get_genome_align
Martin Asser Hansen edited this page Oct 2, 2015
·
5 revisions
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
get_genome_align [options] -g <genome>
or
... | get_genome_align [options] -g <genome>
[-? | --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.
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.
Martin Asser Hansen - Copyright (C) - All rights reserved.
August 2007
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
get_genome_align is part of the Biopieces framework.