Preface - Quickstart

For those who don’t want to read the docs before jumping in, try the code snippets below to get going with parabam as quickly as possible.

First open your terminal and install parabam:

sudo pip install parabam

Then in your terminal create a directory to run your parabam analysis on:

cd ~
mkdir parabam-analysis
cd parabam-analysis

Now let’s create an instruction file for our analysis. Create the file:

touch instruction.py

Open the instruction.py file in your favourite text editor and paste this code into your new file:

def rule(read,constants,master):
        if "ATCGATCG" in read.seq:
                return True
        return False

Now locate the BAM file you wish to run parabam analysis on. Then type the following into your terminal command line:

parabam subset -v2 -i instructions -b /path/to/bam/file_name.bam

After a while (depending on how large your input BAM file was) parabam will be finished and you will be left with a result in <file_name>_subset.bam.

Congratulations - you just ran parabam subset. Read on to find out more.

Introduction

So, you’ve got this far through the documentation which means you are at least reasonably curious about parabam. Great!

The goal of parabam is to allow the user to inspect large BAM files in a timely manner whilst making the most of their computational resources and without having to write too much code. The most direct way to use parabam is via the command line, but it can also be invoked programaticaly via interface classes, and also support full incorporation via OOP inheritance.

If any of the words in the pragraph above don’t make sense: don’t worry. Parabam is easy to run for beginniners. All you need is to know a little bit of Unix (how to make and change directories) and a little bit of Python. Just follow the instructions and you’ll be conducting high-throughput analysis in no time. If you have any questions, feel free to email me.

Alternatively, if you understood every word of the above and want to get more in-depth with parabam then pay close attention to the programmatic and inheritance based interfaces.

Installing parabam

First, we have to get parabam running on your computer. This section will guide you through installing parabam.

Currently, parabam is only available to POSIX compliant systems (Linux, Mac OSX, etc) and not Windows.

The easy way

The easiest way to install parabam is as follows:

sudo pip install parabam

This will also place an executable in a location on your path. So after typing this command you should be able to do the following:

>>> parabam
>>> parabam
    ----------------------------------------------------------------

    About:
        Parabam - analyse bam file in parallel

    Usage:
        parabam <command> [options] instruction:{Python} input:{BAM} output:{BAM/CSV}

    Command:

        stat     Genereate stats regarding the BAM file
        subset   Create a subsetted BAM file

If typing parbam into your terminal yields the result above, you have succesfully installed parabam.

The manual way

Some users may wish to install from source. The source may be downloaded from here. This part of the documentation isn’t written yet, but if you want to do this you probably know how to do it anyway.

The precompiled way

If you really can’t be bothered, then perhap you could try some of the precompiled binaries listed here.

Simply copy these to a location on your path and type:

It should work out of the box if you picked the right binary.

Running parabam on a cluster

Some users may wish to run parabam on a high powered computing service like a cluster. On systems such as these you may not have root access, so you may not be able to install to the Python system directories. In these cases you may wish to use parabam within a virtualenv.