bio | Bioinformatics utilities | Genomics library
kandi X-RAY | bio Summary
kandi X-RAY | bio Summary
NOTE: Exploratory work in progress. Major changes may be introduced at any time. bio - command-line utilities to make bioinformatics explorations more enjoyable. where task can be: fetch, convert, align and many others.
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Top functions reviewed by kandi - BETA
- Run alignment
- Log an error message
- Align two sequences
- The main router
- Parse an XML document
- Generate records from a single record
- Return a JSON - ready representation of a value
- Parse the description
- Format run information as a CSV file
- Return a safe integer
- Get records from fnames
- Yield filenames from fnames
- Close the thread
- Read lines from stream
- Parse aliases
- Yield stream of streams
- Terminate the database
- Call an object
- Parse an XML string
- Calculate start and end coordinates based on start and end
- The main function
- Main thread
- Unparse a dictionary
- Parse a string
- Yield streams from fnames
- Get a logger
- Download a tarball
- Format a GFF record
bio Key Features
bio Examples and Code Snippets
Lines of Code : 8License : Permissive (MIT)
Copy# Fetch multiple accession numbers from genbank
bio fetch NC_045512 MN996532 > genomes.gb
# Convert Genbank to FASTA.
bio convert genomes.gb --fasta
# Convert Genbank to GFF.
bio convert genomes.gb --gff
conda install r-bookdown r-servr
make
make docs
make sync
pip install pytest
make test
import re
string = 'VATLDSCBACSKVNDNVKNKVKVKNVKMLDHHHV'
re.findall(r"B[^P]C|M[^P]D", string)
['BAC', 'MLD']
import re # import the RE module
import Bio
from Bio import SeqIO
seqs = SeqIO.parse(X, 'fasta')
for sequence in seqs:
line = sequence.se
RE = r'B[A-OQ-Z]C|M[A-OQ-Z]D'
# [A-OQ-Z] : Match from A to O and from Q to Z (exl.class UserProfileView(ListView):
model = Post
template_name = 'forum/user_profile.html'
context_object_name = 'posts'
paginate_by = 1
def get_queryset(self):
user = get_object_or_404(User, username=self.kwargs.get('username'))
retfrom redis_om import HashModel, Migrator
# Define a customer model
class Customer(HashModel):
first_name: str
last_name: str
age: int
bio: str
# Create some customers
cust1 = Customer(
first_name="Customer",
last_
super().__init__(*args, **kwargs)
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
for field in self.fields:
self.fields[field].widget.attrs['class']import sys
from typing import Optional
from Bio import AlignIO
from Bio.Align import AlignInfo
from Bio.Seq import Seq
import Bio
def getWitConsensus(alignment: Optional[Bio.Align.MultipleSeqAlignment], threshold=0.25) -> Bio.Seq.Seq:
from Bio import SeqIO
Lines = []
Counter = 0
with open("ids_to_extract.txt") as f:
lines = f.readlines()
original_file = r"input_sequences.fasta"
corrected_file = r"extracted_sequences.fasta"
with open(original_file) as oCommunity Discussions
Trending Discussions on bio
QUESTION
Profile.py
...ANSWER
Answered 2021-Jun-13 at 09:25You can filter the queryset with:
QUESTION
I have met some issue on my "HomeScreen" but it's work before not sure what's going on it's not working right now. Also have a doubt there because I've been add a container and the column also inside of the container why the column will overflow?
I would like to have a "Container" for display image on left side and right side for display "UserInformation" that fetch from database however it's showing column issue even though have been added "Flexible" or "Expanded" also not working.
"HomeScreen Display"
...ANSWER
Answered 2021-Jun-13 at 06:57The problem is that you have your ListView.builder as the child of a Column() and Columns does not scroll, change that column for a ListView and your issue sould be solved.
Also check if you are trying to access a null value and provide a default value for the text widget, a text widget's data can not be null.
QUESTION
I am trying to web scrape a government public page that contains speeches and biography of ministers. At the end I would like a dictionary like this:
...ANSWER
Answered 2021-Jun-13 at 02:24Based on the provided target data structure above, you appear to be using a dictionary. It isn't clear what you would like your keys to be so I would probably suggest using a list/array.
