bedtools | A powerful toolset

I have a very large file (~700M rows) and I would like to reduce the size by grouping mostly matching rows. Specifically, the file is sorted by fields 1 and 2 and I would like to group rows where field 2 contains consecutive numbers but all other fields match. If there is a gap in field 2 or if any other fields do not match the previous row then I would like to start a new interval. Ideally, I would like the output to return the interval range for the grouped rows and would prefer a solution that works in bash with awk and/or sed. I'm open to other solutions as well as long as they don't require re-sorting or other operations that might crash with such a long file.

The input file looks something like this.

I'm doing an internship (= yes I'm a newbie). My supervisor gave told me to create a conda environment. She passed me a log file containing many packages.

A quick qwant.com search shows me how to create envs via the

to speed up a my workflow I would like to do something similar to snakemake-unknown-output-input-files-after-splitting-by-chromosome

I would like to input a variable in the place of a file in the command below, is this possible?

I would like to generate some FASTA files using the programme bedtools getfasta. Typically I would order the input files first using the awk to bedtools sort commands below. The output is then piped into an output file. This output file would then follow the -bed flag in bedtools getfasta so I can create the FASTA files I require, e.g.

I am trying to extract fasta sequences from a genome using a bed file (homemade). The bed file looks like this (tab separated):

I'm trying to learn how to code. I have to say that I'm using the Ubuntu app on the Windows system, so I don't know if my problems are related to this system. I established these variables in the terminal

I have a data table in R which I want to count the number of overlapping windows for. This is essentially a pileup command and seems to be something that could be done using bedtools, but I can't figure out how to do so without leaving R.

Is there an R function to do this already, or any suggestions about what may be an efficient approach?

In case it's helpful, here is a mini example of what I'm trying to do. Thanks in advance!

input:

I have two bedfiles as dataframes in R, for which I want to map all overlapping regions to each other (similar to what bedtools closest would be able to do).

BedA:

I would like to combine two command lines as one single to avoid the intermediate files.