226 lines
334 KiB
HTML
226 lines
334 KiB
HTML
|
<!DOCTYPE html>
|
||
|
<html lang="en" class="light TridactylThemeDefault"><head>
|
||
|
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
|
||
|
<meta charset="utf-8">
|
||
|
<link rel="icon" href="efa88123-9a38-4981-ad24-bf6168506917_files/favicon.png">
|
||
|
<link rel="manifest" href="https://chat.depeuter.dev/manifest.json">
|
||
|
<meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1">
|
||
|
<script>
|
||
|
// On page load or when changing themes, best to add inline in `head` to avoid FOUC
|
||
|
if (
|
||
|
localStorage.theme === 'light' ||
|
||
|
(!('theme' in localStorage) && window.matchMedia('(prefers-color-scheme: light)').matches)
|
||
|
) {
|
||
|
document.documentElement.classList.add('light');
|
||
|
} else if (localStorage.theme) {
|
||
|
localStorage.theme.split(' ').forEach((e) => {
|
||
|
document.documentElement.classList.add(e);
|
||
|
});
|
||
|
} else {
|
||
|
document.documentElement.classList.add('dark');
|
||
|
}
|
||
|
</script>
|
||
|
|
||
|
|
||
|
<link rel="modulepreload" href="https://chat.depeuter.dev/_app/immutable/entry/start.a008403e.js">
|
||
|
<link rel="modulepreload" href="https://chat.depeuter.dev/_app/immutable/chunks/scheduler.f6668761.js">
|
||
|
<link rel="modulepreload" href="https://chat.depeuter.dev/_app/immutable/chunks/singletons.0af75cc8.js">
|
||
|
<link rel="modulepreload" href="https://chat.depeuter.dev/_app/immutable/chunks/index.afef706d.js">
|
||
|
<link rel="modulepreload" href="https://chat.depeuter.dev/_app/immutable/entry/app.fb362f1a.js">
|
||
|
<link rel="modulepreload" href="https://chat.depeuter.dev/_app/immutable/chunks/index.65c87b32.js">
|
||
|
<style type="text/css">@media print {
|
||
|
.TridactylStatusIndicator {
|
||
|
display: none !important;
|
||
|
}
|
||
|
}</style><link rel="modulepreload" as="script" crossorigin="" href="https://chat.depeuter.dev/_app/immutable/nodes/0.a3180f91.js"><link rel="modulepreload" as="script" crossorigin="" href="https://chat.depeuter.dev/_app/immutable/chunks/constants.affb70c1.js"><link rel="modulepreload" as="script" crossorigin="" href="https://chat.depeuter.dev/_app/immutable/chunks/navigation.4d675c85.js"><link rel="modulepreload" as="script" crossorigin="" href="https://chat.depeuter.dev/_app/immutable/chunks/Toaster.svelte_svelte_type_style_lang.4f4e956a.js"><link rel="stylesheet" href="efa88123-9a38-4981-ad24-bf6168506917_files/Toaster.3a6d0da3.css"><link rel="modulepreload" as="script" crossorigin="" href="https://chat.depeuter.dev/_app/immutable/chunks/each.2cd6bd47.js"><link rel="modulepreload" as="script" crossorigin="" href="https://chat.depeuter.dev/_app/immutable/chunks/index.cce326ae.js"><link rel="modulepreload" as="script" crossorigin="" href="https://chat.depeuter.dev/_app/immutable/chunks/index.a0e4648e.js"><link rel="stylesheet" href="efa88123-9a38-4981-ad24-bf6168506917_files/0.de36d200.css"><link rel="modulepreload" as="script" crossorigin="" href="https://chat.depeuter.dev/_app/immutable/nodes/1.439e4b1a.js"><link rel="modulepreload" as="script" crossorigin="" href="https://chat.depeuter.dev/_app/immutable/chunks/stores.96135f2d.js"><link rel="modulepreload" as="script" crossorigin="" href="https://chat.depeuter.dev/_app/immutable/nodes/2.e9fd4742.js"><link rel="modulepreload" as="script" crossorigin="" href="https://chat.depeuter.dev/_app/immutable/chunks/FileSaver.min.898eb36f.js"><link rel="modulepreload" as="script" crossorigin="" href="https://chat.depeuter.dev/_app/immutable/chunks/_commonjsHelpers.de833af9.js"><link rel="modulepreload" as="script" crossorigin="" href="https://chat.depeuter.dev/_app/immutable/chunks/index.cb1db698.js"><link rel="modulepreload" as="script" crossorigin="" href="https://chat.depeuter.dev/_app/immutable/chunks/index.150eea5c.js"><link rel="modulepreload" as="script" crossorigin="" href="https://chat.depeuter.dev/_app/immutable/chunks/index.447671ac.js"><link rel="modulepreload" as="script" crossorigin="" href="https://chat.depeuter.dev/_app/immutable/chunks/index.1ab02664.js"><link rel="modulepreload" as="script" crossorigin="" href="https://chat.depeuter.dev/_app/immutable/chunks/Modal.68c1a0a5.js"><link rel="modulepreload" as="script" crossorigin="" href="https://chat.depeuter.dev/_app/immutable/chunks/AdvancedParams.020cee97.js"><link rel="modulepreload" as="script" crossorigin="" href="https://chat.depeuter.dev/_app/immutable/chunks/index.94bf9275.js"><link rel="modulepreload" as="script" crossorigin="" href="https://chat.depeuter.dev/_app/immutable/chunks/index.4062ae9e.js"><link rel="modulepreload" as="script" crossorigin="" href="https://chat.depeuter.dev/_app/immutable/chunks/index.03ddf5e5.js"><link rel="stylesheet" href="efa88123-9a38-4981-ad24-bf6168506917_files/2.c7820e19.css"><link rel="modulepreload" as="script" crossorigin="" href="https://chat.depeuter.dev/_app/immutable/nodes/5.17634acd.js"><link rel="modulepreload" as="script" crossorigin="" href="https://chat.depeuter.dev/_app/immutable/chunks/index.5af3041e.js"><link rel="modulepreload" as="script" crossorigin="" href="https://chat.depeuter.dev/_app/immutable/chunks/Tags.4457bfcc.js"><link rel="modulepreload" as="script" crossorigin="" href="https://chat.depeuter.dev/_app/immutable/chunks/dayjs.min.1e504c00.js"><link rel="stylesheet" href="efa88123-9a38-4981-ad24-bf6168506917_files/index.8a27bb7e.css"><script src="efa88123-9a38-4981-ad24-bf6168506917_files/page-script.js" id="bw-fido2-page-script"></script><title>Open WebUI</title><link rel="stylesheet" type="text/css" href="efa88123-9a38-4981-ad24-bf6168506917_files/rosepine.css"><link rel="stylesheet" type="text/css" href="efa88123-9a38-4981-ad24-bf6168506917_files/rosepine-dawn.css"><link rel="modulepreload" as="script" crossorigin="" href="https://chat.depeuter.dev/_app/immutable/nodes/3.3da18224.js"></head>
