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Martin Asser Hansen edited this page Oct 1, 2015 · 5 revisions

Biopiece: read_fixedstep

Description

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

Usage

read_fixedstep [options] -i <fixedstep file(s)>

Options

[-?          | --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.

Examples

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'

See also

write_fixedstep

Author

Martin Asser Hansen - Copyright (C) - All rights reserved.

mail@maasha.dk

August 2007

License

GNU General Public License version 2

http://www.gnu.org/copyleft/gpl.html

Help

read_fixedstep is part of the Biopieces framework.

http://www.biopieces.org

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