From 1a4044866a02808cda59e3e7afe22035b9364b81 Mon Sep 17 00:00:00 2001 From: Luis Pedro Coelho Date: Thu, 27 Jun 2024 23:32:17 +1000 Subject: [PATCH] RLS Version 1.4.0 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 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)). --- ChangeLog | 2 +- docs/whatsnew.md | 4 +++- macrel/macrel_version.py | 2 +- tests/contigs.cluster/expected.prediction | 2 +- tests/contigs.nosmorfs/expected.percontigs | 2 +- tests/contigs.nosmorfs/expected.prediction | 2 +- tests/contigs/expected.percontigs | 2 +- tests/contigs/expected.prediction | 2 +- tests/peptides/expected.prediction | 2 +- tests/reads.se/expected.percontigs | 2 +- tests/reads.se/expected.prediction | 2 +- tests/reads/expected.percontigs | 2 +- tests/reads/expected.prediction | 2 +- 13 files changed, 15 insertions(+), 13 deletions(-) diff --git a/ChangeLog b/ChangeLog index c6d553b..0331832 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,4 +1,4 @@ -Unreleased +Version 1.4.0 2024-06-27 * Query AMPSphere online Version 1.3.0 2023-12-05 diff --git a/docs/whatsnew.md b/docs/whatsnew.md index aefbc74..a205501 100644 --- a/docs/whatsnew.md +++ b/docs/whatsnew.md @@ -1,6 +1,8 @@ # What's new? (History) -## Unreleased +## Version 1.4.0 + +*Released 27 June 2024* - 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)). diff --git a/macrel/macrel_version.py b/macrel/macrel_version.py index 19b4f1d..96e3ce8 100644 --- a/macrel/macrel_version.py +++ b/macrel/macrel_version.py @@ -1 +1 @@ -__version__ = '1.3.0' +__version__ = '1.4.0' diff --git a/tests/contigs.cluster/expected.prediction b/tests/contigs.cluster/expected.prediction index 8f7f4f3..5652ab2 100644 --- a/tests/contigs.cluster/expected.prediction +++ b/tests/contigs.cluster/expected.prediction @@ -1,4 +1,4 @@ -# Prediction from macrel v1.3.0 +# Prediction from macrel v1.4.0 Access Sequence AMP_family AMP_probability Hemolytic Hemolytic_probability smORF_2 RFLIKMVKVNLMNGKLIRKISLM CLP 0.634 Hemo 0.871 smORF_19 FFNDGKGTIYYGIKKYFRIYF CLP 0.673 Hemo 0.822 diff --git a/tests/contigs.nosmorfs/expected.percontigs b/tests/contigs.nosmorfs/expected.percontigs index 741381d..4b348cf 100644 --- a/tests/contigs.nosmorfs/expected.percontigs +++ b/tests/contigs.nosmorfs/expected.percontigs @@ -1,4 +1,4 @@ -# Prediction from macrel v1.3.0 +# Prediction from macrel v1.4.0 # Macrel calculated for the sample a density of 0.000 AMPs / Mbp. contig length ORFs smORFs AMPs scaffold2530_2_MH0058 1324 1 0 0 diff --git a/tests/contigs.nosmorfs/expected.prediction b/tests/contigs.nosmorfs/expected.prediction index 3542bc6..fc80bd4 100644 --- a/tests/contigs.nosmorfs/expected.prediction +++ b/tests/contigs.nosmorfs/expected.prediction @@ -1,2 +1,2 @@ -# Prediction from macrel v1.3.0 +# Prediction from macrel v1.4.0 Access Sequence AMP_family AMP_probability Hemolytic Hemolytic_probability diff --git a/tests/contigs/expected.percontigs b/tests/contigs/expected.percontigs index 