janxkoci

name: grass
channels:
  - conda-forge
dependencies:
  - proj
  - gdal
  - parallel # for parallelization
  - flex
  - bison # yacc parser
  - pdal

janxkoci

AWK(1)                                         General Commands Manual                                         AWK(1)

awk

NAME
       awk - pattern-directed scanning and processing language

SYNOPSIS
       awk [ -F fs ] [ -v var=value ] [ 'prog' | -f progfile ] [ file ...  ]

janxkoci

--- dropbox.py
+++ dropbox.py
@@ -134,11 +134,12 @@
         FatalVisibleError("Platform not supported")

 def is_dropbox_running():
-    pidfile = os.path.expanduser("~/.dropbox/dropbox.pid")
-
     try:
-        with open(pidfile, "r") as f:

janxkoci

SAM and BAM filtering one-liners

@author: David Fredman, [email protected] (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)

janxkoci

#!/usr/bin/awk -f

function usage()
{
	print "Convert legofit model with estimates to slendr simulation script." > "/dev/stderr"
	print "usage: estlgo2slendr.awk model.lgo" > "/dev/stderr"
	err_exit = 1
	exit 1
}

janxkoci

#!/bin/bash
#PBS -l select=1:ncpus=64:mem=1gb,walltime=24:00:00

## GO TO WORKDIR
cd $PBS_O_WORKDIR || exit

## EXPORT PATH
export PATH="/storage/brno2/home/jena/bin:$PATH"
export PATH="/storage/brno2/home/jena/miniconda3/bin:$PATH"

janxkoci

# julia shebang here

# mean fasta length
# non-fasta input may lead to division by zero !!
# use at your own risk

# add global constants for vars in loop below
# actually - requires julia v1.8+
nseq::Int = 0
len::Int = 0

janxkoci

#!/bin/bash

## bash vcf2hetfa.sh input.vcf.gz

VCF=$1
OUT=$(basename -s .vcf.gz $VCF).hetfa.fa
TMP=${OUT}.tmp

rm $OUT # output build by appending, so remove old versions first

janxkoci

#!/usr/bin/awk -f

BEGIN {
	OFS = "\t"
	print "chrom_pos", "ref", "alt", "aa", "da", "Altai", "Denisova3", "Chagyrskaya", "Vindija", "Africa"
}

$4 == $5 {		# chimp matches gorilla
	
	## concatenate African genotypes to a string (columns 10..NF)

janxkoci

#!/usr/bin/env Rscript

# library(seqinr)

## ARGS
args <- commandArgs(trailingOnly=TRUE)
if (length(args) != 2) stop("Two input files must be supplied.", call.=FALSE)

## INPUT
fastafile <- grep(".fa", args, val=T) # args[1] # "mez1_chr21-22.fa"