kandi X-RAY | pyranges Summary
kandi X-RAY | pyranges Summary
GenomicRanges and genomic Rle-objects for Python. "Finally ... This was what Python badly needed for years." - Heng Li.
Top functions reviewed by kandi - BETA
- 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
pyranges Key Features
pyranges Examples and Code Snippets
Trending Discussions on pyranges
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.
ANSWERAnswered 2020-Jun-24 at 19:25
gr = pr.PyRanges(df) gr['chr1', 125:126]
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:...
ANSWERAnswered 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:
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.
ANSWERAnswered 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
keys in this
dict are used when you do the
You need to also update the dict
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:...
ANSWERAnswered 2020-May-22 at 23:54
This should do the trick:
Pyranges class from similarly named package has two methods with slightly different functionality:
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
overlap intended to reveal full intervals that do overlap at least at one position?
ANSWERAnswered 2020-May-11 at 15:06
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:...
ANSWERAnswered 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.
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