calc_density
calc_density read BED entries from stream and calculate the density (count or total SCOREs of BED entries) within each sliding window.
... | calc_density [options]
[-? | --help] # Print full usage description.
[-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.
[-w <window_size> | --window_size=<sliding window size>] # Set the size of sliding window - Default=10000
[-s <increment> | --step_size=<increment>] # Set the size of increment - Default=window_size
Consider the following BED entries in the file test.bed:
Chr10 1026 1051
Chr10 10027 10051
Chr10 13032 13056
Chr10 11351 11368
To read in this BED file, use read_bed to calculate density distribution over a chromosome:
read_bed -i test.bed | calc_density -w 10000 -s 5000
(all records from the input-stream)
---
WIN_CHR: Chr10
WIN_CHR_BEG: 0
WIN_CHR_END: 10000
WIN_DENSITY: 1
---
WIN_CHR: Chr10
WIN_CHR_BEG: 5000
WIN_CHR_END: 15000
WIN_DENSITY: 3
---
WIN_CHR: Chr10
WIN_CHR_BEG: 10000
WIN_CHR_END: 20000
WIN_DENSITY: 3
---
All records piped into the calc_density are kept and emitted ahead of its actual results, so that they can be used for other biopieces.
If a BED file contains SCORE field, calc_density uses the SCORE for the density calculation.
For example, for a BED file (test2.bed) shown below:
Chr10 1026 1051 chr10_tag1 1
Chr10 10027 10051 chr10_tag2 10
Chr10 13032 13056 chr10_tag3 2
Chr10 11351 11368 chr10_tag4 3
The result of calc_density is:
read_bed -i test2.bed | calc_density -w 10000 -s 5000
(all records from the input-stream)
---
WIN_CHR: Chr10
WIN_CHR_BEG: 0
WIN_CHR_END: 10000
WIN_DENSITY: 1
---
WIN_CHR: Chr10
WIN_CHR_BEG: 5000
WIN_CHR_END: 15000
WIN_DENSITY: 15
---
WIN_CHR: Chr10
WIN_CHR_BEG: 10000
WIN_CHR_END: 20000
WIN_DENSITY: 15
---
The window slide from the beginning of a chromosome through to the last BED entry in the same chromosome.
For example, for a BED file below (test3.bed):
Chr10 37301 37325 Chr10_tag5 7
The result of calc_density is:
read_bed -i test3.bed | calc_density -w10000
(all records from the input-stream)
---
WIN_CHR: Chr10
WIN_CHR_BEG: 0
WIN_CHR_END: 10000
WIN_DENSITY: 0
---
WIN_CHR: Chr10
WIN_CHR_BEG: 10000
WIN_CHR_END: 20000
WIN_DENSITY: 0
---
WIN_CHR: Chr10
WIN_CHR_BEG: 20000
WIN_CHR_END: 30000
WIN_DENSITY: 0
---
WIN_CHR: Chr10
WIN_CHR_BEG: 30000
WIN_CHR_END: 40000
WIN_DENSITY: 7
---
Chol-Hee JUNG - Copyright (C) - All rights reserved.
December 2010
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
calc_density is part of the Biopieces framework.