pyranges | Performant Pythonic GenomicRanges | Genomics library

by biocore-ntnu Python Version: 0.0.111 License: MIT

X-Ray Key Features Code Snippets Community Discussions(6)Vulnerabilities Install Support

kandi X-RAY | pyranges Summary

pyranges is a Python library typically used in Artificial Intelligence, Genomics applications. pyranges has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has high support. You can download it from GitHub.

GenomicRanges and genomic Rle-objects for Python. "Finally ... This was what Python badly needed for years." - Heng Li.

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Support

pyranges has a highly active ecosystem.

It has 340 star(s) with 37 fork(s). There are 11 watchers for this library.

It had no major release in the last 12 months.

There are 78 open issues and 100 have been closed. On average issues are closed in 61 days. There are 4 open pull requests and 0 closed requests.

It has a positive sentiment in the developer community.

The latest version of pyranges is 0.0.111

Quality

pyranges has 0 bugs and 0 code smells.

Security

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

pyranges code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

pyranges 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

pyranges releases are available to install and integrate.

Build file is available. You can build the component from source.

Installation instructions, examples and code snippets are available.

pyranges saves you 2389 person hours of effort in developing the same functionality from scratch.

It has 5209 lines of code, 334 functions and 69 files.

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

Top functions reviewed by kandi - BETA

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

Calculate k nearest neighbors
Concatenate multiple pyranges
Return a copy of the DataFrame
Process results dictionary
Split the range
Write a bigwig to a bigwig file
Return the lengths of the DataFrames in the DataFrame
Merge the ranges
Count the number of overlapping gaps
Apply a function to this range
Return a pandas DataFrame containing only the intersections
Remove duplicate positions
Apply the bounds to the given chromosome
Tiles a genome
Return a spliced subseq
Find the closest cluster in a scipy
Apply chunks from f to f
Compute tss of the protein sequence
Generate a dataframe of random chromosomes
Return a subset of this range
Calculate the nearest range to other
Return a subset of the ranges
Split this range into a PyRanges
Calculate similarity for each chromosome
Return an iterator of grs
Write this chromosome to a bigwig file
Returns a string representation of the Ranges

Get all kandi verified functions for this library.

pyranges Key Features

No Key Features are available at this moment for pyranges.

pyranges Examples and Code Snippets

No Code Snippets are available at this moment for pyranges.

Community Discussions

Trending Discussions on pyranges

Using pyranges library, How to check if a chromosome position is contained in any interval?

Fishers Exact Test from Pandas Dataframe

How to convert chromosome name to same format in pyranges before performing a join

Grouping the range of intervals based on 2 columns

Difference between overlap and intersect methods in Pyranges

Finding overlaps between millions of ranges/intervals

QUESTION

Using pyranges library, How to check if a chromosome position is contained in any interval?

Asked 2020-Oct-01 at 16:37

I have a .vcf file containing variants information and a .bed file containing region studied information. I am using pyranges library to read the .bed file. I want to filter out all the variants in .vcf file that lies in the region studied intervals specified in .bed file. Since, pyranges provides a pandas dataframe, i could iterate over each row and check for containment of my variant position; But, I am looking for an API that helps me achieve this.

Example:

...

ANSWER

Answered 2020-Jun-24 at 19:25

gr = pr.PyRanges(df)
gr['chr1', 125:126]

Source https://stackoverflow.com/questions/62561215

QUESTION

Fishers Exact Test from Pandas Dataframe

Asked 2020-Sep-30 at 21:06

I'm trying to work out the best way to create a p-value using Fisher's Exact test from four columns in a dataframe. I have already extracted the four parts of a contingency table, with 'a' being top-left, 'b' being top-right, 'c' being bottom-left and 'd' being bottom-right. I have started including additional calculated columns via simple pandas calculations, but these aren't necessary if there's an easier way to just use the 4 initial columns. I have over 1 million rows when including an additional set (x.type = high), so want to use an efficient method. So far this is my code:

...

ANSWER

Answered 2020-Sep-30 at 21:05

Following the answer here which came from the author of pyranges (i think), let's say you data is something like:

Source https://stackoverflow.com/questions/64134929

QUESTION

How to convert chromosome name to same format in pyranges before performing a join

Asked 2020-Aug-01 at 06:17

I have multiple .bed files and I want to perform join, intersection etc. operation on them. I am using pyranges library to read the .bed files and perform these operations. As .bed files allows naming chromosome with or without "chr" prefix, I would like to format all chromosome name in different .bed files to the same format before performing the operations. Therefore, operations results in outputs as expected.

I tried,

...

ANSWER

Answered 2020-Aug-01 at 06:17

The data in PyRanges class are stored in multiple places. Apart from .Chromosome, you have .dfs which is a dict. This keys in this dict are used when you do the py1["1"] call.

You need to also update the dict

Source https://stackoverflow.com/questions/62972436

QUESTION

Grouping the range of intervals based on 2 columns

Asked 2020-May-23 at 00:09

I am a geologist needing to clean up data. I have a .csv file containing drilling intervals, that I imported as a pandas dataframe that looks like this:

...

ANSWER

Answered 2020-May-22 at 23:54

This should do the trick:

Source https://stackoverflow.com/questions/61964744

QUESTION

Difference between overlap and intersect methods in Pyranges

Asked 2020-May-12 at 07:17

Pyranges class from similarly named package has two methods with slightly different functionality: intersect and overlap. Intersect method description is quite similar to overlap's one: Return overlapping subintervals. vs Return overlapping intervals. I can't quite glimpse the difference between those two (Yeah, I noticed that sub prefix).

Is overlap intended to reveal full intervals that do overlap at least at one position?

...

ANSWER

Answered 2020-May-11 at 15:06

Setup:

Source https://stackoverflow.com/questions/61186491

QUESTION

Finding overlaps between millions of ranges/intervals

Asked 2019-Aug-19 at 08:37

I am trying to find pairs of intervals that overlap by at least some minimum overlap length that is set by the user. The intervals are from this pandas dataframe:

...

ANSWER

Answered 2019-Jul-15 at 03:55

Here's an algorithm.

Prepare a set of intervals sorted by starting point. Initially the set is empty.
Sort all starting and ending points.
Traverse the points. If a starting point is encountered, add the corresponding interval to the set. If an ending point is encountered, remove the corresponding interval from the set.
When removing an interval, look at other intervals in the set. They all overlap the interval being removed, and they are sorted by the length of the overlap, longest first. Traverse the set until the length is too short, and report each overlap.

Source https://stackoverflow.com/questions/57032580

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

Vulnerabilities

No vulnerabilities reported

Install pyranges

The preferred way to install pyranges is through the bioconda channel:.

Support

most importantly, cite pyranges if you use it. It is the main metric funding sources care about.use pyranges in Stack Overflow/biostars questions and answersstar the repo (possibly important for github visibility and as a proxy for project popularity)if you are a business using pyranges, please give to one of the charities listed at https://www.givewell.org/

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