Merge pull request #30 from klebgenomics/development

Bump to version 3.0.0b1

docs/source/Installation.rst

@@ -9,7 +9,7 @@ Kaptive requires the following software and libraries to be installed and availa
 
 * `Python <https://python.org/>`_ >=3.9
 * `Biopython <https://biopython.org/>`_ >=1.83
-* `minimap2 <https://lh3.github.io/minimap2/>`_.
+* `minimap2 <https://lh3.github.io/minimap2/>`_
 * `DNA Features Viewer <https://edinburgh-genome-foundry.github.io/DnaFeaturesViewer/>`_
 
 
@@ -18,10 +18,14 @@ Download and install Kaptive
 
 With pip::
 
-   git clone https://github.com/klebgenomics/Kaptive.git
-   pip install Kaptive/
-
+    pip install kaptive
 
 With conda::
 
-   conda install -c bioconda kaptive
+    conda install -c bioconda kaptive
+
+From source::
+
+    git clone https://github.com/klebgenomics/Kaptive.git
+    python -m pip install Kaptive/
+

kaptive/__main__.py

@@ -26,7 +26,8 @@
 
 from kaptive.version import __version__
 from kaptive.log import bold, quit_with_error
-from kaptive.misc import check_python_version, check_programs, get_logo, check_cpus, check_dir, check_file
+from kaptive.misc import (check_python_version, check_biopython_version, check_programs, get_logo, check_cpus,
+                          check_dir, check_file)
 from kaptive.database import Database, get_database
 from kaptive.assembly import typing_pipeline, TypingResult
 
@@ -276,7 +277,8 @@ def plot_result(result: TypingResult, outdir: Path, fmt: str):
 
 # Main -----------------------------------------------------------------------------------------------------------------
 def main():
-    check_python_version()
+    check_python_version(3, 9)
+    check_biopython_version(1, 83)
     args = parse_args(sys.argv[1:])
 
     # Assembly mode ----------------------------------------------------------------------------------------------------

kaptive/assembly.py

@@ -236,6 +236,8 @@ def typing_pipeline(
             previous_result = gene_result  # Set the previous result to the current result
         # FINALISE CONTIG ---------------------------------------------------------------------------------------------
         for piece in pieces:  # Add sequences to pieces and add them to the result
+            if not piece.expected_genes: # If the piece has no expected genes, skip it
+                continue
             piece.strand = "+" if max(i.strand == i.gene.strand for i in piece.expected_genes) else "-"
             piece.sequence = contig.sequence[piece.start:piece.end] if piece.strand == "+" else \
                 contig.sequence[piece.start:piece.end].reverse_complement()

kaptive/misc.py

@@ -88,6 +88,15 @@ def check_python_version(major: int = 3, minor: int = 8):
         quit_with_error(f'Python version {major}.{minor} or greater required')
 
 
+def check_biopython_version(major: int = 1, minor: int = 79):
+    try:
+        from Bio import __version__ as biopython_version
+    except ImportError:
+        quit_with_error('BioPython is required')
+    if (major_version := int(biopython_version.split('.')[0])) < major or (minor_version := int(biopython_version.split('.')[1])) < minor:
+        quit_with_error(f'Biopython version {major}.{minor} or greater required, got {major_version}.{minor_version}')
+
+
 def parse_fasta(fasta: Path, skip_plasmids: bool = False, verbose: bool = False) -> Generator[tuple[str, str, str], None, None]:
     log(f'Parsing {fasta.name}', verbose)
     with open(fasta, 'rb') as f:  # Read the first two bytes to determine the compression format

kaptive/typing.py

@@ -130,7 +130,7 @@ def phenotype(self) -> str:
     def problems(self) -> str:
         if self._problems is not None:
             return self._problems
-        problems = f'?{x}' if (x := len(self.pieces)) > 1 else ''
+        problems = f'?{x}' if (x := len(self.pieces)) != 1 else ''
         problems += '-' if self.missing_genes else ''
         problems += '+' if self.unexpected_genes_inside_locus else ''
         problems += '*' if any(

kaptive/version.py

@@ -14,4 +14,4 @@
 If not, see <https://www.gnu.org/licenses/>.
 """
 
-__version__ = '3.0.0b'
+__version__ = '3.0.0b1'

pyproject.toml

@@ -0,0 +1,34 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "kaptive"
+authors = [
+    {name="Tom Stanton", email="[email protected]" },
+]
+description = "In silico serotyping"
+readme = {file = "README.md", content-type = "text/markdown"}
+requires-python = ">=3.9"
+dependencies = ["biopython", "dna_features_viewer"]
+keywords = ["bioinformatics", "serotyping", "microbiology"]
+license = {file = "LICENSE"}
+classifiers = [
+    "Environment :: Console",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+]
+dynamic = ["version"]
+
+[project.scripts]
+kaptive = "kaptive.__main__:main"
+
+[tool.setuptools.packages.find]
+include = ["kaptive"]
+exclude = ["test", 'development']
+
+[tool.setuptools.package-data]
+kaptive = ['../reference_database/*']
+
+[tool.setuptools.dynamic]
+version = {attr = "kaptive.version.__version__"}