11603cf..aa32044 100644 --- a/tests/contigs/expected.percontigs +++ b/tests/contigs/expected.percontigs @@ -1,4 +1,4 @@ -# Prediction from macrel v1.3.0 +# Prediction from macrel v1.4.0 # Macrel calculated for the sample a density of 45.062 AMPs / Mbp. contig length ORFs smORFs AMPs C4060843_1_MH0058 518 1 1 0 diff --git a/tests/contigs/expected.prediction b/tests/contigs/expected.prediction index a69fceb..121e266 100644 --- a/tests/contigs/expected.prediction +++ b/tests/contigs/expected.prediction @@ -1,4 +1,4 @@ -# Prediction from macrel v1.3.0 +# Prediction from macrel v1.4.0 Access Sequence AMP_family AMP_probability Hemolytic Hemolytic_probability scaffold75334_1_MH0058_1 RFLIKMVKVNLMNGKLIRKISLM CLP 0.634 Hemo 0.871 scaffold33693_17_MH0058_2 FFNDGKGTIYYGIKKYFRIYF CLP 0.673 Hemo 0.822 diff --git a/tests/peptides/expected.prediction b/tests/peptides/expected.prediction index 2973b71..411ca5f 100644 --- a/tests/peptides/expected.prediction +++ b/tests/peptides/expected.prediction @@ -1,4 +1,4 @@ -# Prediction from macrel v1.3.0 +# Prediction from macrel v1.4.0 Access Sequence AMP_family AMP_probability Hemolytic Hemolytic_probability AP00002|AMP YVPLPNVPQPGRRPFPTFPGQGPFNPKIKWPQGY CLP 0.861 Hemo 0.663 AP00007|AMP GNNRPVYIPQPRPPHPRL CLP 0.970 Hemo 0.515 diff --git a/tests/reads.se/expected.percontigs b/tests/reads.se/expected.percontigs index 744ef17..9df5423 100644 --- a/tests/reads.se/expected.percontigs +++ b/tests/reads.se/expected.percontigs @@ -1,4 +1,4 @@ -# Prediction from macrel v1.3.0 +# Prediction from macrel v1.4.0 # Macrel calculated for the sample a density of 59.743 AMPs / Mbp. contig length ORFs smORFs AMPs k47_0 3379 4 2 0 diff --git a/tests/reads.se/expected.prediction b/tests/reads.se/expected.prediction index f670ad6..7a677cf 100644 --- a/tests/reads.se/expected.prediction +++ b/tests/reads.se/expected.prediction @@ -1,4 +1,4 @@ -# Prediction from macrel v1.3.0 +# Prediction from macrel v1.4.0 Access Sequence AMP_family AMP_probability Hemolytic Hemolytic_probability k47_10_1 RFLIKMVKVNLMNGKLIRKISLM CLP 0.634 Hemo 0.871 k47_11_1 FFNDGKGTIYYGIKKYFRIYF CLP 0.673 Hemo 0.822 diff --git a/tests/reads/expected.percontigs b/tests/reads/expected.percontigs index e3ef230..002a1d5 100644 --- a/tests/reads/expected.percontigs +++ b/tests/reads/expected.percontigs @@ -1,4 +1,4 @@ -# Prediction from macrel v1.3.0 +# Prediction from macrel v1.4.0 # Macrel calculated for the sample a density of 57.627 AMPs / Mbp. contig length ORFs smORFs AMPs k77_11 1303 2 1 0 diff --git a/tests/reads/expected.prediction b/tests/reads/expected.prediction index 1eec540..901bcdb 100644 --- a/tests/reads/expected.prediction +++ b/tests/reads/expected.prediction @@ -1,4 +1,4 @@ -# Prediction from macrel v1.3.0 +# Prediction from macrel v1.4.0 Access Sequence AMP_family AMP_probability Hemolytic Hemolytic_probability k77_12_1 RFLIKMVKVNLMNGKLIRKISLM CLP 0.634 Hemo 0.871 k77_15_1 FFNDGKGTIYYGIKKYFRIYF CLP 0.673 Hemo 0.822