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Martin Asser Hansen edited this page Oct 2, 2015 · 6 revisions

Biopiece: BGB_read_track

Description

BGB_read_track reads all records from a specified Biopieces Genome Browser (BGB) track into the stream as KISS type records.

Read more about the KISS format here:

http://code.google.com/p/biopieces/wiki/KissFormat

Usage

BGB_read_track <-u user> <-c clade> <-g genome> <-a assembly> <-t track> [options]

Options

[-?          | --help]               #  Print full usage description.
[-u <string> | --user=<string>]      #  User                           -  Default=<from ~/.biopiecesrc>
[-c <string> | --clade=<string>]     #  Clade.
[-g <string> | --genome=<string>]    #  Genome.
[-a <string> | --assembly=<string>]  #  Assembly version.
[-t <string> | --track=<string>]     #  Track to read.
[-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

BGB_read_track -u maasha -c Bacteria -g S.aureus_COL -a 2006-02-21 -t 05_GenBank_Annotation

See also

BGB_list

BGB_upload

BGB_intersect

Author

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

mail@maasha.dk

December 2009

License

GNU General Public License version 2

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

Help

BGB_read_track is part of the Biopieces framework.

http://www.biopieces.org

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