dammit | just annotate it , dammit | Genomics library
kandi X-RAY | dammit Summary
kandi X-RAY | dammit Summary
dammit is a simple de novo transcriptome annotator. It was born out of the observation that: annotation is mundane and annoying; all the individual pieces of the process exist already; and, the existing solutions are overly complicated or rely on crappy non-free software. Science shouldn't suck for the sake of sucking, so dammit attempts to make this sucky part of the process suck a little less.
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Top functions reviewed by kandi - BETA
- Create a handler for the main
- Create a task to rename transcriptome
- Write data_df to GFF3
- Mangle coordinates in gff3
- Setup a profiler
- Write the result to a CSV file
- Start profiling
- Stop profiling
- Convert a hmm match to a gff3 dataframe
- Create task for Transdecoder
- Return argument parser
- Create a task definition
- Wrapper for cmscan
- Create a task definition for a given db file
- Build a pipeline
- Install a tarball
- Run annotation
- Decorator to turn a function into a context manager
- Parse a list of busco output files
- Create a task for long orfs
- Build the default pipeline
- Download setuptools
- Handle annotate databases
- Execute a BUSCO task
- Wrapper for hmmscan
- Convert cmscan to gff3 dataframe
dammit Key Features
dammit Examples and Code Snippets
Community Discussions
Trending Discussions on dammit
QUESTION
I want a code that input the number of lines (empty ones are counted), then the lines itself, then the word I want to find and finally, where the first occurrence of one character happened. Please with no imports.
I have this rn:
...ANSWER
Answered 2021-May-25 at 19:38Something like this maybe:
QUESTION
I've been using BeautifulSoup on and off for a few years, and I still get tripped up from time to time. I put together this code.
...ANSWER
Answered 2021-Feb-05 at 02:01You can use the .text attribute of the elements returned from the .findAll() method:
QUESTION
I have been trying to do an analysis of news websites which compares how many articles each website has written about covid. I was successfully able to extract articles titles of news websites and also do a word search which tells how many of all the articles extracted had the word "COVID" in it. Now I want to represent the word search result in a bar graph , I used matplotlib, but I'm getting an error which I'm unable to understand. Please help.
Following is the code, (the last part of the code is about the graph where I'm getting an error):
...ANSWER
Answered 2020-Dec-03 at 08:05The left parameter needs to be an array of the x axis values. You're passing a list of strings. And I'm not sure why you're doing this in a loop, when you're plotting the whole set every time.
Also, height needs to be a list of the bar heights, but you're make it a list of a list. Remember, Url_count is already a list.
QUESTION
I have a code which fetches me titles of news articles in webpages. I have used a for loop in which I get the titles of 4 news websites. I have also implemented a word search which tells the number of articles in which the word " coronavirus" is used. I want the word search such that it tells me the number of articles with the word "coronavirus" in each website. Right now I'm getting the output of the number of times the word "coronavirus" is used in all the websites put together. Please help me, I have to submit this project shortly. Following is the code:
...ANSWER
Answered 2020-Dec-02 at 16:29Actually you are getting only the last site count. If you want to get then all, append it to a list, then you can print the count for each site.
First create an empty list and append the final count each iteration:
QUESTION
I've been trying to scrape news titles from the news websites. For that I've come across two python libraries i.e newspaper and beautifulsoup4. Using the beautiful soup library, I've been able to get all the links from a particular news website that lead to news articles. From the code below I've been able to extract the title of a news article from a single link.
...ANSWER
Answered 2020-Nov-20 at 11:20Do you mean something like this?
QUESTION
from bs4 import beautifulsoup4
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
in
----> 1 from bs4 import BeautifulSoup as bs
C:\ProgramData\Anaconda3\lib\site-packages\bs4\__init__.py in
29 import warnings
30
---> 31 from .builder import builder_registry, ParserRejectedMarkup
32 from .dammit import UnicodeDammit
33 from .element import (
ImportError: cannot import name 'builder_registry' from 'bs4.builder' (unknown location)
ANSWER
Answered 2020-Jul-22 at 05:33use this,
QUESTION
I'm trying to convert the solution given here from PyQt4 to PyQt5 as an exercise.
Somehow the collected html code is being lost on the way. I put some print() on the methods to understand what is happening. The print() of Callable method shows the HTML codes. However, when in the handleLoadFinished method it's None and, consequently, the functions funA and funcB have not to work on.
The code I'm working is:
...ANSWER
Answered 2020-Jun-21 at 19:20Obtaining the html in QtWebEngine is asynchronous, so you get None, instead you must pass "self._func" through functools.partial() to add the url:
QUESTION
I have a function executed in parallel using the multiprocessing package, while another one is executed in the main process. The parallel function runs until the main one is finished. Both of them work, but not together. Both functions only share one argument in common (a global variable), and both use the BeautifulSoup package. Also, the functions have internal local variables which have the same name, but I don't think this is a problem. The declaration of the functions is:
...ANSWER
Answered 2020-Mar-07 at 11:03Because i cant recreate your problem , generally i will suggest not to use shared variables between processes ,except you know the state of each every time.Also you need always to have the 2 functions or scripts in the same directory , because many fork issues can show up like errors.
So generally you can solve issues like that by communicating between main and child processes like this with multyprocessing Pipe(),and share real-time the state of the variable:
QUESTION
It doesn't give any errors or show notifications.
...ANSWER
Answered 2018-May-30 at 13:49As written in the Documentation, a small icon is required to be set with SetSmallIcon(), before you call builder.Build(). This is most likely your point of issue, since nothing else seems wrong with your code.
Here is an older SO question that may have relevant information in case you run into more trouble with the Notification Builder How exactly to use Notification.Builder
QUESTION
I created a page where the background colors of a div change every so often. I want to make it so that when the mouse is over(or hovers) the color changer pauses where it is, as long as the mouse hovers there. And when the mouse no longer hovers the div, the colors continue to change where it left off. The closest examples I ran into on this website used JQuery solutions. I am not looking for a JQuery solution. I am looking for a javascript solution. I appreciate any and all of your responses. Thank You!
...ANSWER
Answered 2019-Nov-11 at 14:33While this doesnt really pouse the interval it mimics what you need very closely.. You can use a flag.. something like this:
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Install dammit
You can use dammit like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.
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