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remove_ucsc_tracks
remove_ucsc_tracks removes custom UCSC Genome Browser tracks (or tables) from both the MySQL database and
configuration files. The database is specified with the -d switch and tracks to be removed can be
specified with the -t switch and/or tracks are removed if they exactly match the value of given
record keys of records in the stream.
NB! the config_file will be replaced with machine parsed results so that notes etc. is lost.
A backup configuration file is created with the a ~ suffix.
remove_ucsc_tracks [options] <-d <database>> <-t <tracks>>
or
... | remove_ucsc_tracks [options] <-d <database>> <-k <keys>>
[-? | --help] # Print full usage description.
[-d <string> | --database=<string>] # MySQL database.
[-t <list> | --tracks=<list>] # Comma separated list of tracks.
[-k <list> | --keys=<list>] # Comma separated list of keys.
[-c <file!> | --config_file=<file!>] # Configuration file - Default=~/ucsc/my_tracks.ra
[-u <string> | --user=<string>] # MySQL user name - Default=<fetched from .hg.conf>
[-p <string> | --password=<string>] # MySQL password - Default=<fetched from .hg.conf>
[-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 remove a specific track:
remove_ucsc_tracks -d dm3 -t mah_RM_new
To assimilate a list of tracks to remove do:
read_mysql -d dm3 -q 'show tables' | grab -p test_to_remove | remove_ucsc_tracks -d dm3 -k Tables_in_dm3 -x
Note that read_mysql with the show tables query outputs records of the type:
Tables_in_dm3: mah_test_to_remove
---
Thus we know that the -k value should be Tables_in_dm3.
Martin Asser Hansen - Copyright (C) - All rights reserved.
November 2008
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
remove_ucsc_tracks is part of the Biopieces framework.