dinovski

#!/usr/bin/env python

## get individual genotype from raw vcf
## output is tab-delimited chr \t start \t end \t ref \t alt \t GT \t ref,alt

usage="""
read in tab-delimited bedfile: chr,start,end,ref,alt,gt
usage: python addallgt.py <infile> <outfile>
"""
import sys

dinovski

#! /usr/bin/env python
import os
import sys

try:
    SEQ_DIR = sys.argv[1]
except:
    sys.stderr.write("Usage: python sanger2fastq.py <directory with.seq files>\n")
    sys.exit(1)

dinovski

#!/usr/bin/env python

## calculate N50 from fasta file
## N50 = contig length such that half of the contigs are longer and 1/2 of contigs are shorter

import commands
import sys
import os
from itertools import groupby
import numpy

dinovski

#!/usr/bin/env python

import csv
import string
import datetime
import random
import json
import re
import sys
import os

dinovski

#!/bin/bash

BEDTOOLS=/usr/bin/bedtools/bin
ODIR=/data/dbase/

GENOME=hg19
SLOP=3000
SLOP_OPTS='-l 3000 -r 3000'
GENE_BED=${IDIR}/${GENOME}_3kb.bed

dinovski

---
title: "__RNAseq Summary__"
output: pdf_document
date: '`r Sys.Date()`'
documentclass: article
classoption: a4paper
geometry: margin=2cm
---
  
```{r setup, include=FALSE}

dinovski

#/usr/bin/env/ python

usage="""
# get dbSNP file
wget --timestamping 'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp147Common.txt.gz' -O snp147Common.txt.gz
python dbsnp_clean.py <snp147Common.txt> <snp147common_clean.bed>
"""

if len(sys.argv) != 3:
	print usage

dinovski

#!/usr/bin/env python

usage="""
iupac_change.py <infile> <outfile>
change IUPAC nucleotide codes for tab delimited file with CHR, ID, REF, ALT columns
"""

import sys
import os

dinovski

#!/bin/bash

## calculate Ts/Tv across all sites (includes AC=0)
## file must be b/gzipped
## ./tstv.sh file.vcf.gz

VCF=$1

# get count for transitions:
ag=$(zcat ${VCF} | awk '! /\#/' | awk '{if(length($4) == 1 && length($5) == 1) print}' | \

dinovski

#!/usr/bin/env python

usage="""
## quality score distribution from fastq
gunzip -c fastq.gz | python qualDist.py
"""

import sys
 
num = 0