chromsize

annoyed to have to create an index and cut it?
have to look for that old script every time?
got you. just get your chrom sizes. very fast.

but first, how is this better than any other option? yeah, just check the image below.

googled 'get chromosome sizes from fasta', grab every command/tool I found and benchmarked it. surprisingly, you can lose 14 seconds of your life just waiting for those chrom sizes to be calculated. crazy.

What's new on v.0.0.2?

• now reads .gz!
• CI implementation

Usage

Binary

Usage: chromsize --fasta <FASTA> --output <OUTPUT> [-t <THREADS>]

Arguments:
    -f, --fasta <FASTA>: FASTA file
    -o, --output <OUTPUT>: path to chrom.sizes

Options:
    -t, --threads <THREADS>: number of threads [default: your max ncpus]
    --help: print help
    --version: print version

crate: https://crates.io/crates/chromsize

Installation

to install rust and use chromsize on your system follow this steps:

1. get installer: curl https://sh.rustup.rs -sSf | sh on unix, or go here for other options
2. run cargo install chromsize (make sure ~/.cargo/bin is in your $PATH before running it)
3. use chromsize with the required arguments

Library

use chromsize;

fn main() {
    let input = PathBuf::new("/path/to/fasta.fa");
    let output = PathBuf::new("/path/to/chrom.sizes");

    let sizes: Vec<(String, u64)> = chromsize::chromsize(&input);
    chromsize::write(sizes, &output)
}

Python

build the port to install it as a pkg:

git clone https://github.com/alejandrogzi/chromsize.git && cd chromsize/py-chromsize
hatch shell
maturin develop --release

use it as a binary wrapper:

import chromsize as cs

input = "/path/to/fasta.fa"
output = "/path/to/chrom.sizes"
cs.write_chromsizes(input, output)

or just get them directly

import chromsize as cs

input = "/path/to/fasta.fa"
sizes = cs.get_chromsizes(input)

>>> print(sizes)
[
    ('chr1', 123),
    ('chr2', 456),
    ...
]

Build

to build chromsize from this repo, do:

1. get rust
2. run git clone https://github.com/alejandrogzi/chromsize.git && cd chromsize
3. run cargo run --release -- -i <GTF> -o <OUTPUT>

Container image

to build the development container image:

1. run git clone https://github.com/alejandrogzi/chromsize.git && cd chromsize
2. initialize docker with start docker or systemctl start docker
3. build the image docker image build --tag chromsize .
4. run docker run --rm -v "[dir_where_your_fa_is]:/dir" chromsize -f /dir/<INPUT> -o /dir/<OUTPUT>

Conda (not available yet)

to use chromsize through Conda just:

1. conda install chromsize -c bioconda or conda create -n chromsize -c bioconda chromsize

Nextflow (not available yet)

Benchmark

do not believe me? run the benchmark on your own:

1. get .fa from any species you want (or download the ones I used from UCSC/NCBI)
2. install hyperfine: https://github.com/sharkdp/hyperfine
3. go to chromsize/bench and modify the ASSEMBLIES const with the .fa you've download
4. run cargo run release --bin chromsize-benchmark -- -d /dir/where/my/fastas/are -a show-output ignore-failure

here is all the info and metadata from my experiment:

which tools I used?

Tool	Command	Reference	Discussion
seqkit	seqkit fx2tab --length --name --header-line {assembly} > chrom.sizes	1	2
chromsize	target/release/chromsize -f {assembly} -o chrom.sizes	3
pyfaidx	faidx {assembly} -i chromsizes > chrom.sizes	4	5
samtools	samtools faidx {assembly} && wait | cut -f1,2 {assembly}.fai > chrom.sizes	6	5
faSize	faSize -detailed -tab {assembly} > chrom.sizes	7
awk1	awk '/^>/ {if (seqlen){print seqlen}; print ;seqlen=0;next; } { seqlen += length($0)}END{print seqlen}' {assembly} > chrom.sizes	8	9
awk2	awk '/^>/{if (l!=") print l; print; l=0; next}{l+=length($0)}END{print l}' {assembly} > chrom.sizes	8	9
bioawk1	bioawk -c fastx '{print > $name ORS length($seq)}' {assembly} > chrom.sizes	10	9
awk3	cat {assembly} | awk '$0 ~ > {if (NR > 1) {print c;} c=0;printf substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END { print c; }' > chrom.sizes	8	11
bioawk2	bioawk -c fastx '{ print $name, length($seq) }' < {assembly} > chrom.sizes	10	2

detailed data?