I would suggest a slightly different way to dissect the problem.One potential implementation would be to iterate over each row (paragraph
of the table (div
data array one index at a time.
From here, if the link(s) are present you could then query the external data source (or read from a different location on the page) to collect the respective data. In the example below, I choose to do this in a different iteration of data to help make the code a bit more readable.
I have not used the BeautifulSoap4 library before. I apologise if my solution isn't the most elegant regarding the libraries usage.
QUESTION
I have a dataset that identifies observations based on two variables: Time and Country. The variable of interest is dichotomous, and has the value 0 if the event didn't occur and 1 if it did. For some countries more than one observation is reported per year. The data can be summarized like this:
Country Time Conflict Bio Weapons A 2000 1 0 A 2000 2 0 B 2000 3 1 C 2000 4 0 D 2000 5 1 D 2000 6 0 D 2000 7 0 D 2000 8 1Is it possible two colapse these multiple observations into one observation per year and country with either outcome 0 (if the event never occured) or 1(if the event occured at least once)? Like this?:
Country Time Bio Weapons A 2000 0 B 2000 1 C 2000 0 D 2000 1Thank you in advance !
...ANSWER
Answered 2021-Jun-12 at 18:00Your output is a bit unlcear since it doesn't match with what your description is, but this is what I think you want:
QUESTION
each time i use a plugin to move to the next page on iOS the swipe back will not work like
...ANSWER
Answered 2021-Jun-11 at 07:49in my case. i was using a plugin and the plugin is using
QUESTION
I got this very wierd and unexplainable issue that boggles my mind for quite some time. Each time I run into this issue and I cannot figure out what is wrong since it is the same as it is for the other variables.
I know that there is probably some forum page wedged between the thousands of pages related to this where I could find my answer, however I cannot find that one in a thousand page.
So I am working on a script to run a filter for lines through and it is working fine except for this one stupid and stubbern variable that gives me the error message.
So when I run the following from my Bat-File called Test.bat (to keep names short) it gives me the error message following after.
Code:
...ANSWER
Answered 2021-Jun-10 at 13:50Here a simple batch from your use case illustrating why FINDSTR can't find the files which include %CNAME with your actual script:
QUESTION
I have two tables as follows
user table
subject table
data_id user_id subject 1 1 Math 2 1 Chem 3 1 Bio 4 2 Math 5 2 Phy 6 3 Engwhen I am querying data i am getting results like this:
...ANSWER
Answered 2021-Jun-09 at 06:24You should try using group_concat in MySql to merge subjects in a single column and group by the user_id.
Something like
QUESTION
I'm trying to create a post using the User profile instance. The post is saved but there is no object created in the database
In my user_blog app i have created Profile model for user
blog_users/models.py
...ANSWER
Answered 2021-Jun-08 at 06:37CreatePost is a form for the Post model not the Profile model hence passing it a profile instance is wrong. Instead you need to modify the instance wrapped by the form to set the foreign key to profile. Also from the error NOT NULL constraint failed: posts_post.title it seems you are not providing a value for the title? Your field title is not nullable hence you need to provide a value for that. Make changes to your code like so:
QUESTION
i am sending userID to Profile Page from Selector Page. The error appears once and then disappears. But the app works. Debug console say the error is related with the selectorPage. I think there's a problem in the userInfo function.
here is my selectorPage: I am sending the currentUser to ProfilePage
...ANSWER
Answered 2021-Jun-08 at 00:04Most likely the problem is here:
QUESTION
I am building a React app with Supabase as my backend. I'd like to display the contents from several of my supabase tables, in React. However, I am pulling that data with a promise and I am unsure of how to display it in React. Below is my code:
...ANSWER
Answered 2021-Jun-07 at 17:25I created a custom hook called
useWriteListthis is just another function. Check out this original documentation.useEffectjust calls provided callback function when any of its dependency array changes.
In this case, only called at once when the component rendered for the first time since it's an empty array.
So you can think of it as a declaration like we will call this callback function whenever blabla changes.
Since it's just a declaration it doesn't block rendering flow.
- Inside callback we wait for data and set
listOfWriterswhich will eventually cause a rerender.
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