ccr | Building the constrained coding regions model

by quinlan-lab Python Version: Current License: MIT

X-Ray Key Features Code Snippets Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | ccr Summary

ccr is a Python library typically used in Healthcare, Pharma, Life Sciences applications. ccr has no bugs, it has no vulnerabilities, it has a Permissive License and it has high support. However ccr build file is not available. You can download it from GitHub.

A map of constrained coding regions (CCRs) in the human genome.

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Quality

Security

License

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Support

ccr has a highly active ecosystem.

It has 15 star(s) with 4 fork(s). There are 6 watchers for this library.

It had no major release in the last 6 months.

There are 1 open issues and 2 have been closed. There are no pull requests.

It has a positive sentiment in the developer community.

The latest version of ccr is current.

Quality

ccr has 0 bugs and 0 code smells.

Security

ccr has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

ccr code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

ccr is licensed under the MIT License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

ccr releases are not available. You will need to build from source code and install.

ccr has no build file. You will be need to create the build yourself to build the component from source.

Installation instructions are not available. Examples and code snippets are available.

It has 692 lines of code, 19 functions and 5 files.

It has low code complexity. Code complexity directly impacts maintainability of the code.

Top functions reviewed by kandi - BETA

kandi has reviewed ccr and discovered the below as its top functions. This is intended to give you an instant insight into ccr implemented functionality, and help decide if they suit your requirements.

Read per chromosome
Get a list of ranges from a variant
Returns a list of ranges that overlap a variant
Extract exons from a GTF file
Split ranges into overlapping ranges
Read the coverage of a chromosome
Gets the start and end coordinates of a cdna
Merge multiple rows into a single list
Separate ranges and varflags
Check if two intervals overlap
Calculate the CG content of a sequence
Determine if a csq is functional
Format a value as a string

Get all kandi verified functions for this library.

ccr Key Features

No Key Features are available at this moment for ccr.

ccr Examples and Code Snippets

No Code Snippets are available at this moment for ccr.

Community Discussions

Trending Discussions on ccr

Linux Grep Command - Extract multiple texts between strings

Python: how to extract the LAST substring of a string with separator into another column?

Django ModelForm non-required CharField giving errors

Python : how to extract the first substring of a string with separator into another column?

STM32 I2C Only Transmits Once

Excel VBA listing all unique values from a column, and all corresponding values to each unique value from another column

Performance benefit when using DMA for PWM

How to solve the problem in Javascript code to generate de Bruijn sequences?

Multithreaded File Preview (Lazarus + WinAPI)

NoClassDefFoundError in OSGi although it is exported and imported

QUESTION

Linux Grep Command - Extract multiple texts between strings

Asked 2022-Mar-02 at 15:37

Context;

After running the following command on my server:

zgrep "ResCode-5005" /loggers1/PCRF*/_01_03_2022 > analisis.txt

I get a text file with thousands of lines like this example:

loggers1/PCRF1_17868/PCRF12_01_03_2022_00_15_39.log:[C]|01-03-2022:00:18:20:183401|140404464875264|TRACKING: CCR processing Compleated for SubId-5281181XXXXX, REQNO-1, REQTYPE-3, SId-mscp01.herpgwXX.epc.mncXXX.mccXXX.XXXXX.org;25b8510c;621dbaab;3341100102036XX-27cf0XXX, RATTYPE-1004, ResCode-5005 |processCCR|ProcessingUnit.cpp|423

(X represents incrementing numbers)

Problem:

The output is filled with unnecessary data. The only string portions I need are the MSISDN,IMSI comma separated for each line, like this:

5281181XXXXX,3341100102036XX

Steps I tried

zgrep "ResCode-5005" /loggers1/PCRF*/_01_03_2022| grep -o -P '(?<=SubId-).*?(?=, REQ)' > analisis1.txt

This gave me the first part of the solution

5281181XXXXX

However, when I tried to get the second string located between '334110' and "-"

zgrep "ResCode-5005" /loggers1/PCRF*/_01_03_2022| grep -o -P '(?<=SubId-).?(?=, REQ)' | grep -o -P '(?<=334110).?(?=-)' > analisis1.txt

it doesn't work.

Any input will be appreciated.

...

ANSWER

Answered 2022-Mar-02 at 15:37

To get 5281181XXXXX or the second string located between '334110' and "-" you can use a pattern like:

Source https://stackoverflow.com/questions/71324895

QUESTION

Python: how to extract the LAST substring of a string with separator into another column?

Asked 2022-Feb-25 at 14:04

I have a dataframe with a column "CCR" whose values are as such : "Aaaa;Bbbb;Cccc", or "Bbbb;;Cccc", or "Cccc;Bbbb;Aaaa" or just "Bbbb". I would like to extract the last substring part (after the ";") and put it into another column "LastCCR". If there is only one value and therefore no ';' then the value stays the same in the LastCCR column.

