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.0.0.3? - now adds --accession-only flag to cut fasta headers - fix CI implementation

Usage

Binary

``` rust Usage: chromsize --fasta --output

[-t ]

Arguments: -f, --fasta : FASTA file -o, --output

: path to chrom.sizes

Options: -t, --threads : number of threads [default: your max ncpus] -a, --accession-only only keep the accession id part of the header (stop after blank) --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) 4. use chromsize with the required arguments

Library

``` rust 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: ``` python3 import chromsize as cs

input = "/path/to/fasta.fa" output = "/path/to/chrom.sizes" cs.write_chromsizes(input, output) or just get them directly python3 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

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 |