# intspan
[](https://github.com/wang-q/intspan/actions)
[](https://github.com/wang-q/intspan/actions)
[](https://ci.appveyor.com/project/wang-q/intspan)
[](https://codecov.io/github/wang-q/intspan?branch=master)
[](https://crates.io/crates/intspan)
[](https://github.com//wang-q/intspan)
## Install
Current release: 0.6.7
```bash
cargo install intspan
# or
brew install intspan
```
## SYNOPSIS
* `spanr`
```text
$ spanr help
spanr 0.6.1
wang-q <wang-q@outlook.com>
`spanr` operates chromosome IntSpan files
USAGE:
spanr [SUBCOMMAND]
OPTIONS:
-h, --help Print help information
-V, --version Print version information
SUBCOMMANDS:
combine Combine multiple sets of runlists in a yaml file
compare Compare 1 YAML file against others
convert Convert runlist file to ranges file
cover Output covers on chromosomes
coverage Output detailed depths of coverages on chromosomes
genome Convert chr.size to runlists
gff Convert gff3 to covers on chromosomes
help Print this message or the help of the given subcommand(s)
merge Merge runlist yaml files
range Convert runlist file to ranges file
some Extract some records from a runlist yaml file
span Operate spans in a YAML file
split Split a runlist yaml file
stat Coverage on chromosomes for runlists
statop Coverage on chromosomes for one YAML crossed another
```
* `linkr`
```text
$ linkr help
linkr 0.6.1
wang-q <wang-q@outlook.com>
`linkr` operates ranges on chromosomes and links of ranges
USAGE:
linkr [SUBCOMMAND]
OPTIONS:
-h, --help Print help information
-V, --version Print version information
SUBCOMMANDS:
circos Convert links to circos links or highlights
clean Replace ranges within links, incorporate hit strands and remove nested links
connect Connect bilateral links into multilateral ones
filter Filter links by numbers of ranges or length differences
help Print this message or the help of the given subcommand(s)
merge Merge overlapped ranges via overlapping graph
sort Sort links and ranges within links
```
* `ovlpr`
```text
$ ovlpr help
ovlpr 0.6.1
wang-q <wang-q@outlook.com>
`ovlpr` operates overlaps between sequences
USAGE:
ovlpr [SUBCOMMAND]
OPTIONS:
-h, --help Print help information
-V, --version Print version information
SUBCOMMANDS:
covered Covered regions from .ovlp.tsv files
help Print this message or the help of the given subcommand(s)
paf2ovlp Convert minimap .paf to overlaps
replace Replace fields in *.tsv
restrict Restrict overlaps to known pairs
```
## Concepts
### IntSpans
An IntSpan represents sets of integers as a number of inclusive ranges, for example `1-10,19,45-48`
or `-99--10,1-10,19,45-48`.
The following picture is the schema of an IntSpan object. Jump lines are above the baseline; loop
lines are below it.
Also, [AlignDB::IntSpan](https://github.com/wang-q/AlignDB-IntSpan) and
[jintspan](https://github.com/egateam/jintspan) are implements of IntSpan objects in Perl and Java,
respectively.
### IntSpans on chromosomes
* `chr.sizes`
* Single
* Multi
### Ranges
Examples in [`S288c.ranges`](tests/spanr/S288c.ranges)
```text
I:1-100
I(+):90-150
S288c.I(-):190-200
II:21294-22075
II:23537-24097
```
Simple rules:
* `chromosome` and `start` are required
* `species`, `strand` and `end` are optional
* `.` to separate `species` and `chromosome`
* `strand` is one of `+` and `-` and surround by round brackets
* `:` to separate names and digits
* `-` to separate `start` and `end`
* For `species`:
* `species` should be alphanumeric and without spaces, one exception char is `/`.
* `species` is an identity, you can also treat is as a strain name, a lineage or something else.
```text
species.chromosome(strand):start-end
--------^^^^^^^^^^--------^^^^^^----
```
### Links of ranges
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
## EXAMPLES
### `spanr`
```bash
# cargo install --force --path .
# cargo install --force --git https://github.com/wang-q/intspan
spanr genome tests/spanr/S288c.chr.sizes
spanr genome tests/spanr/S288c.chr.sizes |
spanr stat tests/spanr/S288c.chr.sizes stdin --all
spanr some tests/spanr/Atha.yml tests/spanr/Atha.list
spanr merge tests/spanr/I.yml tests/spanr/II.yml
spanr cover tests/spanr/S288c.ranges
spanr cover tests/spanr/dazzname.ranges
spanr coverage tests/spanr/S288c.ranges -c 2
spanr gff tests/spanr/NC_007942.gff --tag tRNA
spanr range --op overlap tests/spanr/intergenic.yml tests/spanr/S288c.ranges
spanr span --op cover tests/spanr/brca2.yml
spanr combine tests/spanr/Atha.yml
spanr compare \
--op intersect \
tests/spanr/intergenic.yml \
tests/spanr/repeat.yml
spanr compare \
--op intersect \
tests/spanr/I.II.yml \
tests/spanr/I.yml \
tests/spanr/II.yml
spanr split tests/spanr/I.II.yml
spanr stat tests/spanr/S288c.chr.sizes tests/spanr/intergenic.yml
spanr stat tests/spanr/S288c.chr.sizes tests/spanr/I.II.yml
spanr stat tests/spanr/Atha.chr.sizes tests/spanr/Atha.yml
spanr statop \
--op intersect \
tests/spanr/S288c.chr.sizes \
tests/spanr/intergenic.yml \
tests/spanr/repeat.yml
diff <(spanr statop \
--op intersect --all\
tests/spanr/Atha.chr.sizes \
tests/spanr/Atha.yml \
tests/spanr/paralog.yml ) \
<(jrunlist statop \
-o stdout \
--op intersect --all \
tests/spanr/Atha.chr.sizes \
tests/spanr/Atha.yml \
tests/spanr/paralog.yml )
spanr convert tests/spanr/repeat.yml tests/spanr/intergenic.yml |
spanr cover stdin |
spanr stat tests/spanr/S288c.chr.sizes stdin --all
spanr merge tests/spanr/repeat.yml tests/spanr/intergenic.yml |
spanr combine stdin |
spanr stat tests/spanr/S288c.chr.sizes stdin --all
```
### `linkr`
```bash
linkr sort tests/linkr/II.links.tsv -o tests/linkr/II.sort.tsv
linkr merge tests/linkr/II.links.tsv -v
linkr clean tests/linkr/II.sort.tsv
linkr clean tests/linkr/II.sort.tsv --bundle 500
linkr clean tests/linkr/II.sort.tsv -r tests/linkr/II.merge.tsv
linkr connect tests/linkr/II.clean.tsv -v
linkr filter tests/linkr/II.connect.tsv -n 2
linkr filter tests/linkr/II.connect.tsv -n 3 -r 0.99
linkr circos tests/linkr/II.connect.tsv
linkr circos --highlight tests/linkr/II.connect.tsv
```
Steps:
```text
sort
|
v
clean -> merge
| /
| /
v
clean
|
V
connect
|
v
filter
```
#### S288c
```bash
linkr sort tests/S288c/links.lastz.tsv tests/S288c/links.blast.tsv \
-o tests/S288c/sort.tsv
linkr clean tests/S288c/sort.tsv \
-o tests/S288c/sort.clean.tsv
linkr merge tests/S288c/sort.clean.tsv -c 0.95 \
-o tests/S288c/merge.tsv
linkr clean tests/S288c/sort.clean.tsv -r tests/S288c/merge.tsv --bundle 500 \
-o tests/S288c/clean.tsv
linkr connect tests/S288c/clean.tsv -r 0.8 \
-o tests/S288c/connect.tsv
linkr filter tests/S288c/connect.tsv -r 0.8 \
-o tests/S288c/filter.tsv
wc -l tests/S288c/*.tsv
# 229 tests/S288c/clean.tsv
# 148 tests/S288c/connect.tsv
# 148 tests/S288c/filter.tsv
# 566 tests/S288c/links.blast.tsv
# 346 tests/S288c/links.lastz.tsv
# 74 tests/S288c/merge.tsv
# 282 tests/S288c/sort.clean.tsv
# 626 tests/S288c/sort.tsv
cat tests/S288c/filter.tsv |
perl -nla -F"\t" -e 'print for @F' |
spanr cover stdin -o tests/S288c/cover.yml
spanr stat tests/S288c/chr.sizes tests/S288c/cover.yml -o stdout
```
#### Atha
```bash
linkr clean tests/Atha/sort.tsv -o tests/Atha/sort.clean.tsv
linkr merge tests/Atha/sort.clean.tsv -c 0.95 -o tests/Atha/merge.tsv
linkr clean tests/Atha/sort.clean.tsv -r tests/Atha/merge.tsv --bundle 500 -o tests/Atha/clean.tsv
linkr connect tests/Atha/clean.tsv -o tests/Atha/connect.tsv
linkr filter tests/Atha/connect.tsv -r 0.8 -o tests/Atha/filter.tsv
wc -l tests/Atha/*.tsv
# 4500 tests/Atha/clean.tsv
# 3832 tests/Atha/connect.tsv
# 3832 tests/Atha/filter.tsv
# 785 tests/Atha/merge.tsv
# 5416 tests/Atha/sort.clean.tsv
# 7754 tests/Atha/sort.tsv
cat tests/Atha/filter.tsv |
perl -nla -F"\t" -e 'print for @F' |
spanr cover stdin -o tests/Atha/cover.yml
spanr stat tests/Atha/chr.sizes tests/Atha/cover.yml -o stdout
```
### `ovlpr`
```bash
echo "tests/ovlpr/1_4.anchor.fasta;tests/ovlpr/1_4.pac.fasta" |
parallel --colsep ";" -j 1 "
minimap2 -cx asm20 {1} {2} |
ovlpr paf2ovlp stdin |
tsv-sort
minimap2 -cx asm20 {2} {1} |
ovlpr paf2ovlp stdin |
tsv-sort
" |
ovlpr covered stdin --mean
ovlpr covered tests/ovlpr/1_4.pac.paf.ovlp.tsv
ovlpr covered tests/ovlpr/11_2.long.paf --paf
ovlpr covered tests/ovlpr/1_4.pac.paf.ovlp.tsv --base
ovlpr covered tests/ovlpr/1_4.pac.paf.ovlp.tsv --mean
ovlpr paf2ovlp tests/ovlpr/1_4.pac.paf
ovlpr replace tests/ovlpr/1_4.ovlp.tsv tests/ovlpr/1_4.replace.tsv
ovlpr replace tests/ovlpr/1_4.ovlp.tsv tests/ovlpr/1_4.replace.tsv -r
ovlpr restrict tests/ovlpr/1_4.ovlp.tsv tests/ovlpr/1_4.restrict.tsv
```
## License
[](https://app.fossa.io/projects/git%2Bgithub.com%2Fwang-q%2Fintspan?ref=badge_large)