RLS Version 1.5.0

Add support for local querying of the AMPSphere Full `ChangeLog`: - Add support for local searching - Slightly change output format for AMPSphere matching - Add --verbose and --quiet flags
BigDataBiology · Sep 20, 2024 · 83fe40b · 83fe40b
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diff --git a/ChangeLog b/ChangeLog
@@ -1,4 +1,4 @@
-Unreleased
+Version 1.5.0 2024-09-20
 	* Add support for local searching
 	* Slightly change output format for AMPSphere matching
 	* Add --verbose and --quiet flags

diff --git a/README.md b/README.md
@@ -128,17 +128,32 @@ 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:
+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.
+Note that, by default, this command requires internet access as it uses the
+AMPSphere API. Alternatively, you can use the `--local` flag to download a copy
+of the database and run the queries locally. This only requires the network the
+first time.
 
-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).
+```bash
+macrel query-ampsphere \
+    --local \
+    --fasta example_seqs/pep8.faa \
+    --output out_ampsphere
+```
+
+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
 

diff --git a/docs/whatsnew.md b/docs/whatsnew.md
@@ -1,5 +1,13 @@
 # What's new? (History)
 
+## Version 1.5.0
+
+*Released 20 September 2024*
+
+- Add support for local searching when querying the [AMPSphere database](https://ampsphere.big-data-biology.org/)
+- Slightly change output format for AMPSphere matching
+- Add --verbose and --quiet flags
+
 ## Version 1.4.0
 
 *Released 27 June 2024*

diff --git a/macrel/macrel_version.py b/macrel/macrel_version.py
@@ -1 +1 @@
-__version__ = '1.5.0.dev0'
+__version__ = '1.5.0'
diff --git a/tests/contigs.cluster/expected.prediction b/tests/contigs.cluster/expected.prediction
@@ -1,4 +1,4 @@
-# Prediction from macrel v1.5.0.dev0
+# Prediction from macrel v1.5.0
 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
@@ -1,4 +1,4 @@
-# Prediction from macrel v1.5.0.dev0
+# Prediction from macrel v1.5.0
 # 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
@@ -1,2 +1,2 @@
-# Prediction from macrel v1.5.0.dev0
+# Prediction from macrel v1.5.0
 Access	Sequence	AMP_family	AMP_probability	Hemolytic	Hemolytic_probability
diff --git a/tests/contigs/expected.percontigs b/tests/contigs/expected.percontigs
@@ -1,4 +1,4 @@
-# Prediction from macrel v1.5.0.dev0
+# Prediction from macrel v1.5.0
 # 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
@@ -1,4 +1,4 @@
-# Prediction from macrel v1.5.0.dev0
+# Prediction from macrel v1.5.0
 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
@@ -1,4 +1,4 @@
-# Prediction from macrel v1.5.0.dev0
+# Prediction from macrel v1.5.0
 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
@@ -1,4 +1,4 @@
-# Prediction from macrel v1.5.0.dev0
+# Prediction from macrel v1.5.0
 # 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
@@ -1,4 +1,4 @@
-# Prediction from macrel v1.5.0.dev0
+# Prediction from macrel v1.5.0
 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
@@ -1,4 +1,4 @@
-# Prediction from macrel v1.5.0.dev0
+# Prediction from macrel v1.5.0
 # 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
@@ -1,4 +1,4 @@
-# Prediction from macrel v1.5.0.dev0
+# Prediction from macrel v1.5.0
 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