- Modified typing.GeneResult.compare_translation() to translate in all 3 frames and choose the longest translation. Prevents a protein alignment error where the translation is only a single amino acid.

- Fixed partial logic.

Author: tomdstanton

README.md

@@ -7,4 +7,4 @@ Kaptive reports information about surface polysaccharide loci for _Klebsiella pn
 
 A step-by-step tutorial is also available [here](https://bit.ly/kaptive-workshop).
 
-[![DOI](https://zenodo.org/badge/60247148.svg)](https://zenodo.org/badge/latestdoi/60247148)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11257262.svg)](https://doi.org/10.5281/zenodo.11257262)

docs/source/Databases-distributed-with-Kaptive.rst

@@ -123,6 +123,8 @@ same loci, the phenotype will instead be predicted as 'O1ab'.
 This logic is applied during the :ref:`phenotype prediction <Phenotype-prediction>` step of typing and is reported in
 the `Type` column of the Kaptive tabular output.
 
+.. _Distributed-databases:
+
 Databases distributed with Kaptive
 ====================================
 
@@ -331,51 +333,29 @@ Database                                                      Keywords
 
 Extract
 ====================================
-Kaptive 3.0.0 and above include a new command-line option ``--extract`` that allows you to extract features
+Kaptive 3.0.0 and above includes a new command-line mode ``extract`` that allows you to extract features
 from a Kaptive database in the following formats:
 
-* **loci**: Locus nucleotide sequences in fasta (fna) format.
-* **genes**: Gene nucleotide sequences in fasta (fna) format.
-* **proteins**: Protein sequences in fasta (faa) format.
-* **genbank**: Genbank format (same as input but optionally filtered).
-
-Simple usage is as follows::
-
-    kaptive extract <db> <format> [options]
-
-For example, If I wanted to extract the gene nucleotide sequences from the *Klebsiella pneumoniae* K locus primary
-reference database in fasta format, I would run::
-
-    kaptive extract kp_k loci > k_loci.fna
-
-If I wanted to extract all protein sequences from KL1 and KL2, I would run::
+* **fna**: Locus nucleotide sequences in fasta format.
+* **ffn**: Gene nucleotide sequences in fasta format.
+* **faa**: Protein sequences in fasta format.
 
-    kaptive extract kp_k proteins --filter "^KL(1|2)$" > KL1_KL2_proteins.faa
+Usage
+----------
+General usage is as follows::
 
-If I wanted to do the same but output each locus to a separate file, I would run::
+    kaptive extract <db> [formats] [options]
 
-    kaptive extract kp_k proteins --filter "^KL(1|2)$" -d KL1_KL2_proteins
-
-Which would create two files: ``KL1.faa`` and ``KL2.faa``.
-
-Inputs::
-
-  db path/keyword  Kaptive database path or keyword
-  format           Format to extract database
-                    - loci: Loci (fasta nucleotide)
-                    - genes: Genes (fasta nucleotide)
-                    - proteins: Proteins (fasta amino acid)
-                    - genbank: Genbank format
-
-.. note::
-  Combine with ``--filter`` to select loci
+Formats::
 
-Output options::
+  Note, text outputs accept '-' for stdout
 
-  -o , --out       Output file to write/append loci to (default: stdout)
-  -d , --outdir    Output directory for converted results
-                    - Note: This forces the output to be written to files (instead of stdout)
-                            and one file will be written per locus.
+  --fna []         Convert to locus nucleotide sequences in fasta format
+                   Accepts a single file or a directory (default: cwd)
+  --ffn []         Convert to locus gene nucleotide sequences in fasta format
+                   Accepts a single file or a directory (default: cwd)
+  --faa []         Convert to locus gene protein sequences in fasta format
+                   Accepts a single file or a directory (default: cwd)
 
 .. _Database-options:
 
@@ -394,3 +374,27 @@ Other options::
   -V, --verbose    Print debug messages to stderr
   -v , --version   Show version number and exit
   -h , --help      Show this help message and exit
+
+For example, to extract the gene nucleotide sequences from the *Klebsiella pneumoniae* K locus primary
+reference database in fasta format, run::
+
+    kaptive extract kp_k --fna k_loci.fna
+
+To extract all protein sequences from KL1 and KL2, run either one of the following::
+
+    kaptive extract kp_k --filter "^KL(1|2)$" --faa KL1_KL2_proteins.faa
+    kaptive extract kp_k --filter "^KL(1|2)$" --faa - > KL1_KL2_proteins.faa
+
+To do the same but output each locus to a separate file, run either::
+
+    kaptive extract kp_k --filter "^KL(1|2)$" --faa
+    kaptive extract kp_k --filter "^KL(1|2)$" --faa protein_files/
+
+Which would create two files: ``KL1.faa`` and ``KL2.faa``.
+
+        kaptive assembly kpsc_k assembly.fasta -j kaptive_results.json
+
+.. warning::
+ It is possible to write **all** text formats (FNA, FAA and FFN) to the same file (including stdout), however
+ this is not recommended for downstream analysis.
+

docs/source/Databases.rst

@@ -5,7 +5,8 @@ Installation
 Dependencies
 =============
 
-Kaptive requires the following software and libraries to be installed and available in your path:
+Kaptive requires the following software and libraries, if installing from source they will need to be installed and
+available in your path:
 
 * `Python <https://python.org/>`_ >=3.9
 * `Biopython <https://biopython.org/>`_ >=1.83
@@ -16,16 +17,15 @@ Kaptive requires the following software and libraries to be installed and availa
 Download and install Kaptive
 =============================
 
-With pip::
+From PyPI::
 
     pip install kaptive
 
-With conda::
+From Bioconda::
 
     conda install -c bioconda kaptive
 
 From source::
 
-    git clone https://github.com/klebgenomics/Kaptive.git
-    python -m pip install Kaptive/
+    pip install git+https://github.com/klebgenomics/Kaptive.git