Species	Assembly	Size (Gb)	chromsize	seqKit	awk1	awk2	awk3	bioawk1	bioawk2	faSize	pyfaidx	samtools
S. cerevisiae	R64	0.01	0.004	0.016 (X 4.0)	0.043 (X 10.7)	0.043 (X 10.7)	0.05 (X 12.5)	0.03 (X 7.5)	0.03 (X 7.5)	0.054 (X 13.5)	0.101 (X 25.2)	0.064 (X 16.0)
C. elegans	ce11	0.10	0.02	0.103 (X 5.1)	0.409 (X 20.4)	0.408 (X 20.4)	0.492 (X 24.6)	0.274 (X 13.7)	0.274 (X 13.7)	0.426 (X 21.3)	0.225 (X 11.2)	0.472 (X 23.6)
D. melanogaster	dm6	0.14	0.028	0.147 (X 5.2)	0.581 (X 20.7)	0.583 (X 20.8)	0.714 (X 25.5)	0.426 (X 15.2)	0.418 (X 14.9)	0.633 (X 22.6)	0.337 (X 12.0)	0.667 (X 23.8)
D. rerio	danRer11	1.37	0.22	0.742 (X 3.4)	6.815 (X 31.0)	6.803 (X 30.9)	8.216 (X 37.3)	3.946 (X 17.9)	3.95 (X 18.0)	7.202 (X 32.7)	3.029 (X 13.8)	7.633 (X 34.7)
C. familiaris	canFam4	2.48	0.311	1.209 (X 3.9)	10.158 (X 32.7)	10.124 (X 32.6)	12.206 (X 39.2)	6.55 (X 21.1)	6.518 (X 21.0)	10.671 (X 34.3)	4.741 (X 15.2)	11.394 (X 36.6)
H. sapiens	GRCh38	3.10	0.43	1.696 (X 3.9)	12.393 (X 28.8)	12.432 (X 28.9)	13.681 (X 31.8)	7.414 (X 17.2)	7.284 (X 16.9)	13.102 (X 30.5)	6.37 (X 14.8)	14.074 (X 32.7)
B. bombina	aBomBom1	9.80	1.554	8.501 (X 5.5)	41.676 (X 26.8)	41.696 (X 26.8)	49.064 (X 31.6)	24.202 (X 15.6)	24.374 (X 15.7)	43.856 (X 28.2)	19.755 (X 12.7)	45.387 (X 29.2)
A. mexicanum	AmbMex60DD	28.20	3.327	14.375 (X 4.3)	118.923 (X 35.7)	118.422 (X 35.6)	137.781 (X 41.4)	57.626 (X 17.3)	57.591 (X 17.3)	121.257 (X 36.4)	54.82 (X 16.5)	128.374 (X 38.6)
P. annectens	PAN1.0	40.10	4.606	18.664 (X 4.1)	167.85 (X 36.4)	165.701 (X 36.0)	196.833 (X 42.7)	91.747 (X 19.9)	91.924 (X 20.0)	170.475 (X 37.0)	77.707 (X 16.9)	181.562 (X 39.4)

how well performs with .gz?

CHM13-T2T.fa.gz

Tool	Cores	Time
seqkit	16	18.993 s ± 0.132 s
chromsize	default (max_cpus: 16)	7.631 s ± 0.010 s
seqkit	default (4)	18.525 s ± 0.520 s
chromsize	4	8.035 s ± 0.077 s
seqkit	2	18.535 s ± 0.376 s
chromsize	2	8.284 s ± 0.030 s