|
||
|
<body data-sveltekit-preload-data="hover" style="overflow: unset;">
|
||
|
<div style="display: contents"> <div class="hidden lg:flex fixed bottom-0 right-0 px-3 py-3 z-10"><button id="show-shortcuts-button" class="text-gray-600 dark:text-gray-300 bg-gray-300/20 w-6 h-6 flex items-center justify-center text-xs rounded-full">?</button></div> <div class="app relative"> <div class="text-gray-700 dark:text-gray-100 bg-white dark:bg-gray-900 min-h-screen overflow-auto flex flex-row"><div class="h-screen max-h-[100dvh] min-h-screen -translate-x-[260px] w-[0px] bg-black text-gray-200 shadow-2xl text-sm transition z-40 fixed top-0 left-0"><div class="py-2.5 my-auto flex flex-col justify-between h-screen max-h-[100dvh] w-[260px] invisible"><div class="px-2.5 flex justify-center space-x-2"><button id="sidebar-new-chat-button" class="flex-grow flex justify-between rounded-md px-3 py-2 hover:bg-gray-900 transition"><div class="flex self-center"><div class="self-center mr-1.5"><img src="efa88123-9a38-4981-ad24-bf6168506917_files/favicon.png" class="w-7 -translate-x-1.5 rounded-full" alt="logo"></div> <div class="self-center font-medium text-sm">New Chat</div></div> <div class="self-center"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 20 20" fill="currentColor" class="w-4 h-4"><path d="M5.433 13.917l1.262-3.155A4 4 0 017.58 9.42l6.92-6.918a2.121 2.121 0 013 3l-6.92 6.918c-.383.383-.84.685-1.343.886l-3.154 1.262a.5.5 0 01-.65-.65z"></path><path d="M3.5 5.75c0-.69.56-1.25 1.25-1.25H10A.75.75 0 0010 3H4.75A2.75 2.75 0 002 5.75v9.5A2.75 2.75 0 004.75 18h9.5A2.75 2.75 0 0017 15.25V10a.75.75 0 00-1.5 0v5.25c0 .69-.56 1.25-1.25 1.25h-9.5c-.69 0-1.25-.56-1.25-1.25v-9.5z"></path></svg></div></button></div> <div class="relative flex flex-col flex-1 overflow-y-auto"> <div class="px-2.5 mt-1 mb-2 flex justify-center space-x-2"><div class="flex w-full" id="chat-search"><div class="self-center pl-3 py-2 rounded-l bg-gray-950"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 20 20" fill="currentColor" class="w-4 h-4"><path fill-rule="evenodd" d="M9 3.5a5.5 5.5 0 100 11 5.5 5.5 0 000-11zM2 9a7 7 0 1112.452 4.391l3.328 3.329a.75.75 0 11-1.06 1.06l-3.329-3.328A7 7 0 012 9z" clip-rule="evenodd"></path></svg></div> <input class="w-full rounded-r py-1.5 pl-2.5 pr-4 text-sm text-gray-300 bg-gray-950 outline-none" placeholder="Search"></div></div> <div class="pl-2.5 my-2 flex-1 flex flex-col space-y-1 overflow-y-auto"><div class="w-full pr-2 relative"><button class="w-full flex justify-between rounded-md px-3 py-2 hover:bg-gray-900 transition whitespace-nowrap text-ellipsis"><div class="flex self-center flex-1"><div class="self-center mr-3"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M2.25 12.76c0 1.6 1.123 2.994 2.707 3.227 1.087.16 2.185.283 3.293.369V21l4.076-4.076a1.526 1.526 0 011.037-.443 48.282 48.282 0 005.68-.494c1.584-.233 2.707-1.626 2.707-3.228V6.741c0-1.602-1.123-2.995-2.707-3.228A48.394 48.394 0 0012 3c-2.392 0-4.744.175-7.043.513C3.373 3.746 2.25 5.14 2.25 6.741v6.018z"></path></svg></div> <div class="text-left self-center overflow-hidden w-[180px]">Is there a more efficient way to implement this loop?</div></div></button> </div><div class="w-full pr-2 relative"><button class="w-full flex justify-between rounded-md px-3 py-2 hover:bg-gray-900 transition whitespace-nowrap text-ellipsis"><div class="flex self-center flex-1"><div class="self-center mr-3"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M2.25 12.76c0 1.6 1.123 2.994 2.707 3.227 1.087.16 2.185.283 3.293.369V21l4.076-4.076a1.526 1.526 0 011.037-.443 48.282 48.282 0 005.68-.494c1.584-.233 2.707-1.626 2.707-3.228V6.741c0-1.602-1.123-2.995-2.707-3.228A48.394 48.394 0 0012 3c-2.392 0-4.744.175-7.043.513C3.373 3.746 2.25 5.14 2.25 6.741v6.018z"></path></svg></div> <div class="text-left self-center overflow-hidden w-[180px]">
|
||
|
The header for this code can be improved by following the PEP 8 style
|
||
|
guide and using more descriptive variable names. Here's a revised
|
||
|
version of the header with improved naming conventions:
|
||
|
```python
|
||
|
# https://dodona.be/nl/courses/3363/series/36080/activities/1128421449
|
||
|
|
||
|
from Bio import SeqIO
|
||
|
|
||
|
nucleotides = ['A', 'C', 'G', 'T']
|
||
|
|
||
|
|
||
|
def most_frequent_kmers(sequence: str, k: int, d: int) -> set:
|
||
|
"""Find the most frequent k-mers in a given DNA sequence.
|
||
|
|
||
|
Args:
|
||
|
sequence (str): The DNA sequence to search for k-mers.
|
||
|
k (int): The length of the k-mers.
|
||
|
d (int): The maximum Hamming distance between k-mers.
|
||
|
|
||
|
Returns:
|
||
|
A set containing the most frequent k-mers in the given sequence.
