semvec/pypi-packages huggingface dataset:
rcluster 0.2.27
R clusters on AWS
License: MIT
Keywords: r aws cluster cloud

rcluster makes launching and accessing an R cluster on AWS simple and
accessible.

This repository will:

-  Create a connection to your AWS account
-  Create and save an AMI with the software and configuration needed
-  Allow you to launch a manager and a stated number of worker nodes,
   automating the network connections between them and hosting a common
   NFS-based home folder under the default ``cluster`` user:

   -  "/home/cluster" is shared between manager and all workers
   -  "/home/cluster/hostfile" contains the IPs of accessible worker
      nodes and spare manager nodes, repeated based on the number of
      available worker cores
   -  ``cluster`` user's ".Rprofile" defines the R function
      ``defaultCluster()`` that automatically reference the hostfile to
      create a PSOCK-based cluster

After that, login to RStudio Server as normal on the manager, run
``defaultCluster()``, and use the returned parallel cluster object with
``parLapply()`` and its peers.

Getting Started
===============

First, you must create and save locally your AWS access key ID and
secret access key
(`instructions <http://docs.aws.amazon.com/AWSSimpleQueueService/latest/SQSGettingStartedGuide/AWSCredentials.html>`__).

Next, run ``rcluster-config`` from your command line. Note that this
function will, by default, write your AWS access key and secret access
key to a hidden folder in your user directory with no additional
security.

There are currently three functions to launch and manage an R cluster:

-  ``rcluster`` - Launch an R cluster on AWS using the default
   configuration file. This function will open your default browser to
   the RStudio Server login page on the manager instance once it is
   live.
-  ``rcluster-open`` - Access an active R cluster (opens a new tab in
   your web browser to the RStudio Server instance, if available).
-  ``rcluster-terminate`` - Terminate all instances associated with your
   ``rcluster`` configuration.
pyseqfile 0.2
Pyseqfile is a python wrapper on top of [seq_file](https://github.com/noporpoise/seq_file) which allow for reading multiple sequence file formats.
License: MIT

# pyseqfile

Pyseqfile is a python wrapper on top of [seq_file](https://github.com/noporpoise/seq_file) which allow for reading multiple sequence file formats. 

Currently supports:

FASTA & FASTQ

TO DO:

* SAM & BAM (make seq_file with htslib)
* gzipped FASTA
* gzipped FASTQ

# Install
	
	pip install pyseqfile

# Usage

	from pyseqfile import Reader

	reader = Reader('path/to/seqfile{.fq,.fq,.fa,bam,.sam}')
	for r in reader:
	    print(r)

# Benchmarks

pyseqfile is *much* faster than Biopython. 

$ python benchmark.py

	Reading 10k lines 100 times: Biopython : 6.6768401420122245s
	Reading 10k lines 100 times: seqfile : 0.1060560290061403s