alienzj

Hi:

perl -e 'print "hello world!\n"'

A simple filter:

perl -ne 'print if /REGEX/'

Filter out blank lines (in place):

A Brief Tour of the Makepkg Process: What Makes a Pacman Package

This is a terse document covering the anatomy of a package built for the pacman package manager.

The following example commands can mostly run verbatim to manually create a

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.

	#!/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:

	#!/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()

	# 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);
	}
	}

	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)

	#
	# 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

	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