intspan
Install
Current release: 0.7.1
cargo install intspan
cargo install --force --path .
# or
brew install intspan
SYNOPSIS
spanr
$ $ spanr help
spanr 0.7.0
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
$ rgr help
rgr 0.7.0
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
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
* Field numbers start with 1
linkr
$ linkr help
linkr 0.7.0
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
$ ovlpr help
ovlpr 0.7.0
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
Concepts
IntSpans
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.
Runlist - IntSpans on chromosomes
-
Single:
repeat.yml
-
Multi:
Atha.yml
-
chr.sizes
:S288c.chr.sizes
Ranges
An example is S288c.rg
I:1-100
I(+):90-150
S288c.I(-):190-200
II:21294-22075
II:23537-24097
Simple rules:
chromosome
andstart
are requiredspecies
,strand
andend
are optional.
to separatespecies
andchromosome
strand
is one of+
and-
and surround by round brackets:
to separate names and digits-
to separatestart
andend
- For
species
:species
should be alphanumeric with no spaces, the one exception character is/
.- A
species
is an identity that you can also think of as a strain name, an assembly, or something else.
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
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
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
# ctg:I:1 is treated as a range
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.yml tests/rgr/S288c.rg --op overlap
rgr runlist tests/rgr/intergenic.yml tests/rgr/ctg.range.tsv --op non-overlap -H -f 3
rgr prop tests/rgr/intergenic.yml tests/rgr/S288c.rg
rgr prop tests/rgr/intergenic.yml tests/rgr/ctg.range.tsv -H -f 3 --prefix --full
rgr merge tests/rgr/II.links.tsv -c 0.95
rgr replace tests/rgr/1_4.ovlp.tsv tests/rgr/1_4.replace.tsv
rgr replace tests/rgr/1_4.ovlp.tsv tests/rgr/1_4.replace.tsv -r
linkr
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:
sort
|
v
clean -> merge
| /
| /
v
clean
|
V
connect
|
v
filter
S288c
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
# 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
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
# 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
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 restrict tests/ovlpr/1_4.ovlp.tsv tests/ovlpr/1_4.restrict.tsv