CLAM | CLIP-seq Analysis of Multi-mapped reads | Dataset library
kandi X-RAY | CLAM Summary
kandi X-RAY | CLAM Summary
CLAM is a general toolkit for re-aligning multi-mapped reads in CLIP/RIP-seq data and calling peaks. For details, please read our NAR paper. Recently, we updated CLAM to version v1.2.0 with new features:.
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Top functions reviewed by kandi - BETA
- Parse command line arguments
- Intersect GTF regions from GTF files
- Performs peak callers
- Download a genome
- Check if genome data exists
- Perform peak callers
- Filter genotypes based on cov
- Print a time stamp
- Retrieve genomic regions from a BAM file
- Construct a track dictionary given a subset of reads
- Run EM algorithm
- Filter multi - mapped reads
- Call child peak
- Writes the parameter log to a file
- Create a dictionary of genomic regions based on a filter
- Determine alignments for alignment
- Parse an MD string and return error information
- Extract misaligned errors from a CIGAR sequence
- Get md from md string
- Search for a node in the graph
- Make the write content for a write
- Reads a rm output file
- Compare two files
- Read AS score from bam file
- Function to plot a regular expression
- Computes the p - value of the Poisson distribution
- Evaluate EM model
CLAM Key Features
CLAM Examples and Code Snippets
Community Discussions
Trending Discussions on CLAM
QUESTION
I am creating a discord bot (.py) and am wondering how to set/change global variables between functions. Code:
...ANSWER
Answered 2021-Jun-02 at 19:52You can either use global variables:
QUESTION
So I'm trying to build a small app, and I really enjoy the Guizero package and it's easy, event-driven programming.
The only thing it seems to lack is a method to implement theme changes, so it looks really outdated at the moment. Is there a way to apply Tkinter packages or something?
Below is some code I've tried, and it even prints 'vista' out correctly, but it doesn't seem to implement the actual theme change.
...ANSWER
Answered 2021-May-27 at 20:11This is not ttk but you can still style what you want.
QUESTION
I'm trying to understand more about classes. I want to play around with this example Best way to structure a tkinter application? from Bryan Oakley. But now I have a problem, I want to make a simple destroy function (here in the Toolbar, but get only errors. Or do I need to make all functions in the Mainwindow?
ANSWER
Answered 2021-May-06 at 17:37Try using this:
QUESTION
I'm still in my first week of Python, so I'm sorry if this is an obvious mistake...
I want to style a Frame in Tkinter with rounded corners, therefore I got a base64 encoded image, which I applied using ttk.Style following this answer (Tkinter: How to make a rounded corner text widget?) and that worked fine.
My problem is now adapting this into a Class structured program, there the frame is not showing at all.
I replicated the Problem in the code below.
The first window is showing the problem, and the second one how its supposed to look.
How do I make this work? And could there be any new conflicts coming up when I'm not packing the frame to the main window, but into another Frame?
Thanks in advance!
...ANSWER
Answered 2021-Apr-29 at 10:53The problem is pythons garbage collections destroying the PhotoImage instance. You need to keep a reference to it (this is also somewhere in the docs). You probably just wanna save most stuff as an attribute anyway:
QUESTION
following are my files for html, .ts and json . As json data was very extensive therefore i have just added a few states and their cities. my 1st dropdown is showing all states. Now I want to match my 1st dropdown's selected value of state with a key "state" in "cities" object in my json file so i can populate 2nd dropdown with cities relevant to that state. and I want to do this in function "getCitiesForSelectedState". please help me find solution for this.
//.ts file
...ANSWER
Answered 2021-Apr-27 at 16:44You can do it with the $event parameter.
Make sure to compare your values safely.
If your value is not in the right type or has spaces or unwanted chars, this c.state == val might not work.
You can use the trim function to compare your value safely:
c.state.trim() == val.trim()
HTML
QUESTION
We have a java app that needs to use a public class form a JAR file. After much frustration with the main application, we have created a simple repo here to try to figure out what is going on.
The overly simple file that ends up in the JAR file is as follows:
ANSWER
Answered 2021-Apr-07 at 03:52Before adding the jar to library, you may run the command java -jar printStuff.jar to test if it could be executed successfully.
The error occurs because the class must be called with its fully qualified name. To be clear, the name of this class is not printStuff, It's com.mystuff.helpers.printStuff, so the right command should be:
Turn to the folder;
Compile .java file:
javac com\mystuff\helpers\printStuff.javaGenerate .jar:
jar cvfe printStuff.jar com.mystuff.helpers.printStuff .\
Then readd it to referenced libraries and see if the error goes away.
QUESTION
Using the w3schools.com SQL tutorial Northwind database, I'm trying to display the category that has the most products shipped. Additionally, I want to display the net income from all sales in that category. I can't figure out how to take the category with the most products shipped, and use the amount of products shipped to calculate the net income of that category. This is because there are many different products that have the same CategoryID but different prices.
...ANSWER
Answered 2021-Jan-25 at 07:24So first of all you get the income for each product and category and then based on that you find total income for that category and you do this with the help of subquery, then you join this resultant table with the category table and with the help of group by you find the product count and total income for each category, below is the sql query for more indepth understanding
QUESTION
I create this little GUI with Tkinter. But I would like to have my button 'StartDate' and the button '...' and my Combobox aligned with my Entry object. I try to find a solution with pack(), but it's not good.
Do you have any idea?
...ANSWER
Answered 2021-Jan-28 at 18:06They don't line up because you have given them all different values of sticky, pad, and ipad. One way to be sure they all get the same value is to define it in a single dictionary and have them all use that dictionary, like this:
QUESTION
I have am building a Python 3 application using tkinter on a Windows 10 machine. I finished building it out, and now need to add a progress bar for a new feature. The progress bar must change color depending on its value.
My application is already all built using the vista theme, so it is not an option to change to clam theme, as I will have to adjust the GUI for every other element.
I found a discussion here that alludes to the use of state to change the color of the bar. I have tried:
...ANSWER
Answered 2021-Jan-28 at 17:46For anyone having a similar issue, I recommend checking out the answer here about changing the color of an EntryBox.
I used a similar solution to get exactly what I wanted (again, I am using Python 3 on a Windows 10 machine):
QUESTION
How to get the current file type at filedialog in tkinter ?
I want to get the current filetype to help me add .gif or .png at the end when it's not?
for example:
ANSWER
Answered 2021-Jan-26 at 18:46from pathlib import Path
address='C:/temp/data.csv'
Path(address).suffix
>'.csv'
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