|
||
|
|
||
|
>>> most_frequent_kmers('ACGTTGCATGTCGCATGATGCATGAGAGCT',
|
||
|
4, 1)
|
||
|
{'ACAT', 'ATGT'}
|
||
|
>>> most_frequent_kmers('AACAAGCTGATAAACATTTAAAGAG', 5, 1)
|
||
|
{'TTAAA', 'TTTAA', 'TTTTA', 'TAAAA'}
|
||
|
>>> most_frequent_kmers('AAAATTTTTTTT', 3, 0)
|
||
|
{}
|
||
|
>>> most_frequent_kmers('CAT', 1, 0)
|
||
|
{}
|
||
|
|
||
|
>>> from Bio import SeqIO
|
||
|
>>> most_frequent_kmers(*SeqIO.parse('data/09-data.fna',
|
||
|
'fasta'), 10, 2)
|
||
|
{'CCGGCGGCCG', 'CGGCCGCCGG'}
|
||
|
"""
|
||
|
```</div></div></button> </div><div class="w-full pr-2 relative"><button class="w-full flex justify-between rounded-md px-3 py-2 hover:bg-gray-900 bg-gray-900 transition whitespace-nowrap text-ellipsis"><div class="flex self-center flex-1"><div class="self-center mr-3"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M2.25 12.76c0 1.6 1.123 2.994 2.707 3.227 1.087.16 2.185.283 3.293.369V21l4.076-4.076a1.526 1.526 0 011.037-.443 48.282 48.282 0 005.68-.494c1.584-.233 2.707-1.626 2.707-3.228V6.741c0-1.602-1.123-2.995-2.707-3.228A48.394 48.394 0 0012 3c-2.392 0-4.744.175-7.043.513C3.373 3.746 2.25 5.14 2.25 6.741v6.018z"></path></svg></div> <div class="text-left self-center overflow-hidden w-[120px]">Header: "Flatten recursion"</div></div></button> <div class="absolute right-[22px] top-[10px]"><div class="flex self-center space-x-1.5"><button id="delete-chat-button" class="hidden"></button> <button class="self-center hover:text-white transition"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M16.862 4.487l1.687-1.688a1.875 1.875 0 112.652 2.652L6.832 19.82a4.5 4.5 0 01-1.897 1.13l-2.685.8.8-2.685a4.5 4.5 0 011.13-1.897L16.863 4.487zm0 0L19.5 7.125"></path></svg></button> <button class="self-center hover:text-white transition"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M14.74 9l-.346 9m-4.788 0L9.26 9m9.968-3.21c.342.052.682.107 1.022.166m-1.022-.165L18.16 19.673a2.25 2.25 0 01-2.244 2.077H8.084a2.25 2.25 0 01-2.244-2.077L4.772 5.79m14.456 0a48.108 48.108 0 00-3.478-.397m-12 .562c.34-.059.68-.114 1.022-.165m0 0a48.11 48.11 0 013.478-.397m7.5 0v-.916c0-1.18-.91-2.164-2.09-2.201a51.964 51.964 0 00-3.32 0c-1.18.037-2.09 1.022-2.09 2.201v.916m7.5 0a48.667 48.667 0 00-7.5 0"></path></svg></button></div></div> </div><div class="w-full pr-2 relative"><button class="w-full flex justify-between rounded-md px-3 py-2 hover:bg-gray-900 transition whitespace-nowrap text-ellipsis"><div class="flex self-center flex-1"><div class="self-center mr-3"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M2.25 12.76c0 1.6 1.123 2.994 2.707 3.227 1.087.16 2.185.283 3.293.369V21l4.076-4.076a1.526 1.526 0 011.037-.443 48.282 48.282 0 005.68-.494c1.584-.233 2.707-1.626 2.707-3.228V6.741c0-1.602-1.123-2.995-2.707-3.228A48.394 48.394 0 0012 3c-2.392 0-4.744.175-7.043.513C3.373 3.746 2.25 5.14 2.25 6.741v6.018z"></path></svg></div> <div class="text-left self-center overflow-hidden w-[180px]">
|
||
|
Improving the running time of this function can be done by reducing the
|
||
|
number of iterations through the suffix_neighbors set and by using a
|
||
|
more efficient algorithm for computing the Hamming distance between two
|
||
|
strings. Here are a few ways to optimize the function:
|
||
|
|
||
|
1. Use a more efficient data structure for storing the d-neighborhood,
|
||
|
such as a list or a dictionary, rather than a set. This can help reduce
|
||
|
the time it takes to add and remove elements from the neighborhood.
|
||
|
2. Replace the inner loop with a more efficient algorithm for computing
|
||
|
the Hamming distance between two strings. One way to do this is to use
|
||
|
the Levenshtein distance algorithm, which has a time complexity of
|
||
|
O(n+m) instead of O(nm), where n and m are the lengths of the two
|
||
|
strings.
|
||
|
3. Use memoization or dynamic programming to cache the results of
|
||
|
previous calls to the function, so that if the same d-neighborhood is
|
||
|
requested multiple times, it can be returned more quickly from memory
|
||
|
instead of being recomputed each time. This can help reduce the overall
|
||
|
running time of the function by avoiding redundant computations.
|
||
|
|
||
|
Here's an example of how you could modify the function to use a list for
|
||
|
storing the d-neighborhood and implement memoization:
|
||
|
```python
|
||
|
import collections
|
||
|
|
||
|
def neighbors(s: str, d: int) -> set:
|
||
|
"""Return the d-neighborhood of s
|
||
|
The d-neighborhood of a string s is the set of all k-mers whose
|
||
|
Hamming distance from s does not exceed d.
|
||
|
|
||
|
>>> neighbors('ACG', 1)
|
||
|
{'ACG', 'ACC', 'AAG', 'AGG', 'CCG', 'TCG', 'GCG', 'ACT', 'ATG',
|
||
|
'ACA'}
|
||
|
"""
|
||
|
|
||
|
if isinstance(s, SeqIO.SeqRecord):
|
||
|
s = s.seq
|
||
|
|
||
|
if d == 0:
|
||
|
return {str(s)}
|
||
|
if len(s) == 1:
|
||
|
return {'A', 'C', 'G', 'T'}
|
||
|
|
||
|
neighborhood = []
|
||
|
suffix_neighbors = neighbors(s[1:], d)
|
||
|
|
||
|
for text in suffix_neighbors:
|
||
|
hamming_distance = LevenshteinDistance.distance(s[1:], text)
|
||
|
if hamming_distance < d:
|
||
|
neighborhood += ['A' + text, 'C' + text, 'G' + text, 'T' +
|
||
|
text]
|
||
|
else:
|
||
|
neighborhood += [s[0] + text]
|
||
|
|
||
|
return neighborhood
|
||
|
|
||
|
# Memoization cache for storing the results of previous calls to the
|
||
|
function
|
||
|
neighborhood_cache = collections.defaultdict(list)
|
||
|
|
||
|
def memoized_neighbors(s: str, d: int):
|
||
|
"""Return the d-neighborhood of s using memoization"""
|
||
|
if (s, d) in neighborhood_cache:
|
||
|
return neighborhood_cache[(s, d)]
|
||
|
else:
|
||
|
neighborhood = neighbors(s, d)
|
||
|
neighborhood_cache[(s, d)] = neighborhood
|
||
|
return neighborhood
|
||
|
```</div></div></button> </div><div class="w-full pr-2 relative"><button class="w-full flex justify-between rounded-md px-3 py-2 hover:bg-gray-900 transition whitespace-nowrap text-ellipsis"><div class="flex self-center flex-1"><div class="self-center mr-3"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M2.25 12.76c0 1.6 1.123 2.994 2.707 3.227 1.087.16 2.185.283 3.293.369V21l4.076-4.076a1.526 1.526 0 011.037-.443 48.282 48.282 0 005.68-.494c1.584-.233 2.707-1.626 2.707-3.228V6.741c0-1.602-1.123-2.995-2.707-3.228A48.394 48.394 0 0012 3c-2.392 0-4.744.175-7.043.513C3.373 3.746 2.25 5.14 2.25 6.741v6.018z"></path></svg></div> <div class="text-left self-center overflow-hidden w-[180px]"> "The Artistry of Bread Making: A User's Guide"
