read_fixedstep
Martin Asser Hansen edited this page Oct 2, 2015
·
5 revisions
read_fixedstep reads the 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 results in Biopiece records like this:
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
REC_TYPE: fixed_step
---
For more about the fixedStep wiggle format:
http://genome.ucsc.edu/goldenPath/help/wiggle.html
read_fixedstep [options] -i <fixedstep 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 fixedStep entries from a file:
read_fixedstep -i test.wig
To read in only 10 records from a fixedStep file:
read_fixedstep -n 10 -i test.wig
To read all fixedStep entries from multiple files:
read_fixedstep -i test1.wig,test2.wig
To read fixedStep entries from multiple files using a glob expression:
read_fixedstep -i '*.wig'
Martin Asser Hansen - Copyright (C) - All rights reserved.
August 2007
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
read_fixedstep is part of the Biopieces framework.