cooler | A cool place to store your Hi-C | Genomics library

 by   open2c Python Version: 0.10.2 License: BSD-3-Clause

kandi X-RAY | cooler Summary

kandi X-RAY | cooler Summary

cooler is a Python library typically used in Artificial Intelligence, Genomics applications. cooler has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can install using 'pip install cooler' or download it from GitHub, PyPI.

A cool place to store your Hi-C
Support
    Quality
      Security
        License
          Reuse

            kandi-support Support

              cooler has a low active ecosystem.
              It has 159 star(s) with 48 fork(s). There are 13 watchers for this library.
              There were 2 major release(s) in the last 6 months.
              There are 65 open issues and 189 have been closed. On average issues are closed in 73 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of cooler is 0.10.2

            kandi-Quality Quality

              cooler has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              cooler is licensed under the BSD-3-Clause License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              cooler releases are available to install and integrate.
              Deployable package is available in PyPI.
              Build file is available. You can build the component from source.
              Installation instructions, examples and code snippets are available.

            Top functions reviewed by kandi - BETA

            kandi has reviewed cooler and discovered the below as its top functions. This is intended to give you an instant insight into cooler implemented functionality, and help decide if they suit your requirements.
            • Load a histogram
            • Append data to a cooler
            • Put data into a group
            • Set h5 options
            • Calculate a balanced balance factor
            • Load a dataset
            • Open the file
            • Open an hdf5 file
            • Balance a fan
            • Dump a table to a file
            • Return a ~astropy matrix
            • Load data from disk
            • Delete a grp
            • Generate bin counts for each chromosome
            • Coarsen a generator
            • Aggregates pairwise binix files
            • Create a tabixAgg aggregator
            • Read a table from a group
            • Wrapper for the cooler show
            • Main application
            • Aggregate the chromosome
            • Sort chromosomes
            • Create a scool object
            • Perform zoom level
            • Compute pairwise pairs
            • Sanitize chromosome records
            Get all kandi verified functions for this library.

            cooler Key Features

            No Key Features are available at this moment for cooler.

            cooler Examples and Code Snippets

            No Code Snippets are available at this moment for cooler.

            Community Discussions

            QUESTION

            Get for each word the number of the sentences in which appears in a given text
            Asked 2021-Jun-14 at 22:51

            I'm using Spacy and I am looking for a program that counts the frequencies of each word in a text, and output each word with its count and sentence numbers where it appears. Sample input

            ...

            ANSWER

            Answered 2021-Jun-14 at 22:51

            I would split the sentence into words and create a dictionary with each key being a word in the text, like so:

            Source https://stackoverflow.com/questions/67977876

            QUESTION

            How can I set process.env from main process inside of an NPM package?
            Asked 2021-May-10 at 20:06

            I am writing an NPM package that sets environment variables using process.env. Here is the code from the NPM package:

            ...

            ANSWER

            Answered 2021-May-10 at 20:06

            Looks like your function is async and your module exports the function so I would advice you to import the file once in the file when your start your app, and call it and wait for its execution and only then start the rest of your app, otherwise there is no warranty because the code is async.

            Source https://stackoverflow.com/questions/67475682

            QUESTION

            Fade in/out to segment on page
            Asked 2021-May-06 at 04:10

            Currently I have a website where the content is all on a single page.

            The Menu items, when you click them, jump to the relevant part of the page.

            But the jump effect is still jarring and doesn't give a sleek feeling. I think fading in and out would be a cooler effect.

            Is it possible to make the Jump action simulate a FadeIn/FadeOut effect?

            I just have simple Jump HTML code like this:

            ...

            ANSWER

            Answered 2021-May-06 at 03:57

            Switch the href with a data attribute, in our case, data-href.