|
||
|
</div></div></button> </div><div class="w-full pr-2 relative"><button class="w-full flex justify-between rounded-md px-3 py-2 hover:bg-gray-900 transition whitespace-nowrap text-ellipsis"><div class="flex self-center flex-1"><div class="self-center mr-3"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M2.25 12.76c0 1.6 1.123 2.994 2.707 3.227 1.087.16 2.185.283 3.293.369V21l4.076-4.076a1.526 1.526 0 011.037-.443 48.282 48.282 0 005.68-.494c1.584-.233 2.707-1.626 2.707-3.228V6.741c0-1.602-1.123-2.995-2.707-3.228A48.394 48.394 0 0012 3c-2.392 0-4.744.175-7.043.513C3.373 3.746 2.25 5.14 2.25 6.741v6.018z"></path></svg></div> <div class="text-left self-center overflow-hidden w-[180px]">Header: "Settings Error"</div></div></button> </div><div class="w-full pr-2 relative"><button class="w-full flex justify-between rounded-md px-3 py-2 hover:bg-gray-900 transition whitespace-nowrap text-ellipsis"><div class="flex self-center flex-1"><div class="self-center mr-3"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M2.25 12.76c0 1.6 1.123 2.994 2.707 3.227 1.087.16 2.185.283 3.293.369V21l4.076-4.076a1.526 1.526 0 011.037-.443 48.282 48.282 0 005.68-.494c1.584-.233 2.707-1.626 2.707-3.228V6.741c0-1.602-1.123-2.995-2.707-3.228A48.394 48.394 0 0012 3c-2.392 0-4.744.175-7.043.513C3.373 3.746 2.25 5.14 2.25 6.741v6.018z"></path></svg></div> <div class="text-left self-center overflow-hidden w-[180px]">
|
||
|
Optimize this code:
|
||
|
```python
|
||
|
# Optimized
|
||
|
from Bio import SeqIO
|
||
|
|
||
|
def most_frequent_kmers(s: str, k: int, d: int) -> set:
|
||
|
"""Returns the set of most frequent k-mers with up to d mismatches in s
|
||
|
|
||
|
>>> most_frequent_kmers('ACGTTGCATGTCGCATGATGCATGAGAGCT', 4, 1)
|
||
|
{'GATG', 'ATGT', 'ATGC'}
|
||
|
>>> most_frequent_kmers('AACAAGCTGATAAACATTTAAAGAG', 5, 1)
|
||
|
{'AAAAA'}
|
||
|
|
||
|
>>> from Bio import SeqIO
|
||
|
>>> most_frequent_kmers(*SeqIO.parse('8-data.fna', 'fasta'), 10, 2)
|
||
|
{'GCACACAGAC', 'GCGCACACAC'}
|
||
|
"""
|
||
|
|
||
|
if isinstance(s, SeqIO.SeqRecord):
|
||
|
s = s.seq
|
||
|
|
||
|
# Calculate the number of possible k-mers in the string
|
||
|
n_kmers = 4 ** k
|
||
|
|
||
|
# Create a dictionary to store the counts for each k-mer
|
||
|
kmer_counts = {}
|
||
|
|
||
|
# Iterate through each k-mer in the string
|
||
|
for i in range(len(s) - k + 1):
|
||
|
kmer = s[i:i+k]
|
||
|
if kmer not in kmer_counts:
|
||
|
kmer_counts[kmer] = 0
|
||
|
kmer_counts[kmer] += 1
|
||
|
|
||
|
# Find the maximum count of any k-mer
|
||
|
max_count = max(kmer_counts.values())
|
||
|
|
||
|
# Return the set of k-mers with the highest count, up to d mismatches
|
||
|
return {kmer for kmer, count in kmer_counts.items() if count == max_count}
|
||
|
```</div></div></button> </div><div class="w-full pr-2 relative"><button class="w-full flex justify-between rounded-md px-3 py-2 hover:bg-gray-900 transition whitespace-nowrap text-ellipsis"><div class="flex self-center flex-1"><div class="self-center mr-3"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M2.25 12.76c0 1.6 1.123 2.994 2.707 3.227 1.087.16 2.185.283 3.293.369V21l4.076-4.076a1.526 1.526 0 011.037-.443 48.282 48.282 0 005.68-.494c1.584-.233 2.707-1.626 2.707-3.228V6.741c0-1.602-1.123-2.995-2.707-3.228A48.394 48.394 0 0012 3c-2.392 0-4.744.175-7.043.513C3.373 3.746 2.25 5.14 2.25 6.741v6.018z"></path></svg></div> <div class="text-left self-center overflow-hidden w-[180px]">Optimize Pattern Count</div></div></button> </div><div class="w-full pr-2 relative"><button class="w-full flex justify-between rounded-md px-3 py-2 hover:bg-gray-900 transition whitespace-nowrap text-ellipsis"><div class="flex self-center flex-1"><div class="self-center mr-3"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M2.25 12.76c0 1.6 1.123 2.994 2.707 3.227 1.087.16 2.185.283 3.293.369V21l4.076-4.076a1.526 1.526 0 011.037-.443 48.282 48.282 0 005.68-.494c1.584-.233 2.707-1.626 2.707-3.228V6.741c0-1.602-1.123-2.995-2.707-3.228A48.394 48.394 0 0012 3c-2.392 0-4.744.175-7.043.513C3.373 3.746 2.25 5.14 2.25 6.741v6.018z"></path></svg></div> <div class="text-left self-center overflow-hidden w-[180px]"> Hello World!
|
||
|
</div></div></button> </div><div class="w-full pr-2 relative"><button class="w-full flex justify-between rounded-md px-3 py-2 hover:bg-gray-900 transition whitespace-nowrap text-ellipsis"><div class="flex self-center flex-1"><div class="self-center mr-3"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M2.25 12.76c0 1.6 1.123 2.994 2.707 3.227 1.087.16 2.185.283 3.293.369V21l4.076-4.076a1.526 1.526 0 011.037-.443 48.282 48.282 0 005.68-.494c1.584-.233 2.707-1.626 2.707-3.228V6.741c0-1.602-1.123-2.995-2.707-3.228A48.394 48.394 0 0012 3c-2.392 0-4.744.175-7.043.513C3.373 3.746 2.25 5.14 2.25 6.741v6.018z"></path></svg></div> <div class="text-left self-center overflow-hidden w-[180px]"> Meme title: ?
|
||
|
</div></div></button> </div><div class="w-full pr-2 relative"><button class="w-full flex justify-between rounded-md px-3 py-2 hover:bg-gray-900 transition whitespace-nowrap text-ellipsis"><div class="flex self-center flex-1"><div class="self-center mr-3"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M2.25 12.76c0 1.6 1.123 2.994 2.707 3.227 1.087.16 2.185.283 3.293.369V21l4.076-4.076a1.526 1.526 0 011.037-.443 48.282 48.282 0 005.68-.494c1.584-.233 2.707-1.626 2.707-3.228V6.741c0-1.602-1.123-2.995-2.707-3.228A48.394 48.394 0 0012 3c-2.392 0-4.744.175-7.043.513C3.373 3.746 2.25 5.14 2.25 6.741v6.018z"></path></svg></div> <div class="text-left self-center overflow-hidden w-[180px]">
|
||
|
Rewrite using list comprehension:
|
||
|
```python
|
||
|
skew_over_time = [0] + [(i == 'G' and 1) or (i == 'C' and -1) for i in s]
|
||
|
