BamTyper 0.2.6

Working with paired reads in BAM format

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# Overview

Ability to work out the orientation and insert size of a paired read data file
Can estimate relative orientation and gap between pairs of contigs in the bam file (Useful for scaffolding)

# Installation

use pip:

```sh
$ pip install BamTyper
```
# Usage
##As a library:
###Get the type of the reads:
#!/usr/bin/env python
from bamtyper.utilities import BamParser as BTBP
BP = BTBP()
bam_types = BP.getTypes(bamFiles)

Where:
bamFiles - a list of BAM filenames

Returns:
bam_types - a dict containing information about the insert size and
relative orientation of reads in the bam file
{ bam1 : (type, ins, stdev), ... }
Where:
type - orientation type:
0 : OUT : <--- --->
1 : SAME : ---> --->
2 : IN : ---> <---
ins - estimated insert size (of original DNA fragment)
stdev - standard deviation of insert size

###Get linking pairs:
#!/usr/bin/env python
from bamtyper.utilities import BamParser as BTBP
BP = BTBP()
(links, ref_lengths, coverages) = BP.getLinks(bamFiles, doCoverage=True)

Where:
bamFiles - a list of BAM filenames

Returns:
links - a dict containing information about links between two contigs
{c1: (c2, num_links, link_type, gap), ... }
Where:
num_links - Number of paired reads confirming the link
link_type - Relative orientation of the two contigs (Start and End)
SS, SE, ES, EE or ERROR
gap - Estimated gap between te two contigs

coverages - a dict containing the FRAGMENT coverage of each contig n the bam file(s)
{c1 : (cov1, cov2, ..., covN), ... }

ref_lengths - a dict containing the lengths of all contigs
{c1 : len, ... }

Notes:
bamtyper will automatically work out the orientation and insert size of the
reads in each bam file and base it's estimations of link_type and gap on this

##On the command line:

bamtyper type - Parse BAM files and determine reads type

$ bamtyper type bamfile.bam

Determining OT for BAM 'bamfile'
Orientation: IN Insert: 301, Stdev: 29

bamtyper links - Parse BAM files and get linking reads

Usage 1:

$ bamtyper links bamfile.bam

1.
contig2 , [ contig1 , 39 , SE , 69 ]
contig1 , [ contig2 , 39 , ES , 69 ]

implies a layout which looks like:

---1--> 69bp ---2-->

2.
contig3 , [ contig2 , 3 , SS , 58 ]
contig2 , [ contig3 , 3 , SS , 58 ] , [ contig1 , 4 , EE , 45 ]
contig1 , [ contig2 , 4 , EE , 45 ]

implies a layout which looks like:

---1--> 45bp <--2--- 58bp ---3-->

Usage 2: report FRAGMENT coverage too!

$ bamtyper links bamfile1.bam bamfile2.bam -c

contig3 , [ contig2 , 3 , SS , 58 ]
contig2 , [ contig3 , 3 , SS , 58 ] , [ contig1 , 4 , EE , 45 ]
contig1 , [ contig2 , 4 , EE , 45 ]
contig3 0.6206 0.5234
contig2 0.6558 0.0123
contig1 0.6523 0.5634

Where:
contig3 0.6206 0.5234

Reports 0.6206 fragments per base in bamfile1 and 0.5234 in bamfile2
If these were 100bp reads then this would imply
coverages of 62x and 52x respectively

# Administration

Project home page, info on the source tree, documentation, issues and how to contribute, see http://github.com/minillinim/BamTyper

This software is currently unpublished.

Copyright © 2012 Michael Imelfort. See LICENSE.txt for further details.