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write_fixedstep
write_fixedstep outputs fixedStep format, which is one of three formats of the wiggle type in the UCSC Genome Browser. The format consists of entries like this:
fixedStep chrom=chr2L start=1 step=1
0.771
0.780
0.772
0.785
0.780
0.761
0.722
0.710
0.716
0.703
Which is generated from Biopiece records containing either CHR or S_ID keys and
either CHR_BEG or S_BEG keys along with VALS and STEP keys:
STEP: 1
CHR_BEG: 1
VALS: 0.771;0.780;0.772;0.785;0.780;0.761;0.722;0.710;0.716;0.703
CHR: chr2L
---
It is possible to specify an alternative key to VALS holding the fixedStep values
using the -k switch and an alternative step size using the -s switch.
For more about the fixedStep wiggle format:
http://genome.ucsc.edu/goldenPath/help/wiggle.html
... | write_fixedstep [options]
[-? | --help] # Print full usage description.
[-x | --no_stream] # Do not emit records.
[-k <string> | --key=<string>] # Key holding fixedStep values - Default=VALS
[-s <uint> | --step=<uint>] # Step size - Default=1
[-o <file> | --data_out=<file>] # Write result to file.
[-I <file!> | --stream_in=<file!>] # Read input from stream file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output to stream file - Default=STDOUT
[-Z | --compress] # Compress output using gzip.
[-v | --verbose] # Verbose output.
... | write_fixedstep
Or using speficied values:
... | write_fixedstep -k CONTIG
Martin Asser Hansen - Copyright (C) - All rights reserved.
August 2007
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
write_fixedstep is part of the Biopieces framework.