mpkocher

import sys
import random

from pbreports.model.model import Table, Column


def get_columns():
    cs = [Column('person', header="Person Name"),
          Column('color', header="Favorite Color"),
          Column('pid', header='User id')]

mpkocher

<?xml version="1.0" encoding="UTF-8"?>
<workflow>
  <!-- This is similar to the current RS protocol in Portal -->
    <protocol id="pbsmrtpipe.protocols.rs_resequencing">
        <inputs>
            <input><type>MovieFofn</type></input>
            <input><type>ReferenceEntry</type></input>
        </inputs>
        <options>
            <option id="pbsmrtpipe.task_modules.filter.my_option">

mpkocher

# Basic tests
def setup_log(alog, level=logging.INFO, file_name=None, log_filter=None,
              str_formatter='[%(levelname)s] %(asctime)-15s [%(name)s %(funcName)s %(lineno)d] %(message)s'):
    """Core Util to setup log handler

    :param alog: a log instance
    :param level: (int) Level of logging debug
    :param file_name: (str, None) if None, stdout is used, str write to file
    :param log_filter: (LogFilter, None)
    :param str_formatter: (str) log formatting str

mpkocher

<?xml version="1.0" encoding="UTF-8"?>
<report>
    <title>Motifs</title>
    <table>
        <thead>
            <tr>
                <th>Mof</th>
                <th>Modified Position</th>
                <th>Modification Type</th>
                <th>% Motifs Detected</th>

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

# 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"
}