I would like to use a lambda function: I used the code line below to extract the FIRST value but I don't know how to alter it so as to extract the LAST value of my string. Can anyone help ?

...

ANSWER

Answered 2022-Feb-25 at 14:00

df[1stCCR] = df['CCR'].apply(lambda x: x.split(";")[-1])

Source https://stackoverflow.com/questions/71266924

QUESTION

Django ModelForm non-required CharField giving errors

Asked 2022-Jan-31 at 09:37

I have a ModelForm for a model that has a couple of files and with every file, a type description (what kind of file it is). This description field on the model has CHOICES. I have set these file uploads and description uploads as hidden fields on my form, and not required. Now the file upload is working, but the description is giving field errors, the placeholder in the dropdown is not a valid choice, it says. That's true, but since it is not required, I would like it to just be left out of the validation and I am stuck on how.

My codes, shortened them up a bit to keep it concise.

models.py

...

ANSWER

Answered 2022-Jan-31 at 09:37

Your form is submitting desc_1, so there's a an input with name="desc_1" that has a populated value of Type bestand somewhere in your template. blank=True means the value can be left empty. Since your field has choices and blank=True, the submitted value can be either empty or one of the FILE_TYPE_CHOICES.

You're saying that Type bestand is the placeholder for this field, but if you rendered this field as a hidden input ({{ form.desc_1 }} since you have a widget overridden) it would not and should not have a placeholder.

A regular form equivalent would be:

Source https://stackoverflow.com/questions/70920028

QUESTION

Python : how to extract the first substring of a string with separator into another column?

Asked 2022-Jan-07 at 15:25

I have a dataframe with a column "CCR" whose values are as such : "Aaaa;Bbbb;Cccc", or "Bbbb;;Cccc", or "Cccc;Bbbb;Aaaa". I would like to take only the first part (before the ";") and put this into another column "1st CCR". I can't seem to make it work using the split function. With this code I tried, nothing happens. Can you help ?

...

ANSWER

Answered 2022-Jan-07 at 15:25

You can do the following using a lambda function:

Source https://stackoverflow.com/questions/70623175

QUESTION

STM32 I2C Only Transmits Once

Asked 2021-Nov-17 at 18:36

I'm using stm32f3 Datasheet as reference for register level programming instead of HAL. I'm pretty sure I set up everything correctly since I am actually able to transmit bytes of data through I2C peripheral however it fails to send a byte when I change the slave address to a different device (from accelerometer to magnetometer) I get a NACK and Stop condition. Why would that be?

Here is my clock setup:

...

ANSWER

Answered 2021-Nov-17 at 18:36

Not sure why this works but before I switch to another slave on I2C bus, I need to reset the number of bytes I intend to send to value of 0. I use this line in between the 2 slave device transfers to do this:

I2C1->CR2 = 0x00<

I couldn't find anywhere in the datasheet that says I have to reset NBYTES before switching slave devices or any other reason to reset NBYTES but this seems to work for me.

Source https://stackoverflow.com/questions/69995992

QUESTION

Excel VBA listing all unique values from a column, and all corresponding values to each unique value from another column

Asked 2021-Aug-14 at 16:26

I am a novice with VBA/Macros and do not know the technical terms or the best ways to perform many functions. However, I was able to create a Macro that partially does what I need it to, but I can't seem to figure out the rest.

The Situation: I have vulnerability scan results that I'm attempting to parse a certain way so that I can get relevant information out properly so that I can provide it in a clean and concise way to my teams. Currently I get the vuln results into an excel file which has all of the information per vuln, per host (so 1 vuln showing on 6 hosts, produces 6 rows). My current Macro is able to distill the information down so that I can view it as 1 row per vuln (indicated by a unique PluginID), with all of the hosts concatenated into 1 cell delimited by a line break. The current macro accomplishes this well, however there is another column within the vuln results that is very important - "Vulnerability Proof". On some vulns, the "Vulnerability Proof" is the same for all hosts with the vuln, and on some its different. I need to be able to list all unique "vulnerability proofs" with all of the hosts that the proof is related to, so that I get a concise list of "these hosts have this proof, these hosts have this proof etc."

Here some sample source data:

PluginID Description Host Vuln Proof Plugin123 CVE-Plugin123 Host1 Version 1.2.3 detected Plugin123 CVE-Plugin123 Host2 Version 1.2.3 detected Plugin123 CVE-Plugin123 Host3 Version 4.5.6 detected Plugin456 Plugin456-2021 Vuln Host1 Version 7.8.9 detected Plugin456 Plugin456-2021 Vuln Host2 Version 10.11.12 detected Plugin456 Plugin456-2021 Vuln Host3 Version 10.11.12 detected

Currently when I run my macro (below), I get the following output:

PluginID Description Host Vuln Proof Plugin123 CVE-Plugin123 Host1, Host2, Host3 Version 1.2.3 detected, Version 1.2.3 detected, Version 4.5.6 detected Plugin456 Plugin456-2021 Vuln Host1, Host2, Host3 Version 7.8.9 detected, Version 10.11.12 detected, Version 10.11.12 detected

This, while achieving the goal of reviewing by 1 row per vuln, doesn't give a very good way to review the vulnerability proof if/when that proof is long, and/or there are many, many hosts reporting the vuln.

