10 unstable releases (4 breaking)
0.14.0 | Jul 21, 2022 |
---|---|
0.12.0 | Jul 4, 2022 |
0.11.2 | Jul 3, 2022 |
0.11.0 | Nov 8, 2021 |
0.9.11 | Sep 18, 2021 |
#9 in #biological
21 downloads per month
3MB
824 lines
brrrr
brrrr is a CLI to facilitate common informatics tasks, and brrrr-lib is the abstracted code in a cargo installable package.
brrrr
The CLI exposes many of the related brrrr
functionality through a command line
interface. brrrr-lib
is intended for use in other modules.
For the CLI help screen.
brrrr --help
Warning brrrr is very alpha, and may change or break at any time.
Use Case
Use Cases:
- Convert FASTA to JSON
- Convert FASTA to and from parquet
Convert FASTA to JSON
As a quick example, say you have a FASTA file and would like to convert it to json.
; echo ">1\nATCG\n>2\nTAGC\n" | brrrr fa2jsonl | jq
{
"id": "1",
"desc": null,
"seq": "ATCG"
}
{
"id": "2",
"desc": null,
"seq": "TAGC"
}
Convert FASTA to and from parquet
Parquet is a useful file format for large scale data storage, and there exist many tools that can interact with it. For example, DuckDB can be used to query parquet files with SQL.
Starting with the swissprot dataset, use the excellent seqkit to find some summary stats.
$ seqkit stats uniprot-reviewed_yes.fasta
file format type num_seqs sum_len min_len avg_len max_len
uniprot-reviewed_yes.fasta FASTA Protein 561,176 201,758,313 2 359.5 35,213
Convert it to parquet...
$ brrrr fa2pq ./uniprot-reviewed_yes.fasta swissprot.parquet && \
test -f swissprot.parquet && \
echo "swissprot.parquet exists"
swissprot.parquet exists
Load it into DuckDB, select sequences 1000aa and over in length, then create new parquet file.
$ duckdb -c "COPY (SELECT * FROM 'swissprot.parquet' WHERE length("sequence") >= 1000) TO 'swissprot.1000.parquet' (FORMAT PARQUET);"
$ duckdb -c "SELECT COUNT(*) FROM 'swissprot.1000.parquet'"
┌──────────────┐
│ count_star() │
├──────────────┤
│ 18236 │
└──────────────┘
Take it from parquet and convert it back to FASTA, then check the min_len is what's expected.
$ brrrr pq2fa swissprot.1000.parquet swissprot.1000.fasta && seqkit stats swissprot.1000.fasta
file format type num_seqs sum_len min_len avg_len max_len
swissprot.1000.fasta FASTA Protein 18,236 28,228,604 1,000 1,548 35,213
Installation
The CLI is the executable entrypoint, though the library can be separately installed.
CLI
Executables are built for:
x86_64-apple-darwin
x86_64-unknown-linux-musl
aarch64-unknown-linux-gnu
x86_64-pc-windows-msvc
Download the executable from GitHub's release page.
brrrr-lib
brrrr-lib
is a crate contains abstracted code and is used by the CLI.
[dependencies]
brrrr-lib = "0.14.0"
Docs are available here: docs.rs/brrrr-lib.
Dependencies
~23–31MB
~617K SLoC