mafStrander

3 October 2012

Author

Dent Earl

Description

mafStrander is a program to coerce a particular strandedness out for all blocks based the strandedness of a target sequence. When a block contains the target sequence but in the flipped orientation (relative to the --strand option) then the block is flipped, i.e. all start coordinates are transformed, and all sequence fields are reverse-complemented. If the block contains the target sequence multiple times and with conflicing strands (i.e. both + and - strands are observed), then nothing is done.

Installation

1. Download the package.
2. cd into the directory.
3. Type make.

Use

mafStrander --maf alignment.maf --seq hg18 --strand + > positive.maf

Options

• -h, --help show this help message and exit.
• --maf input alignment maf file.
• --seq sequence to base block strandedness upon. (string comparison only done for length of input, i.e. --seq=hg18 will match hg18.chr1, hg18.chr2, etc etc)
• --strand strand to enforce, when possible. may be + or -, defaults to +.

Example

$ mafStrander --maf alignment.maf --seq hg18 --strand + > positive.maf