porterjamesj

import os
import re


xml_file = sys.argv[1]

tree = ET.parse(xml_file)

root = tree.getroot()

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

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

"""
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

[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

(setq inhibit-startup-message t)

(global-set-key (kbd "M-n") 'forward-paragraph)
(global-set-key (kbd "M-p") 'backward-paragraph)

(setq backup-inhibited t)
(setq auto-save-default nil)
(setq create-lockfiles nil)

(defalias 'yes-or-no-p 'y-or-n-p)

porterjamesj

Maui Scheduler General Public License

This product includes software developed for The University of New Mexico High Performance Computing Education and Research Center for use in the Maui Scheduler software.  Copyright (C) 2000 Science and Technology Corporation @ UNM, Software developed for The University of New Mexico.  All Rights Reserved.
Maui Scheduler is a trademark of Science & Technology Corporation @ UNM

THE SOFTWARE IS PROVIDED AS IS AND SCIENCE & TECHNOLOGY CORPORATION @ UNM (STC) AND THE UNIVERSITY OF NEW MEXICO (UNM) DISCLAIM ALL WARRANTIES RELATING TO THE SOFTWARE, WHETHER EXPRESSED OR IMPLIED, INCLUDING BUT NOT LIMITED TO ANY IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.  NEITHER UNM,
STC, NOR ANYONE INVOLVED IN THE CREATION, PRODUCTION, OR DELIVERY OF THE SOFTWARE SHALL BE LIABLE FOR ANY INDIRECT, CONSEQUENTIAL, OR INCIDENTAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE SOFTWARE EVEN IF UNM OR STC HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES OR

porterjamesj

2013-12-30 11:38] torque-node172-16-1-250: Cufflinks on /glusterfs/users/jporter/scale/hg19_scale_project/work2/align/HG00109_1_M_120209_4/3_131109_hg19_scale_project_tophat/3_131109_hg19_scale_project
-sort.bam.
[2013-12-30 11:38] torque-node172-16-1-250: [05:38:07] Loading reference annotation and sequence.
[2013-12-30 12:41] torque-node172-16-1-250: Warning: couldn't find fasta record for 'chr17_ctg5_hap1'!
[2013-12-30 12:41] torque-node172-16-1-250: This contig will not be bias corrected.
[2013-12-30 12:41] torque-node172-16-1-250: Warning: couldn't find fasta record for 'chr17_gl000205_random'!
[2013-12-30 12:41] torque-node172-16-1-250: This contig will not be bias corrected.
[2013-12-30 12:48] torque-node172-16-1-250: Warning: couldn't find fasta record for 'chr19_gl000209_random'!
[2013-12-30 12:48] torque-node172-16-1-250: This contig will not be bias corrected.
[2013-12-30 12:48] torque-node172-16-1-250: Warning: couldn't find fasta record for 'chr1_gl000191_random'!

porterjamesj

function replace_(rep,expr::Expr)
    i = findfirst(x->x==:_,expr.args)
    if i == 0
        # recurse on subexprs one at a time
        # subexprs = expr.args[]
        error("dun goofed")
    else
        return Expr(expr.head,
                    [expr.args[1:i-1]
                     rep