mpkocher

<?xml version="1.0" encoding="UTF-8"?>
<workflow>
    <!-- Not sure this make sense to be here -->
    <settings>
        <param id="pbsmrtpipe.task_modules.filter.my_option">
            <value>12</value>
        </param>
    </settings>
    <abstract-graph id="pbsmrtpipe.abstract_graphs.rs_resequencing">
        <file-node id="2">

mpkocher

"""Unittests for P_Filter module"""
import logging

from pysiv.core.base import TestBase, TestModuleBase
from pysiv.core.utils import monkey_patch_task, monkey_patch_module

from pysiv.validators import FastaValidator, FastqValidator, CsvValidator


log = logging.getLogger(__name__)

mpkocher

import os
import sys
import argparse
import logging

__version__ = '0.1'

log = logging.getLogger(__name__)

mpkocher

#!/usr/bin/env python
from pprint import pformat

__doc__ = """Script to break down post-mapping statistics by movie.

OLD Pre-bax files

m130715_185638_SMRT1_c000000062559900001500000112311501_s1_p0.bas.h5

m{DATE_DATE}_{INSTRUMENT_NAME}_c{CHIP_STRIP_BARCODE}{CELL_NUMBER}_s{

mpkocher

Updating 2.1

Replace $SEYMOUR_HOME/analysis/lib/python2.7/pbpy-0.1-py2.7.egg/pbpy/smrtpipe/modules/P_Control.py in SMRTAnalysis 2.1.

mpkocher

import os
import pandas as pd
import pysiv.toolbook as tb

_STATES = ("RESOLVED", "ASSIGNED", "FIXED")

def make_bug_summary(csv_file_name, output_image, state="RESOLVED"):
    if state not in _STATES:
        raise ValueError("Unsupported state {s}".format(s=state))
    

mpkocher

import os
import logging
import abc
import functools

import networkx as nx
from fabric.api import lcd, local, shell_env, prefix, settings

log = logging.getLogger(__name__)

mpkocher

def compose(*funcs):
    """Functional composition

    [f, g, h] will be f(g(h(x)))
    """
    def compose_two(f, g):
        def c(x):
            return f(g(x))
        return c
    return functools.reduce(compose_two, funcs)

mpkocher

"""
Usage:

python mhouse_runner.py submit my_awesome.csv --debug -m "http://milhouse:9999" internal_test.csv -a '.m2__m_loading_stats' '.m2__gAccuracy' '.m2__gAccuracyByReadLengthBoxplot' -n 'mk_test_01' --description "services-submitted-job"

This is included in the milhouse code (milhouse/src/milhouse/scripts/mhouse_runner.py
"""
import os
from pprint import pformat
import sys

mpkocher

# Add to .bashrc
function seamour() {
        #source $SEYMOUR_HOME/etc/setup.sh
        x=`env | grep SEYMOUR_HOME | awk -F "=" '{print $2}'`
        source $x/etc/setup.sh
        current_version=`get_current_version.sh`
        export PS1="[${current_version}]$PS1"
}