lastZWriter

Documentation

Overview

Package lastZWriter takes in alignment information and creates a file that contains all necessary lastz jobs with all required parameters for any species listed, as well as creating all the directories where data will be stored when those jobs are run.

Index

• func AlignSetUp(pairwise string, species string, reference string, allDists string, m bool, ...) (par []string, mat string)
• func AlignSetUpSimple(pairwise string, species string, reference string)
• func BuildMatrices(mPath string)

Functions

func AlignSetUp

func AlignSetUp(pairwise string, species string, reference string, allDists string, m bool, mPath string) (par []string, mat string)

AlignSetUp takes in the path to the parent directory where all the individual fastas for alignment are being held. In this context the directory below "pairwise" is labeled by a species name, which then contains all the fastas for alignment. It also takes a single aligning species and reference species, as well as a text file that describes the distance between all species in the alignment from all other species in the alignment. This file is make with Phylogenetic Analysis with Space/Time Models or PHAST all_dists function. AlignSetUp then calls its helper functions and returns the results of findParameters.

func AlignSetUpSimple

func AlignSetUpSimple(pairwise string, species string, reference string)

AlignSetUpSimple creates a different output file name structure: ref.species/qName/tName.qName.axt AlignSetupSimple does not generate parameter, matrix

func BuildMatrices

func BuildMatrices(mPath string)

BuildMatrices is used when the user defines m as false and wants to write each potential matrix for the lastZ alignment to a specified directory (mPath).