            Using JavaScript, detect when the user clicks the link. When detected, fade out the document and set a timeout to fade back in in 500 milliseconds. After fading in, select the element defined in the data-href attribute and use .scrollIntoView()

            Source https://stackoverflow.com/questions/67411405

            QUESTION

            How to convert an image in pygame to a numpy array or to a number?
            Asked 2021-Apr-24 at 06:58

            I was wondering how I can convert an image in pygame into a number. I'm making a chess game in python. I have everything made. I first made the chessboard out of string:

            ...

            ANSWER

            Answered 2021-Apr-24 at 06:58

            An easy way is to use numpy.unique with the return_inverse option:

            Find the unique elements of an array.

            return_inverse bool, optional: If True, also return the indices of the unique array

            Example:

            Source https://stackoverflow.com/questions/67238820

            QUESTION

            How to programmatically create a class library DLL using reflection?
            Asked 2021-Apr-01 at 01:05

            Suppose my code possesses the knowledge about the metadata of a nonexistent class library "mytest.dll", such as the types in this library, the functions of the types, the parameters and return types of the functions, etc.

            How does my code manufacture this DLL using techniques such as reflection?

            I know my code can generate the "mytest.cs" text file, then execute the compiler to produce the DLL, then delete the "mytest.cs" file. Just want to know if there are "more advanced" or "cooler" ways to do it.

            Thanks.

            ...

            ANSWER

            Answered 2021-Mar-21 at 22:35

            There are 4 main steps in the process to compile and execute dynamic .net scripts from your application, even really complex scenarios can be simplified in this way:

            1. Generate the code
            2. Compile the script
            3. Load the assembly
            4. Execute the code

            Lets generate a simple Hello Generated C# World App right now!:

            Create a method that will generate an assembly that has 1 class called HelloWorldApp, this class has 1 method called GenerateMessage it will have X input parameters that will be integers, it will return a CSV string of the arguments that were passed in to it.

            This solution requires the following package to be installed:

            Source https://stackoverflow.com/questions/66672329

            QUESTION

            Is there a way to trap the output of Linux "selection" commands that do not meet their match criteria?
            Asked 2021-Mar-28 at 02:19

            By "selection" commands, I mean commands that do filtering such as grep, find, etc.

            Background

            There are at least a few different IBM mainframe environments that support pipeline processing (CMS Pipelines, for example). It's not a shell construct like it is in Bash, but usually a dedicated PIPE command that has its own built-in subcommands (stages) that perform the filtering and data processing.

            One of the cooler features, in my opinion, is that "selection stages" that perform some kind of filtering usually support multiple output streams. Those data lines that meet the selection criteria are passed to the primary output stream, and if specified, those that do not are passed to a secondary output stream, where they can undergo an entirely different processing sequence.

            Taking the example from the Wikipedia page linked above, which might appear in a REXX program:

            ...

            ANSWER

            Answered 2021-Mar-28 at 02:15

            You can easily do both transformations in a single command with GNU sed's negative match operator:

            Source https://stackoverflow.com/questions/66837705

            QUESTION

            Jest tests keep failing for React component that renders various HTML elements based on type by using switch statement
            Asked 2021-Mar-04 at 23:58

            I have a React Component that takes an array and iterates over each node, styling and rendering HTML elements based on the types found within the array.

            I have everything running properly and now I'm trying to write a test using Jest to check that:

            1. The component doesn't render anything when it receives an empty array
            2. The component renders the appropriate HTML elements based on type when it receives a populated array

            I'm relatively new to Jest and testing and I'm not sure how to write the tests to check that the appropriate elements have rendered. Also my null check test keeps failing with the following error message:

            ...

            ANSWER

            Answered 2021-Mar-04 at 23:58

            When you return null from component, React.createElement still creates an element. And there is no way to actually tell if it will render nothing without inspecting resulted markup.

            For example this code will give you proper react element in console, not null:

            Source https://stackoverflow.com/questions/66483793

            QUESTION

            Swift: How do you use a variable in an array?
            Asked 2021-Feb-24 at 08:28

            I am using a pod called iOSDropDown to display a dropdown selection menu for a textfield. I am getting a list of data from php to populate that selection menu that Im storing in a variable.