```</div></div></button> </div><div class="w-full pr-2 relative"><button class="w-full flex justify-between rounded-md px-3 py-2 hover:bg-gray-900 transition whitespace-nowrap text-ellipsis"><div class="flex self-center flex-1"><div class="self-center mr-3"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M2.25 12.76c0 1.6 1.123 2.994 2.707 3.227 1.087.16 2.185.283 3.293.369V21l4.076-4.076a1.526 1.526 0 011.037-.443 48.282 48.282 0 005.68-.494c1.584-.233 2.707-1.626 2.707-3.228V6.741c0-1.602-1.123-2.995-2.707-3.228A48.394 48.394 0 0012 3c-2.392 0-4.744.175-7.043.513C3.373 3.746 2.25 5.14 2.25 6.741v6.018z"></path></svg></div> <div class="text-left self-center overflow-hidden w-[180px]"> "The Basics of Chatbots"
|
||
|
</div></div></button> </div><div class="w-full pr-2 relative"><button class="w-full flex justify-between rounded-md px-3 py-2 hover:bg-gray-900 transition whitespace-nowrap text-ellipsis"><div class="flex self-center flex-1"><div class="self-center mr-3"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M2.25 12.76c0 1.6 1.123 2.994 2.707 3.227 1.087.16 2.185.283 3.293.369V21l4.076-4.076a1.526 1.526 0 011.037-.443 48.282 48.282 0 005.68-.494c1.584-.233 2.707-1.626 2.707-3.228V6.741c0-1.602-1.123-2.995-2.707-3.228A48.394 48.394 0 0012 3c-2.392 0-4.744.175-7.043.513C3.373 3.746 2.25 5.14 2.25 6.741v6.018z"></path></svg></div> <div class="text-left self-center overflow-hidden w-[180px]"> "Home Assistant Integration"
|
||
|
</div></div></button> </div><div class="w-full pr-2 relative"><button class="w-full flex justify-between rounded-md px-3 py-2 hover:bg-gray-900 transition whitespace-nowrap text-ellipsis"><div class="flex self-center flex-1"><div class="self-center mr-3"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M2.25 12.76c0 1.6 1.123 2.994 2.707 3.227 1.087.16 2.185.283 3.293.369V21l4.076-4.076a1.526 1.526 0 011.037-.443 48.282 48.282 0 005.68-.494c1.584-.233 2.707-1.626 2.707-3.228V6.741c0-1.602-1.123-2.995-2.707-3.228A48.394 48.394 0 0012 3c-2.392 0-4.744.175-7.043.513C3.373 3.746 2.25 5.14 2.25 6.741v6.018z"></path></svg></div> <div class="text-left self-center overflow-hidden w-[180px]">
|
||
|
Plant Life</div></div></button> </div><div class="w-full pr-2 relative"><button class="w-full flex justify-between rounded-md px-3 py-2 hover:bg-gray-900 transition whitespace-nowrap text-ellipsis"><div class="flex self-center flex-1"><div class="self-center mr-3"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M2.25 12.76c0 1.6 1.123 2.994 2.707 3.227 1.087.16 2.185.283 3.293.369V21l4.076-4.076a1.526 1.526 0 011.037-.443 48.282 48.282 0 005.68-.494c1.584-.233 2.707-1.626 2.707-3.228V6.741c0-1.602-1.123-2.995-2.707-3.228A48.394 48.394 0 0012 3c-2.392 0-4.744.175-7.043.513C3.373 3.746 2.25 5.14 2.25 6.741v6.018z"></path></svg></div> <div class="text-left self-center overflow-hidden w-[180px]"> Greetings from AI!
|
||
|
</div></div></button> </div><div class="w-full pr-2 relative"><button class="w-full flex justify-between rounded-md px-3 py-2 hover:bg-gray-900 transition whitespace-nowrap text-ellipsis"><div class="flex self-center flex-1"><div class="self-center mr-3"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M2.25 12.76c0 1.6 1.123 2.994 2.707 3.227 1.087.16 2.185.283 3.293.369V21l4.076-4.076a1.526 1.526 0 011.037-.443 48.282 48.282 0 005.68-.494c1.584-.233 2.707-1.626 2.707-3.228V6.741c0-1.602-1.123-2.995-2.707-3.228A48.394 48.394 0 0012 3c-2.392 0-4.744.175-7.043.513C3.373 3.746 2.25 5.14 2.25 6.741v6.018z"></path></svg></div> <div class="text-left self-center overflow-hidden w-[180px]">
|
||
|
"Discord Rich Presence Updater"</div></div></button> </div><div class="w-full pr-2 relative"><button class="w-full flex justify-between rounded-md px-3 py-2 hover:bg-gray-900 transition whitespace-nowrap text-ellipsis"><div class="flex self-center flex-1"><div class="self-center mr-3"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M2.25 12.76c0 1.6 1.123 2.994 2.707 3.227 1.087.16 2.185.283 3.293.369V21l4.076-4.076a1.526 1.526 0 011.037-.443 48.282 48.282 0 005.68-.494c1.584-.233 2.707-1.626 2.707-3.228V6.741c0-1.602-1.123-2.995-2.707-3.228A48.394 48.394 0 0012 3c-2.392 0-4.744.175-7.043.513C3.373 3.746 2.25 5.14 2.25 6.741v6.018z"></path></svg></div> <div class="text-left self-center overflow-hidden w-[180px]">
|
||
|
Backup ZFS with Restic</div></div></button> </div><div class="w-full pr-2 relative"><button class="w-full flex justify-between rounded-md px-3 py-2 hover:bg-gray-900 transition whitespace-nowrap text-ellipsis"><div class="flex self-center flex-1"><div class="self-center mr-3"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M2.25 12.76c0 1.6 1.123 2.994 2.707 3.227 1.087.16 2.185.283 3.293.369V21l4.076-4.076a1.526 1.526 0 011.037-.443 48.282 48.282 0 005.68-.494c1.584-.233 2.707-1.626 2.707-3.228V6.741c0-1.602-1.123-2.995-2.707-3.228A48.394 48.394 0 0012 3c-2.392 0-4.744.175-7.043.513C3.373 3.746 2.25 5.14 2.25 6.741v6.018z"></path></svg></div> <div class="text-left self-center overflow-hidden w-[180px]">
|
||
|
This line uses `curl` with the `--netrc`, `-k`, and `-a` options to transfer a file using SFTP.</div></div></button> </div><div class="w-full pr-2 relative"><button class="w-full flex justify-between rounded-md px-3 py-2 hover:bg-gray-900 transition whitespace-nowrap text-ellipsis"><div class="flex self-center flex-1"><div class="self-center mr-3"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M2.25 12.76c0 1.6 1.123 2.994 2.707 3.227 1.087.16 2.185.283 3.293.369V21l4.076-4.076a1.526 1.526 0 011.037-.443 48.282 48.282 0 005.68-.494c1.584-.233 2.707-1.626 2.707-3.228V6.741c0-1.602-1.123-2.995-2.707-3.228A48.394 48.394 0 0012 3c-2.392 0-4.744.175-7.043.513C3.373 3.746 2.25 5.14 2.25 6.741v6.018z"></path></svg></div> <div class="text-left self-center overflow-hidden w-[180px]">
|
||
|
Meaning of dmesg message</div></div></button> </div><div class="w-full pr-2 relative"><button class="w-full flex justify-between rounded-md px-3 py-2 hover:bg-gray-900 transition whitespace-nowrap text-ellipsis"><div class="flex self-center flex-1"><div class="self-center mr-3"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M2.25 12.76c0 1.6 1.123 2.994 2.707 3.227 1.087.16 2.185.283 3.293.369V21l4.076-4.076a1.526 1.526 0 011.037-.443 48.282 48.282 0 005.68-.494c1.584-.233 2.707-1.626 2.707-3.228V6.741c0-1.602-1.123-2.995-2.707-3.228A48.394 48.394 0 0012 3c-2.392 0-4.744.175-7.043.513C3.373 3.746 2.25 5.14 2.25 6.741v6.018z"></path></svg></div> <div class="text-left self-center overflow-hidden w-[180px]"> Greetings! How can I assist you today?
