restructure

cli.py → clinker/cli.py

@@ -23,8 +23,10 @@ def run(args):
     clusters = []
     print("Parsing GenBank files")
     for file in args.files:
+        print(file)
         records = [record for record in SeqIO.parse(file, "genbank")]
         cluster = Cluster.from_seqrecords(*records, mode=args.mode)
+        print(cluster.name, cluster.loci)
         clusters.append(cluster)
 
     # Scan genes for smCOGs if protein mode specified
@@ -38,9 +40,11 @@ def run(args):
     print("Aligning your clusters")
     aligner = globaligner.align_clusters(*clusters)
 
+    print(aligner)
+
     # Generate the SVG
     print("Generating the figure")
-    figure = visualise.Figure(aligner=aligner, width=args.width).render("maximize")
+    figure = visualise.Figure(aligner=aligner, width=args.width).render("added")
 
     # Write output files
     with open(args.output, "w") as svg:

globaligner.py → clinker/globaligner.py

@@ -193,7 +193,7 @@ def get_cluster(self, cluster):
             raise KeyError("No cluster with this name could be retrieved") from exc
 
     # TODO: check for number of genes vs pure identity score
-    def compute_display_order(self, order="maximize"):
+    def compute_display_order(self, order="first_as_seed"):
         """ Return sorted cluster name list based on specified order scheme.
 
             Arguments:
@@ -221,9 +221,13 @@ def compute_display_order(self, order="maximize"):
             for permutation in permutations(self._clusters.keys()):
                 score = 0
                 for i in range(1, total_clusters):
-                    score += self.get_alignment(
-                        permutation[i - 1], permutation[i]
-                    ).score
+                    try:
+                        score += self.get_alignment(
+                            permutation[i - 1], permutation[i]
+                        ).score
+                    except ValueError:
+                        # no links
+                        continue
                 if score > best_score:
                     best_score = score
                     best_permutation = permutation
@@ -245,12 +249,19 @@ def compute_display_order(self, order="maximize"):
                         continue
 
                     # Grab alignment between last added cluster and next
-                    alignment = self.get_alignment(permutation[-1], target)
-                    if alignment.score > max_score:
-                        max_score = alignment.score
-                        max_cluster = target
+                    try:
+                        alignment = self.get_alignment(permutation[-1], target)
+                    except KeyError:
+                        continue
+                    try:
+                        if alignment.score > max_score:
+                            max_score = alignment.score
+                            max_cluster = target
+                    except ValueError:
+                        continue
 
-                permutation.append(max_cluster)
+                if max_cluster:
+                    permutation.append(max_cluster)
 
             return permutation
 
@@ -301,6 +312,8 @@ def find_gene(self, gene_name):
     @property
     def score(self):
         """Calculate 'score' of this alignment by summing identities."""
+        if not self.links:
+            raise ValueError("Alignment has no links")
         return sum(link.identity + link.similarity for link in self.links) / len(
             self.links
         )

visualise.py → clinker/visualise.py

@@ -83,7 +83,13 @@ def render(self, order):
         genes = ""
 
         for count, cluster_name in enumerate(display_order):  # cluster names
-            cluster = self.aligner.get_cluster(cluster_name)
+            print(count, cluster_name)
+
+            try:
+                cluster = self.aligner.get_cluster(cluster_name)
+            except:
+                continue
+
             cluster_maps.append(
                 cluster.map_cluster(
                     locus_spacing=self.locus_spacing, scale_factor=scale_factor
@@ -105,6 +111,8 @@ def render(self, order):
                     lower = previous_cluster.genes[index]
                     upper = previous_cluster.genes[previous_total - index - 1]
 
+                    print(lower, upper)
+
                     if first and last:
                         break
 

setup.py

@@ -0,0 +1,39 @@
+import re
+
+from pathlib import Path
+from setuptools import setup, find_packages
+
+with open("README.md") as readme:
+    long_description = readme.read()
+
+
+def get_version():
+    """Get version number from __init__.py"""
+    version_file = Path(__file__).resolve().parent / "synthaser" / "__init__.py"
+    version_match = re.search(
+        r"^__version__ = ['\"]([^'\"]*)['\"]", version_file.read_text(), re.M
+    )
+    if version_match:
+        return version_match.group(1)
+    raise RuntimeError("Failed to find version string")
+
+
+setup(
+    name="clinker",
+    author="Cameron Gilchrist",
+    version=get_version(),
+    description="",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    url="https://github.com/gamcil/clinker",
+    packages=find_packages(),
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "License :: OSI Approved :: MIT License",
+        "Operating System :: OS Independent",
+    ],
+    install_requires=["genome2json"],
+    python_requires=">=3.6",
+    entry_points={"console_scripts": ["synthaser=clinker.main:main"]},
+    include_package_data=True,
+)