From cc4fdb181e6ef48ded534692715dd968307964d4 Mon Sep 17 00:00:00 2001 From: Luis Pedro Coelho Date: Thu, 27 Jun 2024 23:08:45 +1000 Subject: [PATCH] DOC Document query-ampsphere subcommand --- README.md | 14 ++++++++++++++ docs/usage.md | 16 ++++++++++++++++ docs/whatsnew.md | 2 +- 3 files changed, 31 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index dbe28d2..b7125a4 100644 --- a/README.md +++ b/README.md @@ -126,6 +126,20 @@ name of the AMPs and the second with the number of reads mapped back to each pep using the given reference. An example of this output using the example file can be found at `test/abundances/expected.abundance.txt`. +### AMPSphere Querying + +Macrel also supports querying the [AMPSphere database](https://ampsphere.big-data-biology.org/) (described in [Santos-Júnior et al., 2024](https://doi.org/10.1016/j.cell.2024.05.013)). To do so, use the `query-ampsphere` subcommand: + +```bash +macrel query-ampsphere \ + --fasta example_seqs/pep8.faa \ + --output out_ampsphere +``` + +Note that this command requires internet access as it uses the AMPSphere API. + +By default it performs exact matching, but you can also use MMSeqs2 to perform approximate matching by using the `--query-mode=mmseqs` (or `--query-mode=hmm` for HMMER). + ### Community Macrel is actively maintained to fix all issues and assimilate suggestions we diff --git a/docs/usage.md b/docs/usage.md index 8962421..973cb34 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -136,3 +136,19 @@ This mode returns a table of abundances containing two columns, the first with t name of the AMPs and the second with the number of reads mapped back to each peptide using the given reference. An example of this output using the example file can be found at `test/abundances/expected.abundance.txt`. + +### AMPSphere Querying + +Macrel also supports querying the [AMPSphere database](https://ampsphere.big-data-biology.org/) (described in [Santos-Júnior et al., 2024](https://doi.org/10.1016/j.cell.2024.05.013)). To do so, use the `query-ampsphere` subcommand: + +```bash +macrel query-ampsphere \ + --fasta example_seqs/pep8.faa \ + --output out_ampsphere +``` + +Note that this command requires internet access as it uses the AMPSphere API. Future versions of macrel will allow you to use a local database. + +By default it performs exact matching (equivalent to passing in `--query-mode=exact`), but you can also use MMSeqs2 to perform approximate matching by using the `--query-mode=mmseqs` (or `--query-mode=hmm` for HMMER). + +Note that since these use the API, you do not need to have the AMPSphere database downloaded locally or installed MMSeqs2/HMMER. diff --git a/docs/whatsnew.md b/docs/whatsnew.md index adada8a..aefbc74 100644 --- a/docs/whatsnew.md +++ b/docs/whatsnew.md @@ -2,7 +2,7 @@ ## Unreleased -- Adds `query-ampsphere` command to query the AMPsphere database +- Adds `query-ampsphere` command to query the [AMPsphere database](https://ampsphere.big-data-biology.org/) (described in [Santos-Júnior et al., 2024](https://doi.org/10.1016/j.cell.2024.05.013)). ## Version 1.3.0