flankTE

Scripts to extract SNPs in the flanking regions of TE insertions. SNPs are extracted from whole-genome consensus sequences of the sample WGS datasets used for the TE calling analyses.

There are two types of the scripts.

1. flankTE-SNP.py extract various types of SNP that support specific groupings of the samples, that need to be configured in the script itself.
2. flankTE-tree.py Extract SNPs that according to various branches on a species tree. This also requires configuration in the script file.

Dependencies

Resolve dependencies i.e. using pip

pip install biopython pyfaidx dendropy ete2

flankTE runs on Python 2.7

Usage

python flankTE-tree.py 
usage: flankTE-tree.py [-h] -i FASTA -f FLANK [-o OVERLAPPING]
                                [-w WINDOWSIZE] -m MATRIX

Command line arguments

• -i Whole-genome consensus sequence (fasta format), supplied for each taxa that is analysed, e.g. -i A.cons.fa -i B.cons.fa ...
• -f Size of flanking regions in base pairs (i.e. 10000). Note that the first 500 bp surrounding the breakpoint will not be analysed in order to account for spuriously mapped reads.
• -o True/[False]. Indicate whether the window size should be extended in each round (True) or if windows should be distinct regions of size [windowssize] (This is the default)
• -w Window size in base pairs [1000]
• -m Tab-separated files with presence information on TE insertions (see below for details).

Overlapping windows

The default behaviour is to count SNPs in distinct windows of size W surrounding the insertion site (breakpoint).

|<--W-4-->|<--W-3-->|<--W-2-->|<--W-1-->|<500bp omitted><BREAKPOINT><500bp omitted>|<--W+1-->|<--W+2-->|<--W+3-->|<--W+4-->|

With -o True the program returns the increasing window sizes. This is most meaningful if the window size equals the flanking size, i.e. only a specific window around the breakpoint is investigated.

Window 1:         |<--W-->|<500bp omitted><BREAKPOINT><500bp omitted>|<--W-->|

Window 2: |<------W------>|<500bp omitted><BREAKPOINT><500bp omitted>|<------W------>|

etc...

Format of matrix file

chr1    10000  10001    sampleA,sampleB
chr1    20000  20001    sampleA,sampleC
...