daler

"""
Requirements:

    - access to an external, publicly-accessible server. The user
    authentication will redirect here. You can tail the logs on that server to
    see the response.

    - Access Key ID (akid) from LabArchives support. This requires a ticket and
    approval from whoever is running the LabArchives instance. It is expected
    that this is passed as an env var, LA_AKID.

daler

On an m4.10xlarge:

sudo apt-get install imagemagick xorg libx11-dev libglu1-mesa-dev htop

Then fire up R as root, and run the following (note that biocLite nowadays will install from CRAN which is pretty nice!)

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from __future__ import print_function
import pybedtools

import subprocess as sp
print('pbt:', pybedtools.__version__)
pybedtools.debug_mode(True)
print(
    sp.check_output(['which', 'bedtools'], universal_newlines=True).strip(),
    '(',
    sp.check_output(['bedtools', '--version'], universal_newlines=True).strip(),

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recipe	check	info	already_in_bioconda	bat_file	exists_in_channels	fix	missing_hash	missing_home	missing_license	missing_summary	no_tests	parse_error	uses_git_url
recipes/multiqc-bcbio	missing_hash	"{'fix': 'add md5, sha1, or sha256 hash to ""source"" section', 'missing_hash': True}"				"add md5, sha1, or sha256 hash to ""source"" section"	True						
recipes/multiqc-bcbio	uses_git_url	{'fix': 'use tarballs whenever possible', 'uses_git_url': True}				use tarballs whenever possible							True
recipes/moreutils	missing_hash	"{'fix': 'add md5, sha1, or sha256 hash to ""source"" section', 'missing_hash': True}"				"add md5, sha1, or sha256 hash to ""source"" section"	True						
recipes/vt	missing_hash	"{'fix': 'add md5, sha1, or sha256 hash to ""source"" section', 'missing_hash': True}"				"add md5, sha1, or sha256 hash to ""source"" section"	True						
recipes/bcdoc	in_other_channels	{'exists_in_channels': {'conda-forge'}, 'fix': 'consider deprecating'}			{'conda-forge'}	consider deprecating							
recipes/bcdoc	

daler

"""
Run the script to see example output.

Modify the features in a, b, and c to see how they affect the output

pybedtools.contrib.plotting.BinaryHeatmap uses the "cluster" method,
but unclustered and naive merge versions are shown as well.
"""

import numpy as np

daler

Shiny app for exploring Fisher's exact tests.

See a running demo at https://daler.shinyapps.io/lcdb_fet/

Run locally with the following command in this directory:

Rscript -e "shiny::runApp()"

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#!/usr/bin/env python

# Install into new environment and activate it before running this script:
#
#   conda create -n biostars-212519 python=3 requests numpy pandas
#   source activate biostars-212519
#   python identify_encode_controls.py

import pandas
import numpy as np

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# Example for https://www.biostars.org/p/193145

import pybedtools
import pysam

# Use an example BAM file included with pybedtools
fn = pybedtools.example_filename('x.bam')
bam = pysam.Samfile(fn, 'r')

# Filter reads using pysam. Since all aspects of the SAM-format read

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Setup

Using bioconda, you can install everything you need for this example with

conda install --channel bioconda pybedtools bedtools htslib matplotlib 

Run

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git clone https://gist.github.com/cb33c735c7cf3f3cf8e8.git r-and-sql-demo
cd r-and-sql-demo
pwd

Open RStudio, set working directory to whatever pwd reported, and open the demo.R script to follow along.