Current release: 0.7.2
```shell cargo install intspan
cargo install --force --path .
brew install intspan
export CARGOTARGETDIR=/tmp cargo build cargo run --bin fasr help
cargo doc --open
```
An example is S288c.rg.
The information presented in this format is very similar to formats such as the BED.
I chose this format because of its compactness, readability, and embeddability into other tab-separated files.
```text I:1-100 I(+):90-150 S288c.I(-):190-200 II:21294-22075 II:23537-24097
```
The schema of an Range object is shown below.
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 --------^^^^^^^^^^--------^^^^^^----
```
In this toolset, rgr is used to operate ranges in .rg and .tsv files.
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.
Very often, we need to deal with many genomic intervals of the same property, e.g., all the exons of a gene, all the promoters of a gene family, all the repeats in a genome, and so on.
Existing formats, such as bedGraph, can partially deal with such situations, but often face
problems of intuitiveness, performance, etc. At the same time, there are only a very limited number
of tools that can handle files in such proprietary formats.
Saving IntSpan to a JSON file is the solution of this toolset, where spanr
handles this job.
repeat.jsonjson
{
"I": "-",
"II": "327069-327703",
"III": "-",
"IV": "512988-513590,757572-759779,802895-805654,981142-987119,1017673-1018183,1175134-1175738,1307621-1308556,1504223-1504728",
"IX": "-",
"V": "354135-354917",
"VI": "-",
"VII": "778784-779515,878539-879235",
"VIII": "116405-117059,133581-134226",
"X": "366757-367499,712641-713226",
"XI": "162831-163399",
"XII": "64067-65208,91960-92481,451418-455181,455933-457732,460517-464318,465070-466869,489753-490545,817840-818474",
"XIII": "609100-609861",
"XIV": "-",
"XV": "437522-438484",
"XVI": "560481-561065"
}
Atha.jsonjson
{
"AT1G01010.1": {
"1": "3631-3913,3996-4276,4486-4605,4706-5095,5174-5326,5439-5899"
},
"AT1G01020.1": {
"1": "5928-6263,6437-7069,7157-7232,7384-7450,7564-7649,7762-7835,7942-7987,8236-8325,8417-8464,8571-8737"
},
"AT1G01020.2": {
"1": "6790-7069,7157-7450,7564-7649,7762-7835,7942-7987,8236-8325,8417-8464,8571-8737"
},
"AT2G01008.1": {
"2": "1025-1272,1458-1510,1873-2810,3706-5513,5782-5945"
},
"AT2G01021.1": {
"2": "6571-6672"
}
}
chr.sizes: S288c.chr.sizesTypes 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
rgr help``text
rgr` operates ranges in .rg and .tsv files
Usage: rgr [COMMAND]
Commands: count Count each range overlapping with other range files field Create/append ranges from fields merge Merge overlapped ranges via overlapping graph prop Proportion of the ranges intersecting a runlist file replace Replace fields in .tsv file runlist Filter .rg and .tsv files by comparison with a runlist file sort Sort .rg and .tsv files by a range field help Print this message or the help of the given subcommand(s)
Options: -h, --help Print help -V, --version Print version
```
spanr help``text
spanr` operates chromosome IntSpan files
Usage: spanr [COMMAND]
Commands: genome Convert chr.size to runlists some Extract some records from a runlist json file merge Merge runlist json files split Split a runlist json file stat Coverage on chromosomes for runlists statop Coverage on chromosomes for one JSON crossed another combine Combine multiple sets of runlists in a json file compare Compare one JSON file against others span Operate spans in a JSON file cover Output covers on chromosomes coverage Output minimum or detailed depth of coverage on chromosomes gff Convert gff3 to covers on chromosomes convert Convert runlist file to ranges file help Print this message or the help of the given subcommand(s)
Options: -h, --help Print help -V, --version Print version
```
fasr help``text
fasr` operates block fasta files
Usage: fasr [COMMAND]
Commands: axt2fas Convert axt to block fasta check Check genome locations in block fasta headers concat Concatenate sequence pieces of the same species consensus Generate consensus sequences by POA create Create block fasta files from links of ranges link Output bi/multi-lateral range links maf2fas Convert maf to block fasta name Output all species names separate Separate block fasta files by species split Split block fasta files to per-alignment/chromosome fasta files subset Extract a subset of species help Print this message or the help of the given subcommand(s)
Options: -h, --help Print help -V, --version Print version
```
linkr help``text
linkr` operates ranges on chromosomes and links of ranges
