porterjamesj

[2014-02-27 16:02:13]  DEBUG lt-chitcpd <<< New state: CLOSING
[2014-02-27 16:02:13]  DEBUG lt-chitcpd <<< Finished handling event PACKET_ARRIVAL on state FIN_WAIT_1
[2014-02-27 16:02:13]  DEBUG lt-chitcpd >>> Handling event PACKET_ARRIVAL on state CLOSING
[2014-02-27 16:02:13]  DEBUG lt-chitcpd <<< New state: CLOSING
[2014-02-27 16:02:13]  DEBUG lt-chitcpd >>> TCP data BEFORE handling:
[2014-02-27 16:02:13]  DEBUG lt-chitcpd    ······················································
[2014-02-27 16:02:13]  DEBUG lt-chitcpd                          CLOSING
[2014-02-27 16:02:13]  DEBUG lt-chitcpd
[2014-02-27 16:02:13]  DEBUG lt-chitcpd             ISS:        3949           IRS:        3949
[2014-02-27 16:02:13]  DEBUG lt-chitcpd         SND.UNA:        3950

porterjamesj

"""
Traceback (most recent call last):
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 22, in run
    _do_run(cmd, checks)
  File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 113, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command '/usr/local/share/bcbio-nextgen/anaconda/bin/cutadapt --times=2 --quality-base=33 --quality-cutoff=20 --format=fastq --minimum-length=0 --output=/glusterfs/netapp/infvol/PORT
ERJAMESJ/brca/work/trim/tx/tmpCEp9YB/111101_UNC13-SN749_0133_BC04U8ABXX.5_2_trimmed.fastq /glusterfs/netapp/infvol/PORTERJAMESJ/brcafqs/111101_UNC13-SN749_0133_BC04U8ABXX.5_2.fastq
Traceback (most recent call last):
  File "/usr/local/share/bcbio-nextgen/anaconda/bin/cutadapt", line 10, in <module>

porterjamesj

from pipeline.main import pipeline_from_config
from pipeline.tools import async

from genomics_tools import parse_bowtie_output


with pipeline_from_config("/path/to/config.yaml") as p:
    with async():
        p.run("cutadapt --quality-base=33 --quality-cutoff=20 --format=fastq --minimum-length=0 --output={path1}/{name1}.trimmed.fastq {path1}/{name1}.fastq")
        p.run("cutadapt --quality-base=33 --quality-cutoff=20 --format=fastq --minimum-length=0 --output={path2}/{name2}.trimmed.fastq {path2}/{name1}.fastq")

porterjamesj

porterjamesj

# some further optimizations

# Parameters
const S0 = 600; # current bitcoin price
const r = 0.02; # risk neutral payoff, assumed 2% for this exercise, in reality probably less.
const sigma = 2; # extremely high sigma due to spike in bitcoin prices late last year
const T = 1.0; # 1 Time cycle
const M = 100; # 100 steps
const dt = T / M # dt

porterjamesj

import os
import re


xml_file = sys.argv[1]

tree = ET.parse(xml_file)

root = tree.getroot()

porterjamesj

def balanced(s):
    raise NotImplementedError("Implement me!")


def test():
    for s in ["{}", "[]", "()", "a(b)c", "abc[d]", "a(b)c{d[e]}"]:
        assert balanced(s)
    for s in ["{]", "(]", "a(b]c", "abc[d}", "a(b)c{d[e}"]:
        assert not balanced(s)
        

porterjamesj

using BinDeps

@BinDeps.setup

gumbo = library_dependency("libgumbo")

provides(Sources,
         URI("https://github.com/google/gumbo-parser/archive/master.zip"),
         gumbo,
         unpacked_dir="gumbo-parser-master")

porterjamesj

function do_computation_then_print(message::String)
    sum = 1
    for i = 1:(rand() * 10^7)
        sum *= i
    end
    # print out the sum so the compiler doesn't elide the loop
    print("$message: $sum\n")
end

porterjamesj

import asyncio


@asyncio.coroutine
def server_callback(reader, writer):
    while True:
        data = yield from reader.readline()
        yield from asyncio.sleep(1)
        writer.write(data)
        yield from writer.drain()