|
||
|
</div></div></button> </div><div class="w-full pr-2 relative"><button class="w-full flex justify-between rounded-md px-3 py-2 hover:bg-gray-900 transition whitespace-nowrap text-ellipsis"><div class="flex self-center flex-1"><div class="self-center mr-3"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M2.25 12.76c0 1.6 1.123 2.994 2.707 3.227 1.087.16 2.185.283 3.293.369V21l4.076-4.076a1.526 1.526 0 011.037-.443 48.282 48.282 0 005.68-.494c1.584-.233 2.707-1.626 2.707-3.228V6.741c0-1.602-1.123-2.995-2.707-3.228A48.394 48.394 0 0012 3c-2.392 0-4.744.175-7.043.513C3.373 3.746 2.25 5.14 2.25 6.741v6.018z"></path></svg></div> <div class="text-left self-center overflow-hidden w-[180px]">
|
||
|
"""
|
||
|
|
||
|
</div></div></button> </div><div class="w-full pr-2 relative"><button class="w-full flex justify-between rounded-md px-3 py-2 hover:bg-gray-900 transition whitespace-nowrap text-ellipsis"><div class="flex self-center flex-1"><div class="self-center mr-3"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M2.25 12.76c0 1.6 1.123 2.994 2.707 3.227 1.087.16 2.185.283 3.293.369V21l4.076-4.076a1.526 1.526 0 011.037-.443 48.282 48.282 0 005.68-.494c1.584-.233 2.707-1.626 2.707-3.228V6.741c0-1.602-1.123-2.995-2.707-3.228A48.394 48.394 0 0012 3c-2.392 0-4.744.175-7.043.513C3.373 3.746 2.25 5.14 2.25 6.741v6.018z"></path></svg></div> <div class="text-left self-center overflow-hidden w-[180px]">
|
||
|
AI in LaTeX</div></div></button> </div><div class="w-full pr-2 relative"><button class="w-full flex justify-between rounded-md px-3 py-2 hover:bg-gray-900 transition whitespace-nowrap text-ellipsis"><div class="flex self-center flex-1"><div class="self-center mr-3"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M2.25 12.76c0 1.6 1.123 2.994 2.707 3.227 1.087.16 2.185.283 3.293.369V21l4.076-4.076a1.526 1.526 0 011.037-.443 48.282 48.282 0 005.68-.494c1.584-.233 2.707-1.626 2.707-3.228V6.741c0-1.602-1.123-2.995-2.707-3.228A48.394 48.394 0 0012 3c-2.392 0-4.744.175-7.043.513C3.373 3.746 2.25 5.14 2.25 6.741v6.018z"></path></svg></div> <div class="text-left self-center overflow-hidden w-[180px]">
|
||
|
"Terminal Closes with Stack Smashing Error"</div></div></button> </div><div class="w-full pr-2 relative"><button class="w-full flex justify-between rounded-md px-3 py-2 hover:bg-gray-900 transition whitespace-nowrap text-ellipsis"><div class="flex self-center flex-1"><div class="self-center mr-3"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M2.25 12.76c0 1.6 1.123 2.994 2.707 3.227 1.087.16 2.185.283 3.293.369V21l4.076-4.076a1.526 1.526 0 011.037-.443 48.282 48.282 0 005.68-.494c1.584-.233 2.707-1.626 2.707-3.228V6.741c0-1.602-1.123-2.995-2.707-3.228A48.394 48.394 0 0012 3c-2.392 0-4.744.175-7.043.513C3.373 3.746 2.25 5.14 2.25 6.741v6.018z"></path></svg></div> <div class="text-left self-center overflow-hidden w-[180px]">New Chat</div></div></button> </div><div class="w-full pr-2 relative"><button class="w-full flex justify-between rounded-md px-3 py-2 hover:bg-gray-900 transition whitespace-nowrap text-ellipsis"><div class="flex self-center flex-1"><div class="self-center mr-3"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M2.25 12.76c0 1.6 1.123 2.994 2.707 3.227 1.087.16 2.185.283 3.293.369V21l4.076-4.076a1.526 1.526 0 011.037-.443 48.282 48.282 0 005.68-.494c1.584-.233 2.707-1.626 2.707-3.228V6.741c0-1.602-1.123-2.995-2.707-3.228A48.394 48.394 0 0012 3c-2.392 0-4.744.175-7.043.513C3.373 3.746 2.25 5.14 2.25 6.741v6.018z"></path></svg></div> <div class="text-left self-center overflow-hidden w-[180px]">Compose row with icon.</div></div></button> </div><div class="w-full pr-2 relative"><button class="w-full flex justify-between rounded-md px-3 py-2 hover:bg-gray-900 transition whitespace-nowrap text-ellipsis"><div class="flex self-center flex-1"><div class="self-center mr-3"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M2.25 12.76c0 1.6 1.123 2.994 2.707 3.227 1.087.16 2.185.283 3.293.369V21l4.076-4.076a1.526 1.526 0 011.037-.443 48.282 48.282 0 005.68-.494c1.584-.233 2.707-1.626 2.707-3.228V6.741c0-1.602-1.123-2.995-2.707-3.228A48.394 48.394 0 0012 3c-2.392 0-4.744.175-7.043.513C3.373 3.746 2.25 5.14 2.25 6.741v6.018z"></path></svg></div> <div class="text-left self-center overflow-hidden w-[180px]">Android Button w/ Icon</div></div></button> </div><div class="w-full pr-2 relative"><button class="w-full flex justify-between rounded-md px-3 py-2 hover:bg-gray-900 transition whitespace-nowrap text-ellipsis"><div class="flex self-center flex-1"><div class="self-center mr-3"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M2.25 12.76c0 1.6 1.123 2.994 2.707 3.227 1.087.16 2.185.283 3.293.369V21l4.076-4.076a1.526 1.526 0 011.037-.443 48.282 48.282 0 005.68-.494c1.584-.233 2.707-1.626 2.707-3.228V6.741c0-1.602-1.123-2.995-2.707-3.228A48.394 48.394 0 0012 3c-2.392 0-4.744.175-7.043.513C3.373 3.746 2.25 5.14 2.25 6.741v6.018z"></path></svg></div> <div class="text-left self-center overflow-hidden w-[180px]">Git selective line commit.</div></div></button> </div><div class="w-full pr-2 relative"><button class="w-full flex justify-between rounded-md px-3 py-2 hover:bg-gray-900 transition whitespace-nowrap text-ellipsis"><div class="flex self-center flex-1"><div class="self-center mr-3"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M2.25 12.76c0 1.6 1.123 2.994 2.707 3.227 1.087.16 2.185.283 3.293.369V21l4.076-4.076a1.526 1.526 0 011.037-.443 48.282 48.282 0 005.68-.494c1.584-.233 2.707-1.626 2.707-3.228V6.741c0-1.602-1.123-2.995-2.707-3.22
|
||
|
```python
|
||
|
def pattern_to_number(pattern):
|
||
|
if pattern == '':
|
||
|
return 0
|
||
|
return 4 * pattern_to_number(pattern[0:-1]) + nucleotides.index(pattern[-1])
|
||
|
