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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)
use pip:
$ pip install BamTyper##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
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.