https://github.com/mbhall88/ontime
Extract subsets of ONT (Nanopore) reads based on time
https://github.com/mbhall88/ontime
bioinfomatics fastq filter nanopore subset time
Last synced: 7 months ago
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Extract subsets of ONT (Nanopore) reads based on time
- Host: GitHub
- URL: https://github.com/mbhall88/ontime
- Owner: mbhall88
- License: mit
- Created: 2023-01-11T05:41:50.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2024-09-12T01:28:24.000Z (about 1 year ago)
- Last Synced: 2025-03-11T03:40:51.980Z (7 months ago)
- Topics: bioinfomatics, fastq, filter, nanopore, subset, time
- Language: Rust
- Homepage:
- Size: 148 KB
- Stars: 21
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
Awesome Lists containing this project
README
# ONTime
[](https://github.com/mbhall88/ontime/actions/workflows/ci.yaml)
[](https://crates.io/crates/ontime)
[](https://opensource.org/licenses/MIT)
[](https://github.com/mbhall88/ontime/releases)
[](https://doi.org/10.5281/zenodo.7533053)
Extract subsets of ONT (Nanopore) reads based on time
- [Motivation](#motivation)
- [Install](#install)
- [Examples](#examples)
- [Usage](#usage)
- [Time range format](#specifying-a-time-range)
- [Cite](#cite)
## Motivation
Some collaborators wanted to know how long they need to perform sequencing on the
Nanopore
device until they got "sufficient" data (sufficient is obviously application-dependent).
They were just going to do multiple runs for different amounts of time. So instead, I
created `ontime`
to easily grab reads from the first hour, first two hours, first three hours etc. and
run those
subsets through the analysis pipeline that was the intended application. This way they
only
needed to do one (longer) run.
## Install
**tl;dr**: precompiled binary
```shell
curl -sSL ontime.mbh.sh | sh
# or with wget
wget -nv -O - ontime.mbh.sh | sh
```
You can also pass options to the script like so
```
$ curl -sSL ontime.mbh.sh | sh -s -- --help
install.sh [option]
Fetch and install the latest version of ontime, if ontime is already
installed it will be updated to the latest version.
Options
-V, --verbose
Enable verbose output for the installer
-f, -y, --force, --yes
Skip the confirmation prompt during installation
-p, --platform
Override the platform identified by the installer [default: apple-darwin]
-b, --bin-dir
Override the bin installation directory [default: /usr/local/bin]
-a, --arch
Override the architecture identified by the installer [default: x86_64]
-B, --base-url
Override the base URL used for downloading releases [default: https://github.com/mbhall88/ssubmit/releases]
-h, --help
Display this help message
```
### Conda
[](https://anaconda.org/bioconda/ontime)
[](https://anaconda.org/bioconda/ontime)
```shell
$ conda install -c bioconda ontime
```
### Cargo
```shell
$ cargo install ontime
```
### Container
Docker images are hosted at [quay.io].
#### `singularity`
Prerequisite: [`singularity`][singularity]
```shell
$ URI="docker://quay.io/mbhall88/ontime"
$ singularity exec "$URI" ontime --help
```
The above will use the latest version. If you want to specify a version then use a
[tag][quay.io] (or commit) like so.
```shell
$ VERSION="0.1.0"
$ URI="docker://quay.io/mbhall88/ontime:${VERSION}"
```
#### `docker`
[](https://quay.io/repository/mbhall88/ontime)
Prerequisite: [`docker`][docker]
```shhell
$ docker pull quay.io/mbhall88/ontime
$ docker run quay.io/mbhall88/ontime ontime --help
```
You can find all the available tags on the [quay.io repository][quay.io].
### Build from source
```shell
$ git clone https://github.com/mbhall88/ontime.git
$ cd ontime
$ cargo build --release
$ target/release/ontime -h
```
## Examples
I want the reads that were sequenced **in the first hour**
```shell
$ ontime --to 1h in.fq
```
The same, but using a BAM file as input
```shell
$ ontime --to 1h in.bam
```
I want the reads that were sequenced **after the first hour**
```shell
$ ontime --from 1h in.fq
```
I want all reads **except those sequenced in the last hour**
```shell
$ ontime --to -1h in.fq
```
I want reads sequenced **between the third and fourth hours**
```shell
$ ontime --from 3h --to 4h in.fq
```
Check what the earliest and latest start times in the fastq are
```shell
$ ontime --show in.fq
Earliest: 2022-12-12T15:17:01.0Z
Latest : 2022-12-13T01:16:27.0Z
```
I like to be specific, give me the reads that were sequenced **while I was eating dinner** (
see [note on time formats](#time-format))
```shell
$ ontime --from 2022-12-12T20:45:00Z --to 2022-12-12T21:17:01.5Z in.fq
```
I want to save the output to a Gzip-compressed file
```shell
$ ontime --to 2h -o out.fq.gz in.fq
```
## Usage
```
Extract subsets of ONT (Nanopore) reads based on time
Usage: ontime [OPTIONS]
Arguments:
Input fastq/fasta/BAM/SAM file
Options:
-o, --output Output file name [default: stdout]
-O, --output-type (fastq/a output only) u: uncompressed; b: Bzip2; g: Gzip; l: Lzma
-L, --compress-level <1-21> Compression level to use if compressing fastq output [default: 6]
-f, --from Earliest start time; otherwise the earliest time is used
-t, --to Latest start time; otherwise the latest time is used
-s, --show Show the earliest and latest start times in the input and exit
-h, --help Print help (see more with '--help')
-V, --version Print version
```
#### Specifying a time range
The `--from` and `--to` options are used to restrict the timeframe you want reads from.
