moonwatcher

#!/bin/sh
# Protocol for setting up an environemnt for bcl2fastq 1.8.4
# See: http://seqanswers.com/forums/showpost.php?p=141026&postcount=29
# lior.galanti@nyu.edu
# for bcl2fastq2 see http://backwardincompatible.com/post/169360794395/compiling-illumina-bcl2fastq-220-on-ubuntu-with

# On Ubuntu
sudo apt-get install \
libexpat1-dev \
libexpat1 \

moonwatcher

#ifndef WIN32
        boost::property_tree::write_xml(os, treeWithIndexAttributes, boost::property_tree::xml_writer_make_settings(' ', 2));
#else
        boost::property_tree::write_xml(os, treeWithIndexAttributes, boost::property_tree::xml_writer_make_settings<std::string>(' ', 2));
#endif
    }
    else
    {
#ifndef WIN32
        boost::property_tree::write_xml(os, tree, boost::property_tree::xml_writer_make_settings(' ', 2));

moonwatcher

import base64
import struct

# s is the original string
s = "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

moonwatcher

#!/usr/bin/env python3
# -*- coding: utf-8 -*-

import json
import os
from subprocess import Popen, PIPE

inode_type = lambda path: ( os.path.isfile(path) and 'file' ) or 'directory'

def to_json(node):

moonwatcher

#!/bin/bash
SOURCE="$1"
TARGET="$2"
NAME="$3"
EMAIL="eegi"

LOG_DIR="/var/log/scope/$NAME";
FILTER_FILE="/var/lib/scope/filter/$NAME"
TIMESTAMP="$(date +%Y-%m-%d-%H-%M-%S)";
CHMOD="a+rwx,g+rwx,o-w"

moonwatcher

Comment                             leading VH J558.1.85*01 is non functional P
R    name        strain  S F I G P  c57bl6b01t01spfb1a | @M00595:21:000000000-A4G6U:1:1101:14408:3540 1:N:0:ATAGG | VH : J558.1.85 | DH : DFL16.1 | JH : IGHJ4 | CDR3 : -6.2 2156 | in frame | Q 36.47
                                    0  2   5   8   11  14  17  20  23  26  29  32  35  38  41  44  47  50  53  56  59  62  65  68  71  74  77  80  83  86  89  92  95  98  101 104 107 110 113 116 119 122 125 128 131 134 137 140 143 
                                    AA TCC TCC AGC ACA GCC TAC ATG CAA CTC AGC AGC CTG ACA TCT GAG GAC TCT GCG GTC TAT TAC TGT GCA TAT TAC TAC GGT AGT AGC TAC TAT GCT ATG GAC TAC TGG GGT CAA GGA ACC TCA GTC ACC GTC TCC TCA GGT AAG 
                                    GG BGG AHH HGF HGG HD? HHH GHH EGF B4H HGH HHH FGF FFH GHH HGF GHH CCG GEB FHG FHH FGH GHH FHH GGD ABA EFE GDD FFF FHH GHH HHB FGB HHH GDH HFE 2EG 3GB HHG FGH HFC C5D GAF EEE AGA G2F AFF FCF FFF 
                                       S   S   S

moonwatcher

R    name      F  c57bl6b01t01spffo | @M00595:21:000000000-A4G6U:1:1106:14825:11935 1:N:0:GGTAC | VH : J558.8.98 | DH : DQ52 | JH : IGHJ2 | CDR3 : -2.6 1197 | out of frame | premature | Q 38.25
                  0 1   4   7   10  13  16  19  22  25  28  31  34  37  40  43  46  49  52  55  58  61  64  67  70  73  76  79  82  85  88  91  94  97  100 103 106 109 112 115 118 121 124 127 130 133 136 139 142 145 
                  T CTC TGT AGA CCG GTC CTC CAG CAC AGT GTA CAT GGT GTT GAA CAG CCT GAC ATC TGA GGA CCC TGC TGT CTA TTA CTG TGG GGA TCT GGG GCC CTT GAC TAC TGG GGC CAA GGC ACC ACT CTC ACA GTC TCC TCA GGT GAG TCC T 
                  G HHG HHH GGG GGH HGG HHH HGH HHH HHH HHH HHH GGH HHH HHH HHH HHH HHH FHH HHH HHG GHH HHH HHH HHH HHH HGG HGH HHH EGG GGG GGF HHH HHH HHG GGH HHH HHH HHF FFF B4F FHH FHH GHG GFB GGG FGG FFB FFF F 
                    L   C   R   P   V   L   Q   H   S   V   H   G   V   E   Q   P   D   I   *   G   P   C   C   L   L   L   W   G   S   G   A   L   D   Y   W   G   Q   G   T   T   L 

moonwatcher

#!/usr/bin/env python3
# -*- coding: utf-8 -*-

# Author: Lior Galanti < lior.galanti@nyu.edu >
# NYU Center for Genetics and System Biology 2015

import sys
import io
import json
import uuid

moonwatcher

# content of main.R
source("CSI.R")

#Cenix
data <- read.delim("../../Cenix_Digimap_raw_040820.csv", header = TRUE, row.names = 1, sep = "\t")
input_m <- data[,2:46]
phenoSig  <- as.matrix(input_m) 
phenoSig[ which(phenoSig <=1) ] = 0 
phenoSig[ which(phenoSig >1) ] = 1 

moonwatcher

#!/bin/bash
#
# GNU GCC COMPILER INSTALLATION SCRIPT
#
# Copyright (c) 2014 Benjamin Beurdouche. All rights reserved.
#
# You might want to modify the first line to specify your own install location.
# Prerequisites : binutils autoconf automake libtool autogen gettext cloog dejagnu