            The PHP data passed stored in a swift variable looks like this when printed -> "option01","option02","option03"... and so on. This is dynamic data that will change that is why I am retrieving from PHP/MYSQL Database instead of just manually typing in the options in the Swift array.

            Below is my code. What I am trying to do is use the "dropdownData" variable that holds the options for the array. Each option should be in its own row and separately selectable. What I am getting is one option, one string of coding with all my options as shown in the picture below.How would I use the dropdownData variable to display options instead of one string, one option?

            dropdownData = "option01","option02","option03"... etc. ALL OPTIONS STORED IN THIS ONE ARRAY

            ...

            ANSWER

            Answered 2021-Feb-24 at 08:28

            Seems like dumpsArray[indexPath.row] as AnyObject).value(forKey: "dropdownData") returns a String where names are comma separated,

            so

            Source https://stackoverflow.com/questions/66347055

            QUESTION

            Looping error in C++ when trying to write to a file
            Asked 2021-Jan-01 at 16:25

            I'm making an extremely crude command based text editor in C++. It works just fine in outputting a .txt's contents. But when writing it gets more complicated. It encounters no problems when writing a single word to a .txt but has this problem when writing input with one or more spaces. Firstly my code looks like this.

            ...

            ANSWER

            Answered 2021-Jan-01 at 16:25

            Two things,

            1. you should change your variable name from filename to something else cause it is hard to interpret what you mean with that.
            2. The issue you are having is that cin ignores spaces. a better approach would be to use std::getline(std::cin, filewrite); This will read till a null terminated \0 or a new line \n. To get this to read multiple lines put it in a while loop. Another thing to watch out for with this is any extraneous new line characters. To avoid this add a dummy variable string and getline for that string to ensure it is going to read properly.

            NOTE: With std::cin, before the read in another option is to put std::cin >> std::noskipws >> varname, but this can sometimes have undefined behaviour

            Source https://stackoverflow.com/questions/65528475

            QUESTION

            Map angles to a 0-1 range
            Asked 2020-Dec-25 at 04:16

            Let's say you have two angles, and you label them 0 and 1. Then you have another angle x. You also know if you'll be going Clockwise or Counter Clockwise to get from angle 0 to angle 1. How do you calculate a number that can describe that third angle?

            Examples:

            Angle at 0 Angle at 1 Rotation Direction Target Angle Mapped number (x) 0° 90° CCW 60° 2/3 90° 0° CW 60° 1/3 0° 180° CW 90° 1.5 0° 180° CCW 90° 0.5

            Problems I'm having:

            • When x can't be supported within 0 and 1 (I am fine with it just telling me it couldn't do it, but having the number would be cooler).
            • When switching from Counter-Clock-Wise (CCW) to CW.
            ...

            ANSWER

            Answered 2020-Dec-25 at 04:16

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

            Vulnerabilities

            No vulnerabilities reported

            Install cooler

            Install from PyPI using pip. If you are using conda, you can alternatively install cooler from the bioconda channel. See the docs for more information.
            Python 2.7/3.4+
            libhdf5 and Python packages numpy, scipy, pandas, h5py. We highly recommend using the conda package manager to install scientific packages like these. To get it, you can either install the full Anaconda Python distribution or just the standalone conda package manager.

            Support

            Interested in contributing to cooler? That's great! To get started, check out the contributing guide.
            Find more information at:

            Find, review, and download reusable Libraries, Code Snippets, Cloud APIs from over 650 million Knowledge Items

            Find more libraries
            Install
          • PyPI

            pip install cooler

          • CLONE
          • HTTPS

            https://github.com/open2c/cooler.git

          • CLI

            gh repo clone open2c/cooler

          • sshUrl

            git@github.com:open2c/cooler.git

          • Stay Updated

            Subscribe to our newsletter for trending solutions and developer bootcamps

            Agree to Sign up and Terms & Conditions

            Share this Page

            share link