03:26 PM |
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Thread: To draw a polynomial solution
Post: RE: To draw a polynomial solution
| I finally found the solution. How can I delete the post? |
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pianistseb |
Data Science |
2 |
2,949 |
Nov-13-2018, 01:45 PM |
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Thread: To draw a polynomial solution
Post: To draw a polynomial solution
| I just want to draw a polynomial solution and I have always the same error. I need this program to complete my thesis. I'm new in python. Please help!!!
from sympy.solvers import solve
from sympy impo... |
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pianistseb |
Data Science |
2 |
2,949 |
Nov-13-2018, 12:54 PM |
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Thread: How can I put an np.arange in equation's solution?
Post: RE: How can I put an np.arange in equation's solut...
| Even I put the tab, the problem remains. |
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pianistseb |
General Coding Help |
3 |
2,392 |
Nov-11-2018, 10:12 PM |
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Thread: To put a solution of an equation into a function
Post: RE: To put a solution of an equation into a functi...
| Thank you! But I have the same problem! |
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pianistseb |
Data Science |
6 |
3,325 |
Nov-11-2018, 08:22 PM |
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Thread: How can I put an np.arange in equation's solution?
Post: How can I put an np.arange in equation's solution?
| How can I fix the issue in this code? It says "can't initialize from 'list' without generators". Thank for your help!
from sympy.solvers import solve
from sympy import Symbol
from sympy import solve, ... |
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pianistseb |
General Coding Help |
3 |
2,392 |
Nov-11-2018, 06:31 PM |
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Thread: To put a solution of an equation into a function
Post: RE: To put a solution of an equation into a functi...
| Look at this code!
def f(x,y):
return solve(Poly(x**2*y+(23+y)*x+y**2),y)
x=np.arange(-20,20,0.1)
y=2
print(f(x,y))I think that the problem is in the dimensions but it
has blocked my mind, and ... |
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pianistseb |
Data Science |
6 |
3,325 |
Nov-11-2018, 06:03 PM |
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Thread: To put a solution of an equation into a function
Post: RE: To put a solution of an equation into a functi...
| Stulis I tried something like that. And now I tried your code and it says "can't initialize from 'list' without generators". It has problem in the line 56. It says always the same thing when I do that... |
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pianistseb |
Data Science |
6 |
3,325 |
Nov-11-2018, 04:48 PM |
