Current release: 0.6.9
```bash cargo install intspan
cargo install --force --path .
brew install intspan
```
spanr``text
$ spanr help
spanr 0.6.8
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 minimum or detailed depth of coverage 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 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
```
rgr``text
$ rgr help
rgr 0.6.8
wang-q <wang-q@outlook.com>
rgr` operates ranges in .rg and .tsv files)
USAGE: rgr [SUBCOMMAND]
OPTIONS: -h, --help Print help information -V, --version Print version information
SUBCOMMANDS: count Count each range overlapping with other range files field Create/append ranges from fields help Print this message or the help of the given subcommand(s) merge Merge overlapped ranges via overlapping graph replace Replace fields in *.tsv runlist Compare a runlist file with a range file
```
linkr``text
$ linkr help
linkr 0.6.8
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) sort Sort links and ranges within links
```
ovlpr``text
$ ovlpr help
ovlpr 0.6.8
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 restrict Restrict overlaps to known pairs
```
An IntSpan represents sets of integers as a number of inclusive ranges, for example 1-10,19,45-48.
The following figure shows the schema of an IntSpan object. Jump lines are above the baseline; loop lines are below it.
Also, AlignDB::IntSpan and jintspan are implements of the IntSpan objects in Perl and Java, respectively.
Single: repeat.yml
Multi: Atha.yml
chr.sizes: S288c.chr.sizes
An example is S288c.rg
```text I:1-100 I(+):90-150 S288c.I(-):190-200 II:21294-22075 II:23537-24097
```
Simple rules:
chromosome and start are requiredspecies, strand and end are optional. to separate species and chromosomestrand is one of + and - and surround by round brackets: to separate names and digits- to separate start and endspecies:
species should be alphanumeric with no spaces, the one exception character is /.species is an identity that you can also think of as a strain name, an assembly, or
something else.```text species.chromosome(strand):start-end --------^^^^^^^^^^--------^^^^^^----
```
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
spanr```bash 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.rg spanr cover tests/spanr/dazzname.rg
spanr coverage tests/spanr/S288c.rg -m 2
spanr coverage tests/spanr/S288c.rg -d
spanr gff tests/spanr/NC_007942.gff --tag tRNA
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
```
rgr```shell rgr count tests/rgr/S288c.rg tests/rgr/S288c.rg
rgr field tests/Atha/chr.sizes --chr 1 --start 2 -a -s rgr field tests/spanr/NC_007942.gff -H --chr 1 --start 4 --end 5 --strand 7 --eq 3:tRNA --ne '7:+'
rgr merge tests/rgr/II.links.tsv -c 0.95
rgr replace tests/rgr/14.ovlp.tsv tests/rgr/14.replace.tsv rgr replace tests/rgr/14.ovlp.tsv tests/rgr/14.replace.tsv -r
rgr runlist --op overlap tests/rgr/intergenic.yml tests/rgr/S288c.rg
```
linkr```bash linkr sort tests/linkr/II.links.tsv -o tests/linkr/II.sort.tsv
rgr 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
```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
rgr 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
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
```
```bash gzip -dcf tests/Atha/links.lastz.tsv.gz tests/Atha/links.blast.tsv.gz | linkr sort stdin -o tests/Atha/sort.tsv
linkr clean tests/Atha/sort.tsv -o tests/Atha/sort.clean.tsv
rgr 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
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/14.anchor.fasta;tests/ovlpr/14.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 restrict tests/ovlpr/14.ovlp.tsv tests/ovlpr/14.restrict.tsv
```
