moonwatcher

alias vpn.portodelgato.stop="close.vpn portodelgato"
alias vpn.portodelgato.start="open.vpn portodelgato"
alias vpn.portodelgato.restart="restart.vpn portodelgato"
alias vpn.portodelgato.log="cat /usr/local/var/log/openvpn.portodelgato.log|tail -n 100"

show.vpn() {
    if [ -n "$1" ]; then
        PROCESS="org.openvpn.$1"
        sudo launchctl list $PROCESS
    else

moonwatcher

R    name      F  c57bl6b02t01spfb1a | @M00595:21:000000000-A4G6U:1:1104:14429:18718 1:N:0:CGTGA | VH : S107.3.62 | JH : IGHJ4 | CDR3 : 0.2 1252 | productive | Q 38.67
                  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 
                  TC ACC ATC TCC AGA GAT AAT TCC CAA AGC ATC CTC TAT CTT CAA ATG AAT GCC CTG AGA GCT GAG GAC AGT GCC ACT TAT TAC TGT GCA AGC TAT GCT ATG GAC TAC TGG GGT CAA GGA ACC TCA GTC ACC GTC TCC TCA GGT AAG 
                  HH HHH HHG FHH HHH HHH HHH HGH HHH HHH HHH HHH HHH HHH HHH HHH HHG GHH HHH HHH HHH HHH HHH HHH GHH HHH HHH HHH HHH HHH HHH HHH HHH HHH HHH HHG GGH HHH HHH HHH HGG GHH HGH GGG GGG GGG GGF FFB FFA 
                     T   I   S   R   D   N   S   Q   S   I   L   Y   L   Q   M   N   A   L   R   A   E   D   S   A   T   Y   Y   C   A   S   Y   A   M   D   Y   W   G   Q   G   T   S   V   T   V   S   S   G   K   

moonwatcher

R    name     F  c57bl6b03t03spffo | @M00595:21:000000000-A4G6U:1:1101:4744:10595 1:N:0:ATCAC | VH : SM7.2.49 | DH : DMB1 | JH : IGHJ2 | CDR3 : -8.2 1534 | productive | Q 36.97
                 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 
                 A ACA GCA GAC ACA TCC TCC AAC ACA GCC TAC CCG CAG CTC AGC AGC CTG ACA TCT GAG GAC ACT GCC GTC TAT TAC TGT GCT AAC GAG TAC TAC TTT GAC TAC TGG GGC CAA GGC ACC ACT CTC ACA GTC TCC TCA GGT GAG TCC T 
                 H HHH HHF HGH HGG ?DG GCF HGG FEH HAG EEG GGH HBG E4H FGH GHF HFG HHE GHG DBF FHH HGE EGD HHG HFH GDB FDB GGF FGE FHF FDH HFH HHH HGH FGE EEE CHH HHG FHF FGH HHH HGF GFH GFA BEB 4FG CEB >FB FBF F 
                   T   A   D   T   S   S   N   T   A   Y   P   Q   L   S   S   L   T   S   E   D   T   A   V   Y   Y   C   A   N   E   Y   Y   F   D   Y   W   G   Q   G   T   T   L   T   V   S   S   G   

moonwatcher

##Alphabet α##

Lets consider the most general case of IUPAC encoding. Our alphabet α is:

α = { T, K, H, Y, G, C, W, V, A, D, S, M, B, R, N }

symbol	reverse complement	options	full name
T	A	T	Thymine
K	M	G, T	Keto

moonwatcher

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

# Search for a sequence in a FASTA file
# Author: Lior Galanti < [email protected] >
# NYU Center for Genetics and System Biology 2015
#
# search is free software; you can redistribute it and/or modify it under the terms of
# the GNU General Public License as published by the Free Software Foundation;
# either version 2 of the License, or (at your option) any later version.

moonwatcher

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

# Extract a sequence by coordinates from a FASTA file
# Author: Lior Galanti < [email protected] >
# NYU Center for Genetics and System Biology 2015
#
# crop is free software; you can redistribute it and/or modify it under the terms of
# the GNU General Public License as published by the Free Software Foundation;
# either version 2 of the License, or (at your option) any later version.

moonwatcher

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

# Reverse complement an IUPAC encoded DNA string
# Author: Lior Galanti < [email protected] >
# NYU Center for Genetics and System Biology 2015
#
# complement is free software; you can redistribute it and/or modify it under the terms of
# the GNU General Public License as published by the Free Software Foundation;
# either version 2 of the License, or (at your option) any later version.

moonwatcher

{
    "A": "T",
    "C": "G",
    "G": "C",
    "T": "A",
    "R": "Y",
    "Y": "R",
    "K": "M",
    "M": "K",
    "S": "S",

moonwatcher

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

#   recursive fastq reference resolver for cleaning up the scratch file system
#   Author: Lior Galanti < [email protected] >
#   NYU Center for Genetics and System Biology 2015

import sys
import re
import json

moonwatcher

 /*
    FASTQ Demultiplexer

    Author: Lior Galanti [email protected]

    Build:
        On ubuntu:
            dependencies: sudo apt-get install lib32z1-dev libboost-iostreams-dev libboost-program-options-dev
            compile: g++ -static phenaqs.cpp -lboost_iostreams -lboost_program_options -lz -std=c++11 -o phenaqs