taoliu

#!/usr/bin/env python

# This script is a wrapper in Python to help submit jobs, that need to use CONDA environment, to SLURM.

import subprocess
import sys
import os
import time
import argparse as ap

taoliu

# K-nearest neighbor smoothing based on sNN from clustering
# Inspired by knn-smooth.R: https://github.com/yanailab/knn-smoothing/blob/master/knn_smooth.R
# by Tao Liu <vladimir.liu@gmail.com>

#' kNN-smoothing on a given matrix based on a pre-calculated sNN matrix
#'
#' Note: sparse matrix will be converted to regular matrix, so memory
#' usage will be high.
#'
#' @param M A numeric matrix that will be smoothed. It should have

taoliu

#!/bin/bash
#
# This script will find the consensus peak regions from peak files (in
# BED format) of multiple samples by:
#
# 1. Converting the peak file of each sample into non-overlapping 3
# cols BED file and concatenating them;
#
# 2. Sorting the concatenated file and Building a genome coverage
# track in BedGraph, of which the value (the 3rd col) indicates the

taoliu

#!/usr/bin/env perl -w
# Time-stamp: <2008-03-03 11:24:07 Tao Liu>
#
# By: Tao Liu <vladimir.liu@gmail.com>
#

use strict;

die "need x paras: $0 <options> [y=blah]\n" if @ARGV < x;

taoliu

#!/bin/bash

if [ $# -lt 1 ]; then
    echo "need 1 para!"
    exit
fi

taoliu

#!/usr/bin/env python3
# Time-stamp: <2008-04-07 17:51:27 Tao Liu>

"""Module Description

Copyright (c) 2020 Tao Liu <vladimir.liu@gmail.com>

This code is free software; you can redistribute it and/or modify it
under the terms of the BSD License (see the file COPYING included with
the distribution).

taoliu

#!/usr/bin/env python
# Time-stamp: <2008-01-18 13:42:57 Tao Liu>

import os
import sys
# ------------------------------------
# Main function
# ------------------------------------
def main():
    if len(sys.argv) < x+1:

taoliu

#!/usr/bin/env perl
# A script to convert samtools (>v1.3) depth (with -aa option) output 
# to bedGraph by merging continous positions with the same value.


if ( $#ARGV < 0 ) {
    print "Need 1 parameter! $0 <samtools depth output (with -aa)>\n";
    exit ();
}

taoliu

#!/bin/bash

# set the path to as file for narrowPeak. Locate it in your UCSC source code directory or google...
asfile=/data/db/UCSC_sqls/encode/narrowPeak.as

which bedToBigBed &>/dev/null || { echo "bedToBigBed not found! Download: <http://hgdownload.cse.ucsc.edu/admin/exe/>"; exit 1; }

if [ $# -lt 2 ];then
    echo "Need 2 parameters! <narrowPeak> <chrom info>"
    exit

taoliu

codon_dictionary = {
    'TCA' : 'S',    # Serine
    'TCC' : 'S',    # Serine
    'TCG' : 'S',    # Serine
    'TCT' : 'S',    # Serine
    'TTC' : 'F',    # Phenylalanine
    'TTT' : 'F',    # Phenylalanine
    'TTA' : 'L',    # Leucine
    'TTG' : 'L',    # Leucine
    'TAC' : 'Y',    # Tyrosine