alienzj

# After Ubuntu 16.04, Systemd becomes the default. 
# It is simpler than https://gist.github.com/Doowon/38910829898a6624ce4ed554f082c4dd

[Unit]
Description=Jupyter Notebook

[Service]
Type=simple
PIDFile=/run/jupyter.pid
ExecStart=/home/phil/Enthought/Canopy_64bit/User/bin/jupyter-notebook --config=/home/phil/.jupyter/jupyter_notebook_config.py

alienzj

R Cheat Sheet : Applying functions

• R Cheat Sheet : Applying functions
  • apply(x,index,function)
  • lapply(x,function)
  • sapply(x,function)
  • tapply(x,y,function)
  • mapply(function,x,y,...)
  • References

alienzj

Python version of the MATLAB code in this Stack Overflow post: http://stackoverflow.com/a/18648210/97160

The example shows how to determine the best-fit plane/surface (1st or higher order polynomial) over a set of three-dimensional points.

Implemented in Python + NumPy + SciPy + matplotlib.

alienzj

#
# This script calculates the depth of coverage and breadth of coverage for a given bam. 
# Outputs a dictionary containing the contig/chromosome names and the depth and breadth of coverage for each
# and for the entire genome.
#
# If you optionally specify the name of the mitochondrial chromosome (e.g. mtDNA, chrM, chrMT)
# The script will also generate breadth and depth of coverage for the nuclear genome AND the ratio
# of mtDNA:nuclearDNA; which can act as a proxy in some cases for mitochondrial count within an individual.
# 
# Author: Daniel E. Cook

alienzj

def splitDataFrameList(df,target_column,separator):
    ''' df = dataframe to split,
    target_column = the column containing the values to split
    separator = the symbol used to perform the split

    returns: a dataframe with each entry for the target column separated, with each element moved into a new row. 
    The values in the other columns are duplicated across the newly divided rows.
    '''
    def splitListToRows(row,row_accumulator,target_column,separator):
        split_row = row[target_column].split(separator)

alienzj

pigz -d -c in.fastq.gz |
    | awk 'BEGIN {LN=0; } { if (LN == 1 || LN == 3) { print substr($0, 0, 26) } else { print $0 } ; if (LN == 3) { LN = 0 } else { LN++ } }' \
    | pigz -c - > out.fastq.gz

alienzj

# This function sorts the matrix for better visualization of mutual exclusivity across genes
memoSort <- function(M) {
	geneOrder <- sort(rowSums(M), decreasing=TRUE, index.return=TRUE)$ix;
	scoreCol <- function(x) {
		score <- 0;
		for(i in 1:length(x)) {
			if(x[i]) {
				score <- score + 2^(length(x)-i);
			}
		}

alienzj

#!/usr/bin/env python3

import json
import sys


def merge(inputs):
    """ Merges the data in the given input handles and returns the result """
    assert len(inputs) > 1
    record_ids = set()

alienzj

Source: https://confluence.rcs.griffith.edu.au/display/v20zCluster/Sun+Grid+Engine+SGE+state+letter+symbol+codes+meanings

Category	State	SGE Letter Code
Pending	pending	qw
Pending	pending, user hold	qw
Pending	pending, system hold	hqw
Pending	pending, user and system hold	hqw
Pending	pending, user hold, re-queue	hRwq
Pending	pending, system hold, re-queue	hRwq

alienzj

#!/usr/bin/env python3
"""
Running this script is (intended to be) equivalent to running the following Snakefile:

include: "pipeline.conf"  # Should be an empty file

shell.prefix("set -euo pipefail;")

rule all:
    input: