App::Rangeops - operates ranges and links of ranges on chromosomes
rangeops <command> [-?h] [long options...]
-? -h --help show help
Available commands:
commands: list the application's commands
help: display a command's help screen
circos: range links to circos links or highlight file
clean: replace ranges within links, incorporate hit strands and remove nested links
connect: connect bilaterial links into multilateral ones
create: create blocked fasta files from range links
filter: filter links by numbers of ranges or length difference
merge: merge overlapped ranges via overlapping graph
replace: replace ranges within links and incorporate hit strands
sort: sort links and ranges within links
See rangeops commands for usage information.
Types of links:
-
Bilateral links
I(+):13063-17220 I(-):215091-219225 I(+):139501-141431 XII(+):95564-97485 -
Bilateral links with hit strand
I(+):13327-17227 I(+):215084-218967 - I(+):139501-141431 XII(+):95564-97485 + -
Multilateral links
II(+):186984-190356 IX(+):12652-16010 X(+):12635-15993 -
Merge files aren't links
I(-):13327-17227 I(+):13327-17227
Steps:
sort
|
v
clean -> merge
| /
| /
v
clean
|
V
connect
|
v
filter
Qiang Wang [email protected]
This software is copyright (c) 2016 by Qiang Wang.
This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.