MIXR: Mismatching Isoform eXon Remover

A package for the removal of exons with mismatching isoforms as described in:

A meta-analysis of bat phylogenetics based on whole genomes and transcriptomes of 18 species

John A. Hawkins, Maria E. Kaczmarek, William H. Press, Sara L. Sawyer

(in review)

Installation

The following instructions should work across platforms, except that installing virtualenv with apt-get is Ubuntu specific. For other platforms, install virtualenv appropriately if desired.

First, clone the repository to a local directory:

git clone https://github.com/hawkjo/mixr.git

Optionally, you can install into a virtual environment (recommended):

sudo apt-get install -y virtualenv
cd mixr
virtualenv envmixr
. envmixr/bin/activate

Now install required packages and mixr using pip:

pip install -r requirements.txt && python setup.py install

Usage

Usage:
  mixr <in_prot_dir> <in_cds_dir> <in_exon_pos_file> <out_prot_dir> <out_cds_dir> <out_exon_pos_file> [-v | -vv | -vvv]

Options:
  -h --help     Show this screen.
  --version     Show version.

Required input:

Input protein MSA directory
Input CDS MSA directory
Input protein exon position file
Output protein MSA directory
Output CDS MSA directory
Output protein exon position file

Exon position file format

The exon position file must have the following tab-delimited, one line per MSA:

Name of MSA file (without directory)
The zero-based starting index position of each exon (protein coordinates)
The length of the MSA (protein coordinates)

See the example given in the examples folder.

MSA requirements

Some non-trivial number of alignments must contain sequences from all species.
The record id of each sequence (the defline until the first space) must be the species name.
The file names for corresponding CDS and protein MSAs must be the same.

liu-wq / mixr