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, 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)

janxkoci

#!/bin/bash

FASTA="$1"
awk 'ORS = $1~/>/ ? RS:FS' $FASTA | sed 's/ >/\n>/g' | sed '2~2s/ //g'

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

## USAGE:
# bash melt_table.sh INFILE.tsv > OUTPUT.tsv

# set variables
outfile=/dev/stdout
tot_ncol=$(head -1 $1 | wc -w)
nsample=$(head -1 $1 | cut -f 3- | sed 's/\.[A-Z][A-Z]\>//g' | tr "\t" "\n" | uniq | wc -l)
ncol=$(expr $(expr $tot_ncol - 2) / $nsample)

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

#!/bin/bash

## Launch interactive session for testing purposes (Torque PBS & PBS Pro / OpenPBS)

# set CPUs and RAM (defaults = 8, 16gb)
cores=${1:-8}
ram=${2:-16}

## Torque PBS
qsub -I -N ijob -d . -v PATH -l nodes=1:ppn=${cores},mem=${ram}gb,walltime=48:00:00

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

#!/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

#!/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