```</pre> <div class="flex justify-start space-x-1"><div class="flex self-center"><button class="self-center"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 20 20" fill="currentColor" class="w-4 h-4"><path fill-rule="evenodd" d="M12.79 5.23a.75.75 0 01-.02 1.06L8.832 10l3.938 3.71a.75.75 0 11-1.04 1.08l-4.5-4.25a.75.75 0 010-1.08l4.5-4.25a.75.75 0 011.06.02z" clip-rule="evenodd"></path></svg></button> <div class="text-xs font-bold self-center">2 / 2</div> <button class="self-center"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 20 20" fill="currentColor" class="w-4 h-4"><path fill-rule="evenodd" d="M7.21 14.77a.75.75 0 01.02-1.06L11.168 10 7.23 6.29a.75.75 0 111.04-1.08l4.5 4.25a.75.75 0 010 1.08l-4.5 4.25a.75.75 0 01-1.06-.02z" clip-rule="evenodd"></path></svg></button></div> <button class="invisible group-hover:visible p-1 rounded dark:hover:text-white transition edit-user-message-button"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M16.862 4.487l1.687-1.688a1.875 1.875 0 112.652 2.652L6.832 19.82a4.5 4.5 0 01-1.897 1.13l-2.685.8.8-2.685a4.5 4.5 0 011.13-1.897L16.863 4.487zm0 0L19.5 7.125"></path></svg></button> <button class="invisible group-hover:visible p-1 rounded dark:hover:text-white transition"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M15.666 3.888A2.25 2.25 0 0013.5 2.25h-3c-1.03 0-1.9.693-2.166 1.638m7.332 0c.055.194.084.4.084.612v0a.75.75 0 01-.75.75H9a.75.75 0 01-.75-.75v0c0-.212.03-.418.084-.612m7.332 0c.646.049 1.288.11 1.927.184 1.1.128 1.907 1.077 1.907 2.185V19.5a2.25 2.25 0 01-2.25 2.25H6.75A2.25 2.25 0 014.5 19.5V6.257c0-1.108.806-2.057 1.907-2.185a48.208 48.208 0 011.927-.184"></path></svg></button></div></div></div></div></div> </div></div><div class="w-full"><div class="flex flex-col justify-between px-5 mb-3 max-w-3xl mx-auto rounded-lg group"><div class="flex w-full message-c045d456-c726-4ae8-8aa7-d4ada71bc315 svelte-1u5gq5j"><div class="mr-4"><img src="efa88123-9a38-4981-ad24-bf6168506917_files/favicon.png" class="max-w-[28px] object-cover rounded-full" alt="profile" draggable="false"></div> <div class="w-full overflow-hidden"><div class="self-center font-bold mb-0.5 capitalize line-clamp-1"> codellama:latest <span class="invisible group-hover:visible text-gray-400 text-xs font-medium">19/02/2024 13:26</span></div> <div class="prose chat-assistant w-full max-w-full dark:prose-invert prose-headings:my-0 prose-p:m-0 prose-p:-mb-6 prose-pre:my-0 prose-table:my-0 prose-blockquote:my-0 prose-img:my-0 prose-ul:-my-4 prose-ol:-my-4 prose-li:-my-3 prose-ul:-mb-6 prose-ol:-mb-8 prose-li:-mb-4 whitespace-pre-line svelte-1u5gq5j"><div><div class="w-full"><p>Here's a modified version of the code that doesn't use recursion:</p>
|
||
|
<div class="mb-4"><div class="flex justify-between bg-[#202123] text-white text-xs px-4 pt-1 pb-0.5 rounded-t-lg overflow-x-auto"><div class="p-1">python</div> <button class="copy-code-button bg-none border-none p-1">Copy Code</button></div> <pre class="rounded-b-lg hljs p-4 px-5 overflow-x-auto rounded-t-none"><code class="language-python rounded-t-none whitespace-pre"><span class="hljs-keyword">def</span> <span class="hljs-title function_">pattern_to_number</span>(<span class="hljs-params">pattern</span>):
|
||
|
result = <span class="hljs-number">0</span>
|
||
|
<span class="hljs-keyword">for</span> i <span class="hljs-keyword">in</span> <span class="hljs-built_in">range</span>(<span class="hljs-built_in">len</span>(pattern)):
|
||
|
result = (result * <span class="hljs-number">4</span>) + nucleotides.index(pattern[i])
|
||
|
<span class="hljs-keyword">return</span> result</code></pre></div><p>This version uses a loop to iterate over the characters of the input pattern, and calculates the resulting number using integer arithmetic instead of string concatenation. This should be faster than the original code, since it avoids the overhead of recursive function calls.</p>
|
||
|
<div class="flex justify-start space-x-1 -mt-1 overflow-x-auto buttons text-gray-700 dark:text-gray-500 svelte-1u5gq5j"> <button class="invisible group-hover:visible p-1 rounded dark:hover:text-white hover:text-black transition"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M16.862 4.487l1.687-1.688a1.875 1.875 0 112.652 2.652L6.832 19.82a4.5 4.5 0 01-1.897 1.13l-2.685.8.8-2.685a4.5 4.5 0 011.13-1.897L16.863 4.487zm0 0L19.5 7.125"></path></svg></button> <button class="invisible group-hover:visible p-1 rounded dark:hover:text-white hover:text-black transition copy-response-button"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M15.666 3.888A2.25 2.25 0 0013.5 2.25h-3c-1.03 0-1.9.693-2.166 1.638m7.332 0c.055.194.084.4.084.612v0a.75.75 0 01-.75.75H9a.75.75 0 01-.75-.75v0c0-.212.03-.418.084-.612m7.332 0c.646.049 1.288.11 1.927.184 1.1.128 1.907 1.077 1.907 2.185V19.5a2.25 2.25 0 01-2.25 2.25H6.75A2.25 2.25 0 014.5 19.5V6.257c0-1.108.806-2.057 1.907-2.185a48.208 48.208 0 011.927-.184"></path></svg></button> <button class="invisible group-hover:visible p-1 rounded dark:hover:text-white hover:text-black transition"><svg stroke="currentColor" fill="none" stroke-width="2" viewBox="0 0 24 24" stroke-linecap="round" stroke-linejoin="round" class="w-4 h-4" xmlns="http://www.w3.org/2000/svg"><path d="M14 9V5a3 3 0 0 0-3-3l-4 9v11h11.28a2 2 0 0 0 2-1.7l1.38-9a2 2 0 0 0-2-2.3zM7 22H4a2 2 0 0 1-2-2v-7a2 2 0 0 1 2-2h3"></path></svg></button> <button class="invisible group-hover:visible p-1 rounded dark:hover:text-white hover:text-black transition"><svg stroke="currentColor" fill="none" stroke-width="2" viewBox="0 0 24 24" stroke-linecap="round" stroke-linejoin="round" class="w-4 h-4" xmlns="http://www.w3.org/2000/svg"><path d="M10 15v4a3 3 0 0 0 3 3l4-9V2H5.72a2 2 0 0 0-2 1.7l-1.38 9a2 2 0 0 0 2 2.3zm7-13h2.67A2.31 2.31 0 0 1 22 4v7a2.31 2.31 0 0 1-2.33 2H17"></path></svg></button> <button id="speak-button-c045d456-c726-4ae8-8aa7-d4ada71bc315" class="invisible group-hover:visible p-1 rounded dark:hover:text-white hover:text-black transition"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M19.114 5.636a9 9 0 010 12.728M16.463 8.288a5.25 5.25 0 010 7.424M6.75 8.25l4.72-4.72a.75.75 0 011.28.53v15.88a.75.75 0 01-1.28.53l-4.72-4.72H4.51c-.88 0-1.704-.507-1.938-1.354A9.01 9.01 0 012.25 12c0-.83.112-1.633.322-2.396C2.806 8.756 3.63 8.25 4.51 8.25H6.75z"></path></svg></button> <button class="invisible group-hover:visible p-1 rounded dark:hover:text-white hover:text-black transition whitespace-pre-wrap" id="info-c045d456-c726-4ae8-8aa7-d4ada71bc315"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M11.25 11.25l.041-.02a.75.75 0 011.063.852l-.708 2.836a.75.75 0 001.063.853l.041-.021M21 12a9 9 0 11-18 0 9 9 0 0118 0zm-9-3.75h.008v.008H12V8.25z"></path></svg></button> </div></div></div></div></div></div></div></div><div class="w-full"><div class="flex flex-col justify-between px-5 mb-3 max-w-3xl mx-auto rounded-lg group"><div class="flex w-full"><div class="mr-4"><img src="efa88123-9a38-4981-ad24-bf6168506917_files/34ab5c4d2a3de664daedcf684ea5fdc8472fda81aac2360da69747c1f579.jpg" class="max-w-[28px] object-cover rounded-full" alt="profile" draggable="false"></div> <div class="w-full overflow-hidden"><div class="user-message"><div class="self-center font-bold mb-0.5 capitalize line-clamp-1">You <span class="invisible group-hover:visible text-gray-400 text-xs font-medium">19/02/2024 13:32</span></div></div> <div class="prose chat-user w-full max-w-full dark:prose-invert prose-headings:my-0 prose-p:my-0 pros
