From f66af732124fb11be91f20e429af887775b242ee Mon Sep 17 00:00:00 2001 From: Luis Pedro Coelho Date: Tue, 5 Dec 2023 11:58:12 +1000 Subject: [PATCH] RLS Version 1.3.0 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Output density values - Compatibility with Pyrodigal ≥3.0 --- ChangeLog | 3 ++- docs/whatsnew.md | 8 ++++++++ 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, 21 insertions(+), 12 deletions(-) diff --git a/ChangeLog b/ChangeLog index e16219c7..a91a54e7 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,4 +1,5 @@ -Unreleased +Version 1.3.0 2023-12-05 + * Add compatibility with Pyrodigal ≥3 * Add density estimates to output Version 1.2.0 2022-05-09 diff --git a/docs/whatsnew.md b/docs/whatsnew.md index 0a9fa160..9db85258 100644 --- a/docs/whatsnew.md +++ b/docs/whatsnew.md @@ -1,5 +1,13 @@ # What's new? (History) +## Version 1.3.0 + +*Released 5 December 2023* + +- Adds density estimates to output +- Adds compatibility with Pyrodigal ≥3 + + ## Version 1.2.0 *Released May 9 2022* diff --git a/macrel/macrel_version.py b/macrel/macrel_version.py index 58d478ab..19b4f1d6 100644 --- a/macrel/macrel_version.py +++ b/macrel/macrel_version.py @@ -1 +1 @@ -__version__ = '1.2.0' +__version__ = '1.3.0' diff --git a/tests/contigs.cluster/expected.prediction b/tests/contigs.cluster/expected.prediction index af9a6d1a..8f7f4f32 100644 --- a/tests/contigs.cluster/expected.prediction +++ b/tests/contigs.cluster/expected.prediction @@ -1,4 +1,4 @@ -# Prediction from macrel v1.2.0 +# Prediction from macrel v1.3.0 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 138570d7..741381df 100644 --- a/tests/contigs.nosmorfs/expected.percontigs +++ b/tests/contigs.nosmorfs/expected.percontigs @@ -1,4 +1,4 @@ -# Prediction from macrel v1.2.0 +# Prediction from macrel v1.3.0 # 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 1e0757ff..3542bc6e 100644 --- a/tests/contigs.nosmorfs/expected.prediction +++ b/tests/contigs.nosmorfs/expected.prediction @@ -1,2 +1,2 @@ -# Prediction from macrel v1.2.0 +# Prediction from macrel v1.3.0 Access Sequence AMP_family AMP_probability Hemolytic Hemolytic_probability diff --git a/tests/contigs/expected.percontigs b/tests/contigs/expected.percontigs index 5c6b96ac..f0612a67 100644 --- a/tests/contigs/expected.percontigs +++ b/tests/contigs/expected.percontigs @@ -1,4 +1,4 @@ -# Prediction from macrel v1.2.0 +# Prediction from macrel v1.3.0 # Macrel calculated for the sample a density of 45.062 AMPs / Mbp. contig length ORFs smORFs AMPs scaffold2530_2_MH0058 717 2 2 0 diff --git a/tests/contigs/expected.prediction b/tests/contigs/expected.prediction index f074ed25..a69fcebd 100644 --- a/tests/contigs/expected.prediction +++ b/tests/contigs/expected.prediction @@ -1,4 +1,4 @@ -# Prediction from macrel v1.2.0 +# Prediction from macrel v1.3.0 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 332bac53..2973b714 100644 --- a/tests/peptides/expected.prediction +++ b/tests/peptides/expected.prediction @@ -1,4 +1,4 @@ -# Prediction from macrel v1.2.0 +# Prediction from macrel v1.3.0 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 3565512c..e668cb86 100644 --- a/tests/reads.se/expected.percontigs +++ b/tests/reads.se/expected.percontigs @@ -1,4 +1,4 @@ -# Prediction from macrel v1.2.0 +# Prediction from macrel v1.3.0 # 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 d520697c..f670ad6d 100644 --- a/tests/reads.se/expected.prediction +++ b/tests/reads.se/expected.prediction @@ -1,4 +1,4 @@ -# Prediction from macrel v1.2.0 +# Prediction from macrel v1.3.0 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 62e1c85d..a33fd26b 100644 --- a/tests/reads/expected.percontigs +++ b/tests/reads/expected.percontigs @@ -1,4 +1,4 @@ -# Prediction from macrel v1.2.0 +# Prediction from macrel v1.3.0 # Macrel calculated for the sample a density of 57.627 AMPs / Mbp. contig length ORFs smORFs AMPs k77_3 1270 1 0 0 diff --git a/tests/reads/expected.prediction b/tests/reads/expected.prediction index ede595d7..1eec540a 100644 --- a/tests/reads/expected.prediction +++ b/tests/reads/expected.prediction @@ -1,4 +1,4 @@ -# Prediction from macrel v1.2.0 +# Prediction from macrel v1.3.0 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