Merge pull request #92 from gbouras13/1.0.1

v1.1.0

.github/workflows/ci.yaml

@@ -13,7 +13,7 @@ jobs:
 
     strategy:
       matrix:
-        os: [macos-12, ubuntu-latest]
+        os: [macos-13, ubuntu-latest]
         python-version: ["3.9"]
 
     steps:

HISTORY.md

@@ -1,9 +1,15 @@
 # History
 
+# 1.1.0 (2025-01-13)
+
+* Adds support for reorienting contigs where the gene of interest spands the contig ends - [fixes this issue](https://github.com/gbouras13/dnaapler/issues/90). Thanks @marade @oschwengers.
+  * Specifically, this is done by rotating each contig in the input by half the genome length, then running `MMseqs2` for both the original and rotated contigs. The `MMseqs2` hit with the highest bitscore across the original and rotated contigs will be chosen as the top hit to rotate by, therefor enabling detection of partial hits (on the original contig) that span the contig ends. 
+* This has only been implemented for `dnaapler all` (this should be the command used by 99% of users).
+
 # 1.0.1 (2024-11-22)
 
 * Thanks to the inimitable @[rrwick](https://github.com/rrwick), v1.0.1 is a patch fixing a string-parsing bug.
-* If your contig headers were integers, `dnaapler` did not rotate the found `BLAST/MMseqs2` hits. This was pre-existing (not introduced by v1.0.0).
+* If your contig headers were integers, `dnaapler` did not rotate the found `BLAST/MMseqs2` hits. This was a pre-existing issue (not introduced by v1.0.0).
 
 # 1.0.0 (2024-11-21)
 

README.md

@@ -32,9 +32,16 @@ conda install -c bioconda dnaapler
 # runs dnaapler all 
 dnaapler all -i input_mixed_contigs.fasta -o output_directory_path -p my_bacteria_name -t 8
 
-# runs dnaapler chromosome
-dnaapler chromosome -i input_chromosome.fasta -o output_directory_path -p my_bacteria_name -t 8
+```
+
+* If you have a MacOS machine with Apple Silicon (M1/M2/M3/M4), please try
 
+```
+conda create --platform osx-64 -n dnaapler_env dnaapler
+
+conda activate dnaapler_env
+
+dnaapler all -i input_mixed_contigs.fasta -o output_directory_path -p my_bacteria_name -t 8
 ```
 
 ## Paper
@@ -59,7 +66,15 @@ Larralde, M., (2022). Pyrodigal: Python bindings and interface to Prodigal, an e
 Hyatt, D., Chen, GL., LoCascio, P.F. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010). https://doi.org/10.1186/1471-2105-11-119.
 ```
 
-## v1
+## v1 and other recent changes
+
+# 1.1.0
+
+* Adds support for reorienting contigs where the gene of interest spands the contig ends - [fixes this issue](https://github.com/gbouras13/dnaapler/issues/90). Thanks @marade @oschwengers.
+  * Specifically, this is done by rotating each contig in the input by half the genome length, then running `MMseqs2` for both the original and rotated contigs. The `MMseqs2` hit with the highest bitscore across the original and rotated contigs will be chosen as the top hit to rotate by, therefor enabling detection of partial hits (on the original contig) that span the contig ends. 
+* This has only been implemented for `dnaapler all` (this should be the command used by 99% of users).
+
+# v1.0
 
 * **BREAKING CHANGE** - `dnaapler` now uses `MMSeqs2 v13.45111` rather than `BLAST`. You will need to install [MMSeqs2](https://github.com/soedinglab/MMseqs2) if you upgrade (if you use conda, it should be handled for you). The CLI is identical.
 * There are 2 reasons for this:
@@ -78,7 +93,9 @@ If you don't want to install `dnaapler` locally, you can run `dnaapler all` with
 - [dnaapler](#dnaapler)
   - [Quick Start](#quick-start)
   - [Paper](#paper)
-  - [v1](#v1)
+  - [v1 and other recent changes](#v1-and-other-recent-changes)
+- [1.1.0](#110)
+- [v1.0](#v10)
 - [Google Colab Notebooks](#google-colab-notebooks)
   - [Table of Contents](#table-of-contents)
   - [Description](#description)
@@ -110,6 +127,8 @@ Additionally, you can also reorient multiple bacterial chromosomes/plasmids/phag
 
 If your input FASTA is mixed (e.g. has chromosome and plasmids), you can also use `dnaapler all`, with the option to ignore some contigs with the `--ignore` parameter.
 
+**As of v1, in practice, `dnaapler all` is the only command you will likely need, as it contains all the functionality of `bulk`, `chromosome`, `plasmid`, `phage` but with much more flexibility and user-friendliness**
+
 ## Documentation
 
 The full documentation for `dnaapler` can be found [here](https://dnaapler.readthedocs.io).

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dnaapler"
-version = "1.0.1" # change VERSION too
+version = "1.1.0" # change VERSION too
 description = "Reorients assembled microbial sequences"
 authors = ["George Bouras <[email protected]>"]
 license = "MIT"

src/dnaapler/__init__.py

@@ -21,12 +21,14 @@
 )
 from dnaapler.utils.constants import DNAAPLER_DB
 from dnaapler.utils.external_tools import ExternalTool
+from dnaapler.utils.processing import rotate_input
 from dnaapler.utils.util import (
     begin_dnaapler,
     check_duplicate_headers,
     end_dnaapler,
     get_version,
     print_citation,
+    remove_file,
     run_autocomplete,
 )
 from dnaapler.utils.validation import (
@@ -841,7 +843,7 @@ def bulk(
     default="all",
     type=click.STRING,
     callback=validate_choice_db,
-    help="Lets you choose a subset of databases rather than all 3. Must be one of: 'all', 'dnaa', 'repa', terl', 'dnaa,repa', 'dnaa,terl' or 'repa,terl' ",
+    help="Lets you choose a subset of databases rather than all 4. Must be one of: 'all', 'dnaa', 'repa', terl', 'cog1474', 'dnaa,repa', 'dnaa,terl', 'repa,terl',  'dnaA,cog1474', 'cog1474,terl', 'cog1474,repa', 'dnaa,cog1474,repa', 'dnaa,cog1474,terl' or 'cog1474,repa,terl'",
     show_default=True,
 )
 @click.option(
@@ -968,9 +970,14 @@ def all(
     else:
         custom_db = None
 
+    # rotate all replicons by half the length of the contig
+    # the rotated input for MMSeqs2 will have the original contigs + the rotated ones with suffix "rotated_"
+    rotated_input = os.path.join(output, "rotated_input.fasta")
+    rotate_input(input, rotated_input)
+
     # runs bulk MMseqs2
     run_bulk_MMseqs2(
-        ctx, input, output, prefix, gene, evalue, threads, custom_db=custom_db
+        ctx, rotated_input, output, prefix, gene, evalue, threads, custom_db=custom_db
     )
 
     # rerorients MMseqs2
@@ -998,8 +1005,12 @@ def all(
         autocomplete,
         seed_value,
         custom_db=custom_db,
+        gene=gene,
     )
 
+    # remove the rotated input
+    remove_file(Path(rotated_input))
+
     # end dnaapler
     end_dnaapler(start_time)
 

src/dnaapler/utils/VERSION

@@ -1 +1 @@
-1.0.1
+1.1.0