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frontier

Overview of Contents

.
├── Frontier
│   ├── IO
│   │   ├── AQCReader.py                    Class to read from AQC Matrix Files
│   │   ├── AbstractReader.py               Abstract class to inherit generic file reading
│   │   │                                     methods for users to implement custom readers
│   │   ├── BamcheckReader.py               Class to read from BAMcheckr'd Files
│   │   └── __init__.py                     Package definition
│   │
│   ├── __init__.py                         Package definition
│   └── frontier.py                         Frontier module containing classification
│                                             utilities and the Statplexer class
│
├── Goldilocks
│   ├── __init__.py                         Package definition
│   ├── goldilocks.py                       Goldilocks module
│   └── paths.g                             Paths File used for goldilocks.py
│
│
├── R
│   ├── goldilocks_regionplot.R             R script for plotting variant density vs.
│   │                                         region location as displayed in Chap.9
│   ├── lanemap.r                           R script to investigate potential correlation
│   │                                         between samples, lanes and lanelets
│   └── megabase_regions                    Input data for goldilocks_regionplot.R script
│
│
├── results
│   ├── front
│   │   ├── log
│   │   │   └── *                           Log files generated by Front for each experiment,
│   │   │                                     named in the format yyyy-mm-dd_hhmm__dset_pset_score.txt
│   │   │
│   │   └── pdf
│   │       └── *                           Directories of PDF files generated by Front each
│   │                                         containing 10 trees drawn by graphviz, one for each
│   │                                         training and testing fold.
│   │                                         Named in the format yyyy-mm-dd_hhmm__dset_pset_/
│   │
│   └── goldilocks
│       ├── goldilocks.log                  Latest log file from Goldilocks execution
│       ├── megabase_plot.pdf               PDF containing Figure 9.2
│       └── megabase_plot.png               PNG containing Figure 9.2
│
│
├── tests
│   ├── data
│   │   ├── goldilocks
│   │   │   ├── group0_1.q                  }
│   │   │   ├── group0_2.q                  } Variant Query Files for testing Goldilocks
│   │   │   ├── group1_1.q                  }
│   │   │   └── paths.g                     Paths File locating VQF testing files
│   │   │
│   │   ├── example.aqc.txt                 AQC Matrix example with non-consistent
│   │   │                                     intraclass target labels
│   │   ├── example.aqc.uniq.txt            AQC Matrix example with consistent
│   │   │                                     intraclass target labels
│   │   ├── example.bamcheck.baddups.txt    BAMcheckr'd example containing non matching
│   │   │                                     duplicate summary number entries
│   │   ├── example.bamcheck.dups.txt       BAMcheckr'd example with consistent
│   │   │                                     duplicated summary number entries
│   │   └── example.bamcheck.txt            Valid BAMcheckr'd example
│   │
│   ├── __init__.py                         Package definition
│   ├── aqcreader.py                        AQCReader testing suite
│   ├── bamcheckreader.py                   BamcheckReader testing suite
│   ├── frontier.py                         Frontier and Frontier utils testing suite
│   └── goldilocks.py                       Goldilocks testing suite
│
│
├── .gitignore
├── README.md
├── front.py                                Script using Frontier and scikit-learn for analysis
│                                             of auto_qc data and targets for training, testing
│                                             and documentation of decision tree classifiers.
├── msn_FinalReport_2014.pdf                The final version of the thesis write up
└── ratios.py                               A proof of concept file showing bamcheckr
                                              function can be implemented by Frontier

Other Contributions

Please see the following for examples of contributions to external projects made as a result of this project:

samtools

samtools #200: Fix arbitrary memory leaks in merge and split test harnesses
samtools #188: Add -b option to samtools merge manpage

bamcheckr

seq_autoqc #2: Fix quality_dropoff.r

Installation

Both the Frontier and Goldilocks packages require numpy for its efficient data containers. Additionally the front.py script requires the scikit-learn machine learning framework.

You can install these packages via pip:

pip install scikit-learn numpy

Although included with some distributions, for the plotting of decision trees as PDF files you may need to install graphviz and pydot via your distribution's package manager and pip, respectively.

yum install graphviz
pip install pydot

The R scripts require the R data analysis language to be installed via an appropriate package manager.

yum install R

Once installed, use the R environment to download and install the packages:

install.packages("ggplot2")
install.packages("reshape")
install.packages("plyr")
install.packages("pheatmap")

##Housekeeping

View documentation using pydoc (from this directory)

# Front AQC Module
pydoc front

# Frontier Package
pydoc Frontier
pydoc Frontier.frontier

# Frontier IO Subpackage
pydoc Frontier.IO
pydoc Frontier.IO.AbstractReader
pydoc Frontier.IO.AQCReader
pydoc Frontier.IO.BamcheckReader

# Goldilocks
pydoc Goldilocks
pydoc Goldilocks.goldilocks

Run tests

# Frontier
python -m tests/frontier
python -m tests/aqcreader
python -m tests/bamcheckreader

# Goldilocks
python -m tests/goldilocks