reference_database/Klebsiella_o_locus_primary_reference.gbk

@@ -48,7 +48,7 @@ FEATURES             Location/Qualifiers
                      RDWLYVEDHARALYKVATEGKSGETYNIGGHNERKNIDVVRTICTILDKVVAQKPGNIT
                      HFADLITFVTDRPGHDLRYAIDATKIQHDLGWVPQETFESGIEKTVHWYLNNQTWWQRV
                      LDGSYAGERLGLNN"
-                     /locus_tag="OL101_01_rfbB"
+                     /locus_tag="OL13_01_rfbB"
      gene            1092..1961
                      /gene="rfbA"
      CDS             1092..1961
@@ -67,7 +67,7 @@ FEATURES             Location/Qualifiers
                      PKSDWAVTGLYFYDNNVVEMAKDVKPSERGELEITTLNQMYLEQGDLHVELLGRGFAWL
                      DTGTHDSLMDASQFIHTIEKRQGMKVACLEEIAYRNQWLSAEGVAAQAERLKKTEYGAY
                      LKRLLNER"
-                     /locus_tag="OL101_02_rfbA"
+                     /locus_tag="OL13_02_rfbA"
      gene            1993..2883
                      /gene="rfbD"
      CDS             1993..2883
@@ -86,7 +86,7 @@ FEATURES             Location/Qualifiers
                      KTMLRLAGEKETLTIIDDQHGAPTGAELLADCTATAIRETLRNPALAGTYHLVASGETS
                      WCDYARYVFEVARAHGAELAIQEVKGIPTTAYPTPAKRPLNSRLSNEKFQQAFGVTLPD
                      WRQGVARVVTEVLGK"
-                     /locus_tag="OL101_03_rfbD"
+                     /locus_tag="OL13_03_rfbD"
      gene            2898..3452
                      /gene="rfbC"
      CDS             2898..3452
@@ -103,7 +103,7 @@ FEATURES             Location/Qualifiers
                      VQDNHSQSQKGVLRGLHYQLDPHAQGKLVRCVEGEVFDVAVDIRRSSSTFGKWVGAVLS
                      AENKRQLWIPEGFAHGFMALSDTVQFVYKATNYYAPQSERSIIWNDPEIGIDWPALNDC
                      ALSLSEKDLQAHTLATAEVYA"
-                     /locus_tag="OL101_04_rfbC"
+                     /locus_tag="OL13_04_rfbC"
      gene            3539..4369
                      /gene="wbbL"
      CDS             3539..4369
@@ -121,7 +121,7 @@ FEATURES             Location/Qualifiers
                      LVSFAWVNEYNFVSPQIIYKNGERQYSCRLLPTPSNLFLRRFLPTTAIKYDATYELKDA
                      EYDKVFSPPSVSGCFMLLTNVLLQKLNGFDERYFMYLEDVDLCRRALQLTKIYYCPETT
                      IVHVFNKGSYKSKLLLWYHVRSAITYFNKWGWFFDKKRYAYNESALRNIPRKLS"
-                     /locus_tag="OL101_05_wbbL"
+                     /locus_tag="OL13_05_wbbL"
      gene            4398..5231
                      /gene="wzm"
      CDS             4398..5231
@@ -138,7 +138,7 @@ FEATURES             Location/Qualifiers
                      QIILNNTNYVKKVIFPLETLSVISLVAALFHTTISLLVLLTAFVIFNGFIHWTIIFIPL
                      VFLPLVIFSLGLSWILASLGVFLRDVSQTTVIITTVLMFLSPVFFPISALPEKYHIWIM
                      LNPVTFIIEQARTVLIWGGLPNFMGILLYTVGASIVAWLGFVFFQKTRKGFADVL"
-                     /locus_tag="OL101_06_wzm"
+                     /locus_tag="OL13_06_wzm"
      gene            5221..6552
                      /gene="wzt"
      CDS             5221..6552
@@ -159,7 +159,7 @@ FEATURES             Location/Qualifiers
                      AIQNTQTNSEVDEKRFGSGRAIIEDFSIMKADGTPLSEKPLVKPNEEIYFSFKLNSSEN
                      INDVVLGVSLSRTQGGDIWGDNNIFAGHKIDLAPGLRKLKYKVKLPINTGDYLVHCGLA
                      CFNNGEREELDQRRPIAKVKFWSSRELGGVIHSPVNVIEGDELS"
-                     /locus_tag="OL101_07_wzt"
+                     /locus_tag="OL13_07_wzt"
      gene            6549..10115
                      /gene="wbbB"
      CDS             6549..10115
@@ -192,7 +192,7 @@ FEATURES             Location/Qualifiers
                      RIINWDISFQRMSELWRQAIADFDGFFQQQSVDPMPDVSSETRVDHFYRDYYIRDSWWR
                      ESELGRIDFKTLIDSFYSSDNITIVEEKISQPQGRKEKLLAILWMLRQNPALSWVTKLI
                      PYRLQRYVKRQLSRRALHEIVR"
-                     /locus_tag="OL101_08_wbbB"
+                     /locus_tag="OL13_08_wbbB"
      gene            complement(10274..12064)
                      /gene="glycosylhydrolase"
      CDS             complement(10274..12064)
@@ -215,7 +215,7 @@ FEATURES             Location/Qualifiers
                      GRERTFSHQIAPMFNADWNEEKIAAEDSLKKNNHYNIGLNTYGSAFYGDYLFNWLKTSG
                      IERYGIPEVHPMVENEEVIYDALEHHHNNGAIFISPYYLEIKPDSFGVDKEHEKFSINE
                      NNTNYYSSSFYHALKKIMKE"
-                     /locus_tag="OL101_09_glycosylhydrolase"
+                     /locus_tag="OL13_09_glycosylhydrolase"
 ORIGIN
         1 atgaagattc ttgtcaccgg gggtgcaggc tttatcggtt ctgccgtggt tcgtcatatc
        61 attgaaaata ccctggacga agtccgtgtg atggactgcc tgacctacgc cggcaacctt