nimezhu

/**
 * Created with JetBrains WebStorm.
 * User: zhuxp
 * Date: 13-4-21
 * To change this template use File | Settings | File Templates.
 */


function parseStems(ss)
{

nimezhu

chr1	61735	7035990	CopyNumberRegion_0	2	0
chr1	7036801	7974076	CopyNumberRegion_1	3	0
chr1	7975788	29271013	CopyNumberRegion_2	2	0
chr1	29275883	30265652	CopyNumberRegion_3	4	2
chr1	30271899	31334415	CopyNumberRegion_4	6	2
chr1	31336903	41403766	CopyNumberRegion_5	7	2
chr1	41405663	42601214	CopyNumberRegion_6	4	2
chr1	42602991	44503629	CopyNumberRegion_7	6	2
chr1	44507772	48809180	CopyNumberRegion_8	2	0
chr1	48810111	48824773	CopyNumberRegion_9	7	1

nimezhu

#for i in chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY chrM
for i in   chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chrX chrY chrM
do
echo "samtools mpileup -uf ../hg19.fna ../Mapping/$i.v2.sorted.bam | bcftools view -bvcg - > test_$i.var.raw.bcf"
echo "bcftools view test_$i.var.raw.bcf | vcfutils.pl varFilter -D100000 > test_$i.vcf"
echo "vcf2var.pl test_$i.vcf > test_$i.variants"
echo "samtools view ../Mapping/$i.v2.sorted.bam | extract_hairs --sam stdin --variants test_$i.variants > test_$i.fragments"
done 

nimezhu

venn.overlap <- 
function(r, a, b, target = 0)
{
#
# calculate the overlap area for circles of radius a and b 
# with centers separated by r
# target is included for the root finding code
#
	pi = acos(-1)
	if(r >= a + b) {

nimezhu

#!/bin/sh

inputfile=$1

# you can add friendly code to check the extension and use zcat if it's *.fastq.gz or *.fq.gz...

[[ "$inputfile" =~ ".*\.(fq\.gz$|fastq\.gz$)" ]] && zcat $inputfile | head -n400 | awk '{if(NR%4==0) printf("%s",$0);}' |  od -A n -t u1 | awk 'BEGIN{min=100;max=0;}{for(i=1;i<=NF;i++) {if($i>max) max=$i; if($i<min) min=$i;}}END{if(max<=74 && min<59) print "Phred+33"; else if(max>73 && min>=64) print "Phred+64"; else if(min>=59 && min<64 && max>73) print "Solexa+64"; else print "Unknown score encoding!";}'


[[ "$inputfile" =~ ".*\.(fq$|fastq$)" ]] && head -n400 $inputfile | awk '{if(NR%4==0) printf("%s",$0);}' |  od -A n -t u1 | awk 'BEGIN{min=100;max=0;}{for(i=1;i<=NF;i++) {if($i>max) max=$i; if($i<min) min=$i;}}END{if(max<=74 && min<59) print "Phred+33"; else if(max>73 && min>=64) print "Phred+64"; else if(min>=59 && min<64 && max>73) print "Solexa+64"; else print "Unknown score encoding!";}'

nimezhu

#!/bin/bash

if [ $# -lt 1 ]
    then
    echo "USAGE: test_contamination.sh <fastq_file>"
    exit 0
fi

# modify the following parameters as needed
Sample_Size=5000000

nimezhu

#!/usr/bin/python
# Wei Guifeng, <guifengwei@gmail.com>
# Revised By zhuxp <nimezhu@gmail.com>
# -- coding: utf-8 --
'''
Gencode annotation or Cufflinks transcript.gtf

usage:
    for gene in TableIO.parse("cufflinks.transcript.gtf", 'gtf'):
        print "{0}\t{1}\t{2}".format(gene.chr, gene.strand, (gene.stop - gene.start))

nimezhu

$(function() {
    Backbone.sync = function(method, model, success, error){
        success();
    }
    
CausalityView = Backbone.View.extend({
		el: $('body'), // el attaches to existing element
        attributes: {"width":900,"height":700},
        events: {
            'change #csv': 'render',

nimezhu

#!/usr/bin/env python
# a bar plot with errorbars
import numpy as np
import matplotlib.pyplot as plt

N = 5
menMeans = (20, 35, 30, 35, 27)
menStd =   (2, 3, 4, 1, 2)

ind = np.arange(N)  # the x locations for the groups

nimezhu

##TSS(TTS) POSITION CLASSIFIED

HITS : distance < 10
SHIFT : 10<= distance < 50
ALT_E : 50 < distance and peak in Exon
ALT_E : 50 < distance and peak in Intron

COL14 for gene: number of tss, repr string, number of tts