|
||
|
<div class="mb-4"><div class="flex justify-between bg-[#202123] text-white text-xs px-4 pt-1 pb-0.5 rounded-t-lg overflow-x-auto"><div class="p-1">python</div> <button class="copy-code-button bg-none border-none p-1">Copy Code</button></div> <pre class="rounded-b-lg hljs p-4 px-5 overflow-x-auto rounded-t-none"><code class="language-python rounded-t-none whitespace-pre"><span class="hljs-keyword">def</span> <span class="hljs-title function_">pattern_to_number</span>(<span class="hljs-params">pattern</span>):
|
||
|
<span class="hljs-keyword">if</span> <span class="hljs-built_in">len</span>(pattern) == <span class="hljs-number">0</span>:
|
||
|
<span class="hljs-keyword">return</span> <span class="hljs-number">0</span>
|
||
|
<span class="hljs-keyword">else</span>:
|
||
|
<span class="hljs-keyword">return</span> <span class="hljs-number">4</span> * pattern_to_number(pattern[<span class="hljs-number">0</span>:-<span class="hljs-number">1</span>]) + nucleotides.index(pattern[-<span class="hljs-number">1</span>])</code></pre></div><p>This version of the code uses a recursive function to calculate the result, where the base case is when the input string has zero length, in which case the function returns 0. Otherwise, it calculates the result by multiplying the result of the same function called with the first character removed from the input string, and then adding the value of the last character.</p>
|
||
|
<p>This version of the code should be faster than the previous one, since it avoids the overhead of iterating over the characters of the input string using a loop. However, it is generally considered less efficient than a non-recursive solution, since it can lead to a stack overflow if the input string is too long.</p>
|
||
|
<div class="flex justify-start space-x-1 -mt-1 overflow-x-auto buttons text-gray-700 dark:text-gray-500 svelte-1u5gq5j"> <button class="visible p-1 rounded dark:hover:text-white hover:text-black transition"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M16.862 4.487l1.687-1.688a1.875 1.875 0 112.652 2.652L6.832 19.82a4.5 4.5 0 01-1.897 1.13l-2.685.8.8-2.685a4.5 4.5 0 011.13-1.897L16.863 4.487zm0 0L19.5 7.125"></path></svg></button> <button class="visible p-1 rounded dark:hover:text-white hover:text-black transition copy-response-button"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M15.666 3.888A2.25 2.25 0 0013.5 2.25h-3c-1.03 0-1.9.693-2.166 1.638m7.332 0c.055.194.084.4.084.612v0a.75.75 0 01-.75.75H9a.75.75 0 01-.75-.75v0c0-.212.03-.418.084-.612m7.332 0c.646.049 1.288.11 1.927.184 1.1.128 1.907 1.077 1.907 2.185V19.5a2.25 2.25 0 01-2.25 2.25H6.75A2.25 2.25 0 014.5 19.5V6.257c0-1.108.806-2.057 1.907-2.185a48.208 48.208 0 011.927-.184"></path></svg></button> <button class="visible p-1 rounded dark:hover:text-white hover:text-black transition"><svg stroke="currentColor" fill="none" stroke-width="2" viewBox="0 0 24 24" stroke-linecap="round" stroke-linejoin="round" class="w-4 h-4" xmlns="http://www.w3.org/2000/svg"><path d="M14 9V5a3 3 0 0 0-3-3l-4 9v11h11.28a2 2 0 0 0 2-1.7l1.38-9a2 2 0 0 0-2-2.3zM7 22H4a2 2 0 0 1-2-2v-7a2 2 0 0 1 2-2h3"></path></svg></button> <button class="visible p-1 rounded dark:hover:text-white hover:text-black transition"><svg stroke="currentColor" fill="none" stroke-width="2" viewBox="0 0 24 24" stroke-linecap="round" stroke-linejoin="round" class="w-4 h-4" xmlns="http://www.w3.org/2000/svg"><path d="M10 15v4a3 3 0 0 0 3 3l4-9V2H5.72a2 2 0 0 0-2 1.7l-1.38 9a2 2 0 0 0 2 2.3zm7-13h2.67A2.31 2.31 0 0 1 22 4v7a2.31 2.31 0 0 1-2.33 2H17"></path></svg></button> <button id="speak-button-166e5ba8-331f-430f-8da7-6dba226ec178" class="visible p-1 rounded dark:hover:text-white hover:text-black transition"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M19.114 5.636a9 9 0 010 12.728M16.463 8.288a5.25 5.25 0 010 7.424M6.75 8.25l4.72-4.72a.75.75 0 011.28.53v15.88a.75.75 0 01-1.28.53l-4.72-4.72H4.51c-.88 0-1.704-.507-1.938-1.354A9.01 9.01 0 012.25 12c0-.83.112-1.633.322-2.396C2.806 8.756 3.63 8.25 4.51 8.25H6.75z"></path></svg></button> <button class="visible p-1 rounded dark:hover:text-white hover:text-black transition whitespace-pre-wrap" id="info-166e5ba8-331f-430f-8da7-6dba226ec178"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M11.25 11.25l.041-.02a.75.75 0 011.063.852l-.708 2.836a.75.75 0 001.063.853l.041-.021M21 12a9 9 0 11-18 0 9 9 0 0118 0zm-9-3.75h.008v.008H12V8.25z"></path></svg></button> <button type="button" class="visible p-1 rounded dark:hover:text-white hover:text-black transition regenerate-response-button"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M21 12a9 9 0 1 1-18 0 9 9 0 0 1 18 0Z"></path><path stroke-linecap="round" stroke-linejoin="round" d="M15.91 11.672a.375.375 0 0 1 0 .656l-5.603 3.113a.375.375 0 0 1-.557-.328V8.887c0-.286.307-.466.557-.327l5.603 3.112Z"></path></svg></button> <button type="button" class="visible p-1 rounded dark:hover:text-white hover:text-black transition regenerate-response-button"><svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" stroke-width="1.5" stroke="currentColor" class="w-4 h-4"><path stroke-linecap="round" stroke-linejoin="round" d="M16.023 9.348h4
|
||
|
|
||
|
|
||
|
<span class="cleanslate TridactylStatusIndicator TridactylModenormal" style="border: #37adff var(--tridactyl-indicator-border-style, solid) var(--tridactyl-indicator-border-width, 1.5px) !important">normal</span></body><iframe class="cleanslate hidden" src="efa88123-9a38-4981-ad24-bf6168506917_files/commandline.html" id="cmdline_iframe" loading="lazy" style="height: 0px !important;"></iframe></html>
|