boydgreenfield

from __future__ import print_function
import argparse

import onecodex


if __name__ == "__main__":
    parser = argparse.ArgumentParser(
        description=("Download a set of FASTA/Q files stored in One Codex with their sample IDs."))
    parser.add_argument('samples', metavar='sample ID', nargs='+',

boydgreenfield

'''
:Date: 26 Jul 2016
:Author: Public Health England
'''

"""Detect peaks in data based on their amplitude and other features."""
import argparse

from khmer import khmer_args
import khmer

boydgreenfield

#!/usr/local/bin/Rscript

# Copyright Reference Genomics, Inc. 2016
# Released under the MIT License
#
# Script for fetching analysis results from the One Codex API (v0)
# See https://docs.onecodex.com for full documentation on the REST API
#
# Script can be run from the command line with:
# `Rscript fetch_ocx_analyses.R <API_KEY> <FILE> [-d DATABASE_NAME] [-b BEGINNING_DATE_RANGE -e ENDING_DATE_RANGE]`

boydgreenfield

#
#
#            Nim's Runtime Library
#        (c) Copyright 2015 Andreas Rumpf
#
#    See the file "copying.txt", included in this
#    distribution, for details about the copyright.
#

## The ``tables`` module implements variants of an efficient `hash table`:idx:

boydgreenfield

#!/usr/bin/env python
# Usage: python team_sync.py refgenomics Core [optional list of repos to sync (short name)]
from github import Github
import getpass
import sys


print "Enter user: ",
user = raw_input()
password = getpass.getpass()

boydgreenfield

>A_hydrophila_HiSeq.922
AGGCCCACTGGAAGTTGTAGCCACCGAGCCAGCCGGTCACGTCCACCACCTCGCCGATGAAGTAGAGACCGGCTACCTTGCGCGCCTCCATGGTCTTGGAG
>A_hydrophila_HiSeq.1263
TGACTTGACGTCATCCCCACCTTCCTCCGGTTTATCACNACGGCAGTCTCCCTTGAGTTCCCACCATTACGTGCTGGCAACAAAGGACAGGGGTTGCGCTCGT
>A_hydrophila_HiSeq.2905
GACACCAAGCATATCTTCGACGAGCTGGACATCGACATAGACCCGCGGGTCAAGGTCGGCACCCTCTCCGTCTCCCAGATGCAGATGATCGAGATCGCCAA
>A_hydrophila_HiSeq.4866
TGACCCGCATCCGTAACGGTCAGGCGGCGAGCAAAGTTGNNNCGGTTTCCATGCCTTCTTCCAAGCTGAAAGTGGCTATTGCCAAAGTGCTGAAAGAAGAAGGT
>A_hydrophila_HiSeq.7009
GGTGAACCGTCTAATCCCCATCGTCGCCGACGAGCACGCCGACATGGAGAAGGGCACAGGCTGCGTGAAGATCACCCCGGCCCACGACTTCAACGACAACG

boydgreenfield

#!/usr/bin/env python
"""
No dependency Python script for joining two paired end FASTQ files.

Supports concatenating reads with a separator ("NNNNN") or interleaving reads via the
--interleave option. Auto-detects gzip'd files, offers header checking via a --strict flag,
and supports output to STDOUT a gzip'd FASTQ or an uncompressed FASTQ (--uncompressed flag).
"""
import argparse
import gzip

boydgreenfield

{.push checks: off.}
proc unsafe_mult2(x: int32): int32 =
  result = x * 2
{.pop.}

{.push checks: off.}
proc unsafe_assert(x: int): void =
  assert x == (x + 1)
{.pop.}

boydgreenfield

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boydgreenfield

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