gawbul

# load libraries
library(gdata)
library(reshape2)
library(ggplot2)

# load data - trim last two rows
spectra_data <- read.xls("/Users/stevemoss/Downloads/CORRECTIONS.xls", sheet="Corrected Values")[1:11,]
names(spectra_data)
head(spectra_data)
tail(spectra_data)

gawbul

Family.Description
AMBIGUOUS
DISINTEGRIN AND METALLOPROTEINASE DOMAIN CONTAINING 5 TRANSMEMBRANE METALLOPROTEINASE  DISINTEGRIN  AND CYSTEINE RICH II TMDC II
PROBABLE RIBOSOME BIOGENESIS RLP24 RIBOSOMAL L24 DOMAIN CONTAINING 1
ADENOSINE RECEPTOR A3
TRANSCRIPTION FACTOR 19 TCF 19 TRANSCRIPTION FACTOR SC1
PROLIFERATION ASSOCIATED 2G4 P38 2G4
TRIPARTITE MOTIF CONTAINING 40
ANKYRIN REPEAT AND SOCS BOX ASB
BUTYROPHILIN  2

gawbul

Family.Description
COMPLEMENT C3 COMPLEMENT C3 BETA CHAIN; COMPLEMENT C3 ALPHA CHAIN; C3A ANAPHYLATOXIN; COMPLEMENT
PROTOCADHERIN GAMMA PRECURSOR PCDH GAMMA
UNKNOWN
HISTONE H3
MHC CLASS I POLYPEPTIDE RELATED SEQUENCE PRECURSOR MIC
KERATIN TYPE II CYTOSKELETAL CYTOKERATIN CK KERATIN TYPE II KERATIN
OLFACTORY RECEPTOR
60S RIBOSOMAL L7A
PRAME FAMILY MEMBER

gawbul

Keybase proof

I hereby claim:

• I am gawbul on github.
• I am gawbul (https://keybase.io/gawbul) on keybase.
• I have a public key whose fingerprint is 705F CA8A 945B A999 F7A9 AFE9 59C3 CB71 CBC4 3646

To claim this, I am signing this object:

gawbul

==> Installing maker from homebrew/homebrew-science
/usr/bin/env perl -e use Bio::Perl
/usr/bin/env perl -e use Bit::Vector
/usr/bin/env perl -e use DBD::SQLite
/usr/bin/env perl -e use DBI
/usr/bin/env perl -e use File::Which
/usr/bin/env perl -e use IO::All
/usr/bin/env perl -e use IO::Prompt
/usr/bin/env perl -e use Inline
/usr/bin/env perl -e use Perl::Unsafe::Signals

gawbul

==> Installing mira from homebrew/homebrew-science
couldn't understand kern.osversion `14.3.0'
==> Downloading https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira-4.0.2.tar.bz2
Already downloaded: /Library/Caches/Homebrew/mira-4.0.2.tar.bz2
==> Verifying mira-4.0.2.tar.bz2 checksum
tar xf /Library/Caches/Homebrew/mira-4.0.2.tar.bz2
==> ./configure --disable-debug --disable-dependency-tracking --prefix=/usr/local/Cellar/mira/4.0.2 --with-expat=/usr/local/opt/expat --with-expat-lib=-L/usr/local/opt/expat/lib --with-boost=/usr/local/opt/boost --with-boost-libdir=/usr/local/opt/boost/lib --with-boost-regex=boost_regex-mt --with-boost-system=boost_system-mt --with-boost-filesystem=boost_filesystem-mt --with-boost-iostreams=boost_iostreams-mt --with-tcmalloc --with-tcmalloc-dir=/usr/local/opt/google-perftools/lib
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d

gawbul

#!/usr/bin/env python
# import modules
import os, random, sys

# parse arguments
if len(sys.argv) != 2:
  print "Requires one input filename as an argument."
  sys.exit()
filename = sys.argv[1]

gawbul

#!/usr/bin/env python
# import modules
import mmap, os, random, sys
from Bio import SeqIO
from StringIO import StringIO

# parse arguments
if len(sys.argv) != 3:
  print "Requires an input filename and integer as arguments."
  sys.exit()

gawbul

#!/usr/bin/env python
# import modules
import mmap, os, random, re, sys

# parse arguments
if len(sys.argv) != 3:
  print "Requires an input filename and integer as arguments."
  sys.exit()
filename = sys.argv[1]
try:

gawbul

class Poretools < Formula
  desc "Tools for working with nanopore sequencing data"
  homepage "http://poretools.readthedocs.org/"
  url "https://github.com/arq5x/poretools/archive/v0.5.1.tar.gz"
  sha256 "7cd55a8f30290992dcf8d7792401e7f21efadfde02b3f4604d6680d2f8300479"
  head "https://github.com/arq5x/poretools.git"

  depends_on "hdf5"
  depends_on "r"
  depends_on :python if MacOS.version <= :snow_leopard