These options accept two different formats: duration and timestamp.
**Duration**: The most human-friendly way to provide a range is with duration. For
example, `1h` means 1 hour. Passing `--from 1h` says "I want reads that were generated 1
hour or more after sequencing started" - i.e. the earliest start time in the file plus 1
hour. Likewise, passing `--to 2h` says "I only want reads that were generated before the
second hour of sequencing". Using `--from` and `--to` in combination gives you a range.
We support a range of time/duration units and they can be combined. For example,
`3h45m` to indicate 3 hours and 45 minutes. See the [`duration-str` docs][duration] for
the full list
of support duration units.
Negative durations are also allowed. A negative duration subtracts that duration from
the **latest** start time in the file. So `--to -1h` will exclude reads that were
sequenced in the last hour of the run. Negative ranges are also valid -
i.e. `--from -2h --to -1h` will give you the reads sequenced in the penultimate hour of
the run.
**Timestamp**: If you want to provide date and time for your ranges, that is acceptable
in `--from/--to` also. See [the formatting guide](#time-format) for more information.
To make using timestamps a little easier, you can first run `ontime --show ` to
get the earliest and latest timestamps in the file.
#### Time format
The times that `ontime` extracts are the `start_time=
All times printed by `ontime` and accepted by the `--from/--to` options
are [UTC time][utc]. More recent versions of Guppy also have UTC offsets in
their `start_time`; for simplicity's sake, these offsets are ignored by `ontime`. So, if
you want to provide a timestamp to `--from/--to` based on a timeframe in your local
time, please first [convert it to UTC time][utc].
In general, the timestamp format `ontime` accepts anything that
is [RFC339-compliant][rfc3339].
The basic (recommended) format is `--T::Z` -
e.g. `2022-12-12T18:39:09Z`. Feel free to get precise with
subseconds though if you like...
### Full usage
```
Extract subsets of ONT (Nanopore) reads based on time
Usage: ontime [OPTIONS]
Arguments:
Input fastq/fasta/BAM/SAM file
Options:
-o, --output
Output file name [default: stdout]
Note: you cannot output a fastq if a BAM/SAM input is given and vice versa. Use samtools for post-processing. However, you can output SAM if the input is BAM and vice versa.
-O, --output-type
(fastq/a output only) u: uncompressed; b: Bzip2; g: Gzip; l: Lzma
ontime will attempt to infer the output compression format automatically from the output extension. If writing to stdout, the default is uncompressed (u)
-L, --compress-level <1-21>
Compression level to use if compressing fastq output
[default: 6]
-f, --from
Earliest start time; otherwise the earliest time is used
This can be a timestamp - e.g. 2022-11-20T18:00:00 - or a duration from the start - e.g. 2h30m (2 hours and 30 minutes from the start). See the docs for more examples
-t, --to
Latest start time; otherwise the latest time is used
See --from (and docs) for examples
-s, --show
Show the earliest and latest start times in the input and exit
-h, --help
Print help (see a summary with '-h')
-V, --version
Print version
```
## Cite
`ontime` is archived [at Zenodo](https://doi.org/10.5281/zenodo.7533052).
```bibtex
@software{ontime,
author = {Michael Hall},
title = {mbhall88/ontime: 0.1.3},
month = jan,
year = 2023,
publisher = {Zenodo},
version = {0.1.3},
doi = {10.5281/zenodo.7533053},
url = {https://doi.org/10.5281/zenodo.7533053}
}
```
and replace the version number with whichever you used.
[quay.io]: https://quay.io/repository/mbhall88/ontime
[singularity]: https://sylabs.io/guides/3.5/user-guide/quick_start.html#quick-installation-steps
[docker]: https://docs.docker.com/v17.12/install/
[utc]: https://www.timeanddate.com/worldclock/timezone/utc
[rfc3339]: https://www.rfc-editor.org/rfc/rfc3339#section-5.8
[duration]: https://github.com/baoyachi/duration-str#duration-unit-list
[dorado]: https://github.com/nanoporetech/dorado