Extract subsets of ONT (Nanopore) reads based on time
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.
tl;dr: precompiled binary
```shell curl -sSL ontime.mbh.sh | sh
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
```
shell
$ conda install -c bioconda ontime
shell
$ cargo install ontime
Docker images are hosted at [quay.io].
singularity
Prerequisite: 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 (or commit) like so.
shell
$ VERSION="0.1.0"
$ URI="docker://quay.io/mbhall88/ontime:${VERSION}"
docker
Prerequisite: 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.
shell
$ git clone https://github.com/mbhall88/ontime.git
$ cd ontime
$ cargo build --release
$ target/release/ontime -h
I want the reads that were sequenced in the first hour
shell
$ ontime --to 1h in.fq
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)
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: ontime [OPTIONS]
Arguments:
Options:
-o, --output --help
for more detail)
-V, --version Print version information
```
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.
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 for more information.
To make using timestamps a little easier, you can first run ontime --show <in.fq>
to
get the earliest and latest timestamps in the file.
The times that ontime
extracts are the start_time=<time>
section contained in the
description of each fastq read.
The format of this time has changed a few times, so if you come across a file
which ontime
cannot parse, please raise an issue so I can make it work.
All times printed by ontime
and accepted by the --from/--to
options
are UTC time. 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.
In general, the timestamp format ontime
accepts anything that
is RFC339-compliant.
The basic (recommended) format is <YEAR>-<MONTH>-<DAY>T<HOUR>:<MINUTE>:<SECONDS>Z
- e.g. 2022-12-12T18:39:09Z
. Feel free to get precise with
subseconds though if you like...
``` Extract subsets of ONT (Nanopore) reads based on time
Usage: ontime [OPTIONS]
Arguments:
Options:
-o, --output
-O, --output-type 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 <1-9> Compression level to use if compressing output
[default: 6]
-f, --from
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
See --from (and docs) for examples
-s, --show Show the earliest and latest start times in the input and exit
-h, --help
Print help information (use -h
for a summary)
-V, --version Print version information ```