PoisonAlien

#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <htslib/sam.h>

int main(int argc, char *argv[]){
	
	samFile *fp_in = hts_open(argv[1],"r"); //open bam file
	bam_hdr_t *bamHdr = sam_hdr_read(fp_in); //read header
	bam1_t *aln = bam_init1(); //initialize an alignment

PoisonAlien

#!/bin/bash
#
# AUTHOR: Anand M.
# RNA-Seq variant calling pieline accoring to GATK Best practices.
# https://www.broadinstitute.org/gatk/guide/article?id=3891
#
# Call with following arguments
# bash rna_seq_variant_pipeline.sh <Input_Reads1.fq.gz> <Input_Reads2.fq.gz> <output_basename>
# 
# Assumes STAR aligner is under path

PoisonAlien

__author__ = "Anand M"

'''
Takes output file generated by VarScan2 somatic programme and converts the formats.
'''

import argparse, math, re

parser = argparse.ArgumentParser(
    description="Converts VarScan2 somatic vcf to native format and vice-versa.\nInput is automatically detected")

PoisonAlien

__author__ = 'Anand M'

import argparse, datetime, os


############# parse arguments ########
parser = argparse.ArgumentParser(
    description="wrapper script for STAR aligner. Assumes STAR is installed under path and accessible.",
    formatter_class=argparse.ArgumentDefaultsHelpFormatter)

PoisonAlien

# Usage
# 
# oncotate(maflite, header = FALSE, basename = NULL)
# Arguments
# 
# maflite	
# input tsv file with chr, start, end, ref_allele, alt_allele columns. (rest of the columns, if present will be attached to the output maf)
#
# header	
# logical. Whether input has a header line. Default is FALSE.

PoisonAlien

#Usage: From command line		
#Rscript dnaCopyScan.r <foo.copynumber>
#Author: Anand Mayakonda (Cancer Science Institute of Singapore; NUS)

dnaCopy=function(copynumber_file){
  suppressPackageStartupMessages(library(DNAcopy))
  suppressPackageStartupMessages(library(data.table))
  tn = data.table::fread(copynumber_file, sep="\t", stringsAsFactors=FALSE, header=TRUE, check.names=FALSE)
  colnames(tn)[1] = 'contig'
  tn$contig = gsub(pattern = 'chr', replacement = '', x = tn$contig, fixed = T)

PoisonAlien

#!/usr/bin/env bash

#Usage example: fetch_sra SRR1067272
#Details - Downloads SRA runs with wget. 
#Accepts one or more SRR run ids as input and downloads them into working directory  
#Partially downloaded files will be resumed.
#Author: Anand Mayakonda <[email protected]>

echo "$(tput setaf 3)"
if [ $# -lt 1 ];then

PoisonAlien

Keybase proof

I hereby claim:

• I am poisonalien on github.
• I am anandmt (https://keybase.io/anandmt) on keybase.
• I have a public key ASCo_qLuKorQBwDJ44Rb9fTv-EmjPSFm-A6i3MF-aXvQawo

To claim this, I am signing this object:

PoisonAlien

png(filename = "xx.png", width = 1200, height = 700, res = 70, bg = "white")
par(bg = 'black', mar = c(0, 0, 0, 0))
plot(1:50,1:50, pch = NA, axes = FALSE)
for(i in 1:50){
  x = sample(x = c("A", "T", "G", "C"), size = 50, replace = TRUE)  
  points(x = rep(i, 50), y = 1:50, pch = x, cex = 0.8, col = "green")
}

par(family = "serif")
legend(x = "center", legend = "M E T H R I X", text.col = "green", bg = "black", cex = 3, adj = 0.1)

PoisonAlien

use std::io::{BufRead, BufReader};
use std::fs::File;
use std::env;
use std::process;

fn main() {
    
    let args: Vec<String> = env::args().collect();

    if args.len() < 2{