Usage: linkr [COMMAND]
Commands: circos Convert links to circos links or highlights sort Sort links and ranges within links filter Filter links by numbers of ranges or length differences clean Replace ranges within links, incorporate hit strands and remove nested links connect Connect bilateral links into multilateral ones help Print this message or the help of the given subcommand(s)
Options: -h, --help Print help -V, --version Print version
```
ovlpr help``text
ovlpr` operates overlaps between sequences
Usage: ovlpr [COMMAND]
Commands: covered Covered regions from .ovlp.tsv files paf2ovlp Convert minimap .paf to overlaps restrict Restrict overlaps to known pairs help Print this message or the help of the given subcommand(s)
Options: -h, --help Print help -V, --version Print version
```
spanr```shell 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.json tests/spanr/Atha.list
spanr merge tests/spanr/I.json tests/spanr/II.json spanr merge tests/spanr/I.json tests/spanr/II.other.json --all
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.json
spanr combine tests/spanr/Atha.json
spanr compare \ --op intersect \ tests/spanr/intergenic.json \ tests/spanr/repeat.json
spanr compare \ --op intersect \ tests/spanr/I.II.json \ tests/spanr/I.json \ tests/spanr/II.json
spanr split tests/spanr/I.II.json
spanr stat tests/spanr/S288c.chr.sizes tests/spanr/intergenic.json
spanr stat tests/spanr/S288c.chr.sizes tests/spanr/I.II.json
spanr stat tests/spanr/Atha.chr.sizes tests/spanr/Atha.json
spanr statop \ --op intersect \ tests/spanr/S288c.chr.sizes \ tests/spanr/intergenic.json \ tests/spanr/repeat.json
spanr statop \ --op intersect --all\ tests/spanr/Atha.chr.sizes \ tests/spanr/Atha.json \ tests/spanr/paralog.json
spanr convert tests/spanr/repeat.json tests/spanr/intergenic.json | spanr cover stdin | spanr stat tests/spanr/S288c.chr.sizes stdin --all
spanr merge tests/spanr/repeat.json tests/spanr/intergenic.json | spanr combine stdin | spanr stat tests/spanr/S288c.chr.sizes stdin --all
```
rgr```shell 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 field tests/rgr/ctg.tsv --chr 2 --start 3 --end 4 -H -f 6,1 > tests/rgr/ctg.range.tsv
rgr sort tests/rgr/S288c.rg rgr sort tests/rgr/ctg.range.tsv -H -f 3
rgr sort tests/rgr/S288c.rg tests/rgr/ctg.range.tsv
rgr count tests/rgr/S288c.rg tests/rgr/S288c.rg rgr count tests/rgr/ctg.range.tsv tests/rgr/S288c.rg -H -f 3
rgr runlist tests/rgr/intergenic.json tests/rgr/S288c.rg --op overlap rgr runlist tests/rgr/intergenic.json tests/rgr/ctg.range.tsv --op non-overlap -H -f 3
rgr prop tests/rgr/intergenic.json tests/rgr/S288c.rg rgr prop tests/rgr/intergenic.json tests/rgr/ctg.range.tsv -H -f 3 --prefix --full
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
```
linkr```shell 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
```shell 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.json
spanr stat tests/S288c/chr.sizes tests/S288c/cover.json -o stdout
```
```shell 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.json
spanr stat tests/Atha/chr.sizes tests/Atha/cover.json -o stdout
```
ovlpr```shell 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
```
fasr```shell fasr maf2fas tests/fasr/example.maf
fasr axt2fas tests/fasr/RM111a.chr.sizes tests/fasr/example.axt --qname RM111a
fasr name tests/fasr/example.fas --count
fasr cover tests/fasr/example.fas
fasr cover tests/fasr/example.fas --name S288c --trim 10
fasr concat tests/fasr/name.lst tests/fasr/example.fas
fasr subset tests/fasr/name.lst tests/fasr/example.fas
fasr link tests/fasr/example.fas --pair cargo run --bin fasr link tests/fasr/example.fas --best
samtools faidx tests/fasr/NC000932.fa NC000932:1-10
fasr check tests/fasr/NC000932.fa tests/fasr/Atha.pair.fas
fasr create tests/fasr/genome.fa tests/fasr/I.connect.tsv --name S288c
fasr separate tests/fasr/example.fas -o . --suffix .tmp
spoa tests/fasr/refine.fasta -r 1
cargo run --bin fasr consensus tests/fasr/example.fas cargo run --bin fasr consensus tests/fasr/refine.fas
cargo run --bin fasr split tests/fasr/example.fas --simple cargo run --bin fasr split tests/fasr/example.fas -o . --chr --suffix .tmp
cargo run --bin fasr slice tests/fasr/slice.json tests/fasr/slice.fas --name S288c
cargo run --bin fasr join tests/fasr/S288cvsYJM789.slice.fas --name YJM789 cargo run --bin fasr join \ tests/fasr/S288cvsRM11_1a.slice.fas \ tests/fasr/S288cvsYJM789.slice.fas \ tests/fasr/S288cvsSpar.slice.fas
cargo run --bin fasr stat tests/fasr/example.fas --outgroup
```
