BGB_upload

Biopiece: BGB_upload

Description

Use BGB_upload to upload sequence or track to the Biopieces Genome Browser (BGB).

Usage

... | BGB_upload [options] <-u <user>> <-c <clade>> <-g <genome>> <-a assembly>

Options

[-?          | --help]                  #  Print full usage description.
[-x          | --no_stream]             #  Do not emit records.
[-u <string> | --user=<string>]         #  BGB user -  Default=<from ~/.biopiecesrc>
[-c <string> | --clade=<string>]        #  Clade.
[-g <string> | --genome=<string>]       #  Genome.
[-a <string> | --assembly=<string>]     #  Assembly.
[-t <string> | --track_name=<string>]   #  Track name.
[-T <string> | --track_type=<string>]   #  Track type [linear|wiggle]   -  Default=linear
[-f          | --force]                 #  Force overwrite of sequence.
[-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

read_fasta -i 454AllContigs.fna | BGB_upload -c Bacteria -g S.aureus_M1 -a 2009-02-07 -x

read_kiss -i test.kiss | BGB_upload -c Bacteria -g S.aureus_M1 -a 2009-02-07 -t 454_reads_no_clip -x

See also

read_fasta

read_kiss

BGB_list

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_upload is part of the Biopieces framework.

http://www.biopieces.org