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read_ucsc_config
Martin Asser Hansen edited this page Oct 2, 2015
·
5 revisions
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
---
read_ucsc_config [options] -i <.rc file(s)>
[-? | --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.
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'
Martin Asser Hansen - Copyright (C) - All rights reserved.
November 2008
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
read_ucsc_config is part of the Biopieces framework.