Lincoln D. Stein

NAME

axt2phy.pl - convert AXT pairwise alignment files to GFF, Fasta and wig files

SYNOPSYS

  % axt2phy.pl -species speciesname -axtin AXTinputfile

DESCRIPTION

This program reads an AXT pairwise alignment file and creates the GFF, Fasta and binary wig files to be used for the phylogenetic glyph for the Generic Genome Browser.

AXT alignment files are used by UCSC Genome Broser. A description of the AXT files can be found at:

http://genome.ucsc.edu/goldenPath/help/axt.html

NOTES

The GFF entries make use of the GFF3 CIGAR format which creates gap entries as specified by:

http://www.sequenceontology.org/gff3.shtml

COMMAND-LINE OPTIONS

Required

    -species           Name or label of aligning species
    -axtin             Filename of axt file
    

Optional

    -fa_width          Width of Fasta entries
                         Default = 80
    wigpath            Path of output wig file
                         Default = "."
    wigout             Output wig file
                         Default = axtin_<timestamp>.wig
    gffout             Output GFF file
                         Default = axtin_<timestamp>.gff
    fastaout           Output Fasta file
                         Default = axtin_<timestamp>.fa
    append             Option to append GFF and Fasta entries to file
                         Default = 0
    start              Minimum coordinate for entries to be considered
                         Default = 0
    stop               Maximum coordinate for entries to be considered
                         Default = 0 (off)
    chr                Chromosome of reference sequences to be considered
                         Default = "" (off)

Many options have aliases and can be abbreviated.

SEE ALSO

Bio::Graphics::Wiggle, Bio::Graphics::Glyph::phylo_align, Bio::Graphics::Glyph::wiggle_xyplot, Bio::Graphics::Glyph::wiggle_density, Bio::Graphics::Panel, Bio::Graphics::Glyph, Bio::Graphics::Feature, Bio::Graphics::FeatureFile

AUTHOR

H. Mark Okada <hmokada@hotmail.com>.

Copyright (c) 2008

This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL (either version 1, or at your option, any later version) or the Artistic License 2.0. Refer to LICENSE for the full license text. In addition, please see DISCLAIMER.txt for disclaimers of warranty.