peterdfields peterdfields

## one liner to split a multifasta into separate single fasta
cat hg18.fa | awk '{
        if (substr($0, 1, 1)==">") {filename=(substr($0,2) ".fa")}
        print $0 > filename
}'

## gist:895282

      
              1 file
            
          
              14 forks
            
          
                5 comments
              
            
              44 stars
            
          
                brantfaircloth
                / gist:895282
            
            
              Created
              March 30, 2011 20:55
            
              
                Substitution models in mrbayes
              
          
    ##GTR
lset applyto=() nst=6                           # GTR
lset applyto=() nst=6 rates=propinv             # GTR + I
lset applyto=() nst=6 rates=gamma               # GTR + gamma
lset applyto=() nst=6 rates=invgamma            # GTR + I + gamma
##SYM
lset applyto=() nst=6                           # SYM

prset applyto=() statefreqpr=fixed(equal)

  
## galaxy-init-example
#!/bin/bash

#--- config

SERVICE_NAME=galaxy
RUN_AS=galaxy
RUN_IN=/your/galaxy/directory

#--- main actions

## deinterleave_fastq.sh
#!/bin/bash
# Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress]
#
# Deinterleaves a FASTQ file of paired reads into two FASTQ
# files specified on the command line. Optionally GZip compresses the output
# FASTQ files using pigz if the 3rd command line argument is the word "compress"
#
# Can deinterleave 100 million paired reads (200 million total
# reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s)
#

## unique-bash-history.sh
HISTCONTROL="erasedups"
export HISTCONTROL

## curriculum.md

      
              1 file
            
          
              6 forks
            
          
                11 comments
              
            
              33 stars
            
          
                hadley
                / curriculum.md
            
            
              Created
              September 27, 2013 20:24
            
              
                My first stab at a basic R programming curriculum. I think teaching just these topics without overall motivating examples would be extremely boring, but if you're a self-taught R user, this might be useful to help spot your gaps.
              
          
    Notes:


I've tried to break up in to separate pieces, but it's not always possible: e.g. knowledge of data structures and subsetting are tidy intertwined.


Level of Bloom's taxonomy listed in square brackets, e.g. http://bit.ly/15gqPEx. Few categories currently assess components higher in the taxonomy.


Programming R curriculum

Data structures


## estimate-insert-sizes
#!/usr/bin/env python
doc = """
Quickly estimates insert sizes of read datasets, given some sequence(s) they can be mapped to.
Author: Rayan Chikhi

short usage: <reference> <*.fastq>

example:
         estimate-insert-sizes contigs.fa readsA_1.fq readsA_2.fq readsB_1.fq readsB_2.fq

## install_pyenv.sh
#!/bin/zsh
# pyenv install for CentOS 6.5 x86_64

yum install -y  gcc gcc-c++ make git patch openssl-devel zlib-devel readline-devel sqlite-devel bzip2-devel

git clone git://github.com/yyuu/pyenv.git ~/.pyenv

export PATH="$HOME/.pyenv/bin:$PATH"
eval "$(pyenv init -)"

## bamfilter_oneliners.md

      
              1 file
            
          
              52 forks
            
          
                17 comments
              
            
              154 stars
            
          
                davfre
                / bamfilter_oneliners.md
            
            
              Last active
              January 18, 2025 22:47
            
              
                SAM and BAM filtering oneliners
              
          
    SAM and BAM filtering one-liners
@author: David Fredman, david.fredmanAAAAAA@gmail.com (sans poly-A tail)

@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/
Please extend with additional/faster/better solutions via a pull request!
BWA mapping (using piping for minimal disk I/O)

  
## gist:094e361cb94557878d16
library(Rcpp)

body <- "
SEXP foo(const int len, Rcpp::NumericVector pr)
{
  Rcpp::IntegerVector ret(len);
  RNGScope();

  for (int i=0; i<len; i++)
  {
	cat hg18.fa \| awk '{
	if (substr($0, 1, 1)==">") {filename=(substr($0,2) ".fa")}
	print $0 > filename
	}'
	#!/bin/bash

	#--- config

	SERVICE_NAME=galaxy
	RUN_AS=galaxy
	RUN_IN=/your/galaxy/directory

	#--- main actions
	#!/bin/bash
	# Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress]
	#
	# Deinterleaves a FASTQ file of paired reads into two FASTQ
	# files specified on the command line. Optionally GZip compresses the output
	# FASTQ files using pigz if the 3rd command line argument is the word "compress"
	#
	# Can deinterleave 100 million paired reads (200 million total
	# reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s)
	#
	#!/bin/zsh
	# pyenv install for CentOS 6.5 x86_64

	yum install -y gcc gcc-c++ make git patch openssl-devel zlib-devel readline-devel sqlite-devel bzip2-devel

	git clone git://github.com/yyuu/pyenv.git ~/.pyenv

	export PATH="$HOME/.pyenv/bin:$PATH"
	eval "$(pyenv init -)"
	library(Rcpp)

	body <- "
	SEXP foo(const int len, Rcpp::NumericVector pr)
	{
	Rcpp::IntegerVector ret(len);
	RNGScope();

	for (int i=0; i<len; i++)
	{