read_ucsc_config

Biopiece: read_ucsc_config

Description

read_ucsc_config read in UCSC Genome Browser track configuration from one or more .ra files. Each track is converted to a Biopiece records and emitted in the stream and will looks something like this:

priority: 1
color: 246,186,129
visibility: pack
group: h.oey
shortLabel: GSE13483_hg18_ES_cells
track: ho_GSE13483_human_ES_cells_Divergent_transcription
type: bed 6
longLabel: GSE13483_human_ES_cells_Divergent_transcription_from_active_promoters
---

Usage

read_ucsc_config [options] -i <.rc file(s)>

Options

[-?          | --help]               #  Print full usage description.
[-i <files!> | --data_in=<files!>]   #  Comma separated list of files or glob expression to read.
[-n <uint>   | --num=<uint>]         #  Limit number of records to read.
[-I <file!>  | --stream_in=<file!>]  #  Read input stream from file  -  Default=STDIN
[-O <file>   | --stream_out=<file>]  #  Write output stream to file  -  Default=STDOUT
[-v          | --verbose]            #  Verbose output.

Examples

To read all track entries from a file:

read_ucsc_config -i mytracks.ra

To read in only 10 records from a file:

read_ucsc_config -n 10 -i mytracks.ra

To read all entries from multiple files:

read_ucsc_config -i mytracks1.ra,mytracks2.ra

To read entries from multiple files using a glob expression:

read_ucsc_config -i '*.ra'

See also

write_ucsc_config

remove_ucsc_track

upload_to_ucsc

Author

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

mail@maasha.dk

November 2008

License

GNU General Public License version 2

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

Help

read_ucsc_config is part of the Biopieces framework.

http://www.biopieces.org