Author:         Martin Asser Hansen - Copyright (C) - All rights reserved

Contact:        mail@maasha.dk

Date:           February 2009

License:        GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)

Description:    Extract phastcons scores from a genome either explicitly or using BED/PSL/BLAST entries in stream.

Usage:          $script [options] -g <genome>
Usage:          ... | $script [options] -g <genome>

Options:   [-g <genome> | --genome=<genome>]    -  Genome to get phastcons scores from.
Options:   [-c <string> | --chr=<string>]       -  Chromosome with requested scores.
Options:   [-b <int>    | --beg=<int>]          -  Begin position of interval (first residue=1).
Options:   [-e <int>    | --end=<int>]          -  End position of interval.
Options:   [-l <int>    | --len=<int>]          -  Length of interval.
Options:   [-f <int>    | --flank=<int>]        -  Include flanking region.
Options:   [-I <file>   | --stream_in=<file>]   -  Read input from stream file  -  Default=STDIN
Options:   [-O <file>   | --stream_out=<file>]  -  Write output to stream file  -  Default=STDOUT

Examples:  $script -g hg18 -c chr1 -b 1 -e 10  -  Get the first 10 phastcons scores from human genome chr1.
Examples:  $script -g hg18 -c chr1 -b 1 -l 10  -  Get the first 10 phastcons scores from human genome chr1.
Examples:  ... | $script -g mm8 -f 50          -  Get phastcons scores including 50nt flanks of mouse BED/PSL/BLAST entries.

Keys in:  REC_TYPE  -  Optional record type (BED, PSL, or BLAST).
Keys in:  CHR       -  Chromosome (for use with BED record type).
Keys in:  CHR_BEG   -  Chromosome begin.
Keys in:  CHR_END   -  Chromosome end.
Keys in:  S_ID      -  Chromosome       (for use with PSL and BLAST record type).
Keys in:  S_BEG     -  Chromosome begin (for use with PSL and BLAST record type).
Keys in:  S_END     -  Chromosome end   (for use with PSL and BLAST record type).

Keys out: CHR        -  Chromosome.
Keys out: CHR_BEG    -  Chromosome begin.
Keys out: CHR_END    -  Chromosome end.
Keys out: PHASTCONS  -  Comma separated list of phastcons scores.