How I'd like to receive the output:

PluginID Description Host Vuln Proof Plugin123 CVE-Plugin123 Host1, Host2, Host3 Host1, Host 2: Version 1.2.3 detected
Host 3: Version 4.5.6 detected Plugin456 Plugin456-2021 Vuln Host1, Host2, Host3 Host 1: Version 7.8.9 detected
Host 2, Host3: Version 10.11.12 detected

My current Macro looks like this:

...

ANSWER

Answered 2021-Aug-13 at 22:07

Here's how I'd tackle it - sorry did not have time to try to understand/adapt your code...

Source https://stackoverflow.com/questions/68778018

QUESTION

Performance benefit when using DMA for PWM

Asked 2021-Jun-23 at 06:20

I have a segment of code below as a FreeRTOS task running on an STM32F411RE microcontroller:

...

ANSWER

Answered 2021-Jun-22 at 06:33

First, remember that premature optimization is the cause of uncountably many problems. The question you need to ask is "what ELSE does the processor need to do?". If the processor has nothing better to do, then just poll and save yourself some programming effort.

If the processor does have something better to do (or you are running from batteries and want to save power) then you need to time how long the processor spends waiting between each thing that it needs to do.

In your case, you are using an operating system context switch in place of "waiting". You can time the cost of the switch-write-to-pwm-switch-back cycle by measuring the performance of some other thread.

Set up a system with two threads. Perform some task that you know the performance of in one thread, eg, some fixed computation or processor benchmark. Now set up the other thread to do your timer business above. Measure the performance of the first thread.

Next set up a similar system with only the first thread plus DMA doing the PWM. Measure the performance change, you have you answer.

Obviously this all depends very much on your exact system. There is no general answer that can be given. The closer your test is to your real system the more accurate the answer you will get.

PS: Your PWM will glitch using the above code. Replace the two writes with a single one:

Source https://stackoverflow.com/questions/68075980

QUESTION

How to solve the problem in Javascript code to generate de Bruijn sequences?

Asked 2021-Jun-01 at 17:45

I am trying to convert some C code to JavaScript. I chose one of the simplest rules (PCR4) and removed all irrelevant parts. The goal is to generate a particular de Bruijn sequence for a particular value of n. For example, if n = 6, the output should be

...

ANSWER

Answered 2021-Jun-01 at 17:45

The main issue is that in DB you return a. If you look at the condition of the loop just above that return, you'll see that this loop exits when a consists only of zeroes. So it is no wonder you only get zeroes in the output.

In the C-code you referred to, DB does not return anything. It prints. So if you want to make this a function that returns the result, you should collect the output in a variable at the same spot as where the C-code prints. This could be a JavaScript string, and then the function should return that string:

Source https://stackoverflow.com/questions/67782465

QUESTION

Multithreaded File Preview (Lazarus + WinAPI)

Asked 2021-Apr-16 at 00:20

Hello all,

i am having problems getting the file preview (the one shown on the right side in the Windows Explorer window) for a certain file.
So far fetching the file preview works fine, but it takes a long time (between 0.5 and 2 seconds). Thus i do not want it to be executed in the main thread (as this would interrupt the program gui).

I tried to execute the file preview extraction in a worker thread, but this yields a SIGSEGV.

The call stack is also not really useful, it only shows that the exception is raised in ShellObjHelper in Line 141 (see source code below).

Source Code for main unit:

...

ANSWER

Answered 2021-Apr-13 at 07:07

Thanks to the comment from @IInspectable, that's the hint i needed.

Solution:
Add CoInitialize before calling GetExtractImageItfPtr and add CoUninitialize after receiving the file preview, but still within the worker thread.
Ensure that CoUninitialize is called even if exceptions occur by using try and finally`.

Working source code for main unit with worker thread:

Source https://stackoverflow.com/questions/67056289

QUESTION

NoClassDefFoundError in OSGi although it is exported and imported

Asked 2021-Mar-23 at 21:20

I tried to create a basic virtual reality IDE based on Karaf.

I have 3 maven-projects:

VRServer who connect to a native-component for rendering.
VR Component Toolkit for VR-HMI-Widgets (Having a VRFrame who extends from VRComponent) as a Multi-Module-Maven-Project.
The VR IDE project read/write files and execute lowlevel commands.

I installed all of them into Karaf:

...

ANSWER

Answered 2021-Jan-07 at 13:13

The main problem in the project is true in maven-bundle-plugin. You need to have it in your pom.xml. example code

Source https://stackoverflow.com/questions/65504619

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install ccr

You can download it from GitHub.
You can use ccr 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.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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