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upload_to_ucsc
upload_to_ucsc handles uploading data to the UCSC Genome Browser Database as custom tracks of
BED, PSL, or Wiggle type. A variety of different data formats can be read with the appropriate
Biopieces or the result from a number or other Biopieces can be used directly.
upload_to_ucsc creates a table in the MySQL database and appends an entry in the ~/ucsc/my_tracks.ra file.
The following data formats are supported:
- BED read_bed
- PSL read_psl
- BLAST read_blast_tab
- fixedStep read_fixedstep (creates a Wiggle track)
Results from the following Biopieces can be uploaded directly to the UCSC Genome Browser:
upload_to_ucsc requires a local mirror of the UCSC Genome Browser to be installed.
http://hgdownload.cse.ucsc.edu/downloads.html
... | upload_to_ucsc [options] <-d <genome>> <-t <string>>
[-? | --help] # Print full usage description.
[-d <string> | --database=<string>] # Genome database to upload track to.
[-t <string> | --table=<string>] # Table name of track - NB! prefix with initials. e.g.: mah_test.
[-x | --no_stream] # Do not emit records.
[-s <string> | --short_label=<string>] # Short label for track - Default=<table>
[-l <string> | --long_label=<string>] # Long label for track - Default=<table>
[-g <string> | --group=<string>] # Track group name - Default=<env logname>
[-p <float> | --priority=<float>] # Track display priority - Default=1
[-u | --use_score] # Use the score to grey shade the track.
[-V <string> | --visibility=<string>] # Track visibility: hide|dense|squish|pack|full - Default=pack
[-c <string> | --color=<string>] # Track color e.g. '147,73,42' - Default=<random>
[-C | --check] # Check the integrity of the record.
[-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.
To read in a BED file, first read it with read_bed:
read_bed -i test.bed | upload_to_ucsc -d danRer4 -t mah_test -x
This following entry is appended to the ~/ucsc/my_tracks.ra file:
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
# Track added by 'upload_to_ucsc' 2008-07-03 17:46:58
# Database danRer4
track mah_test
shortLabel mah_test
longLabel mah_test
group m.hansen
priority 1
visibility pack
color 99,96,140
type bed 6
# //
To create a Wiggle track from a fixedStep file consider the following fixedStep file test.fixedStep:
fixedStep chrom=chr2L start=1 step=1
1.869232
1.939519
1.934498
1.934498
1.863323
1.863323
1.863323
1.863323
1.863323
To create a Wiggle track from this file, read it with read_fixedstep:
read_fixedstep -i test.fixedstep | upload_to_ucsc -d <database> -t <table> -x
Read more about Wiggle format here:
http://genome.ucsc.edu/goldenPath/help/wiggle.html
If you want to visualize RNA secondary structure the table name must include rnaSecStr.
See fold_seq for more information.
Martin Asser Hansen - Copyright (C) - All rights reserved.
August 2007
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
upload_to_ucsc is part of the Biopieces framework.