GenomicTools: an open source platform for developing highthroughput analytics in genomics - Open Source Software in Life Science Research - page 190

Table 8.1

Summary of operations of the genomic_regions tool

Operation Description

align Aligns sequences to reference genome (line-based)

bed Converts input regions to BED format (line-based)

bounds Checks interval against chromosome bounds and

removes invalid intervals (line-based)

center Prints center interval (line-based)

connect Connects intervals from minimum start to maximum stop

(line-based)

diff Computes the difference between successive intervals

(line-based)

dist Computes distances between successive intervals

(line-based)

divide Divides intervals in the middle (line-based)

fi x Removes invalid intervals, i.e. start<1 or start>stop

(line-based)

gdist Computes distances of successive regions (fi le-based)

int Computes the intersection of input intervals (line-based)

inv Inverts regions given the genome chromosomal

boundaries (fi le-based)

link Links consecutive regions to produce a non-overlapping

set (fi le-based)

n Computes total interval length, including possible

overlaps (line-based)

pos Modifi es interval start/stop positions (line-based)

￿ ￿ ￿ ￿ ￿

reg Converts to REG format (line-based)

rnd Randomizes region across entire genome (line-based)

select Selects a subset of intervals according to their relative

start positions (line-based)

shift Shifts interval start/stop positions (line-based)

shiftp Shifts interval 5'/3' positions (line-based)

shuffl e Shuffl es intervals within given reference region

(line-based)

sort Sorts intervals (line-based)

split Splits regions into their intervals which are printed on

separate lines (line-based)

strand Modifi es interval strand information (line-based)