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get_genome_phastcons
Martin Asser Hansen edited this page Oct 2, 2015
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get_genome_phastcons extracts phastcons scores from a specified genome that has been preformatted with format_genome. Ths phastcons scores can be extracted either explicitly or using BED/PSL/BLAST entries in the stream. Formatted genomes can be listed using list_genomes.
get_genome_phastcons [options] -g <genome>
or
... | get_genome_phastcons [options] -g <genome>
[-? | --help] # Print full usage description.
[-g <genome> | --genome=<genome>] # Genome to get phastcons scores from.
[-c <string> | --chr=<string>] # Chromosome with requested scores.
[-b <uint> | --beg=<uint>] # Begin position of interval (first residue=1).
[-e <uint> | --end=<uint>] # End position of interval.
[-l <uint> | --len=<uint>] # Length of interval.
[-f <uint> | --flank=<uint>] # Include flanking region.
[-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_phastcons -g hg18 -c chr1 -b 1 -e 10 # Get the first 10 phastcons scores from human genome chr1.
get_genome_phastcons -g hg18 -c chr1 -b 1 -l 10 # Get the first 10 phastcons scores from human genome chr1.
... | get_genome_phastcons -g mm8 -f 50 # Get phastcons scores including 50nt flanks 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_phastcons is part of the Biopieces framework.