get_genome_align

Biopiece: get_genome_align

Description

get_genome_align extracts an alignment from multiple genome alignment either explicitly or using BED/PSL/BLAST entries in the stream.

get_genome_align uses mafFrag from the UCSC Genome Browser toolset and requires a local mirror of the UCSC Genome Browser to be installed.

http://hgdownload.cse.ucsc.edu/downloads.html

Usage

get_genome_align [options] -g <genome>

or

... | get_genome_align [options] -g <genome>

Options

[-?          | --help]               #  Print full usage description.
[-g <genome> | --genome=<genome>]    #  Genome to get alignment from.
[-c <string> | --chr=<string>]       #  Chromosome with requested alignment.
[-b <uint>   | --beg=<uint>]         #  Begin position of alignment (first residue=1).
[-e <uint>   | --end=<uint>]         #  End position of alignment.
[-l <uint>   | --len=<uint>]         #  Length of alignment.
[-s <string> | --strand=<string>]    #  Strand                       -  Default=+
[-I <file!>  | --stream_in=<file!>]  #  Read input from stream file  -  Default=STDIN
[-O <file>   | --stream_out=<file>]  #  Write output to stream file  -  Default=STDOUT
[-v          | --verbose]            #  Verbose output.

Examples

get_genome_align -g hg18 -c chr1 -b 1 -e 10  #  Get the first 10 nucleotides multiz alignment of human genome chr1.
get_genome_align -g hg18 -c chr1 -b 1 -l 10  #  Get the first 10 nucleotides multiz alignment of human genome chr1.
... | get_genome_align -g mm8 -s '-'         #  Get the reverse complement alignment of mouse BED/PSL/BLAST entries.

See also

get_genome_seq

get_genome_phastcons

Author

Martin Asser Hansen - Copyright (C) - All rights reserved.

[email protected]

August 2007

License

GNU General Public License version 2

http://www.gnu.org/copyleft/gpl.html

Help

get_genome_align is part of the Biopieces framework.

http://www.biopieces.org