hello cenote-taker 3

.gitignore

@@ -1,3 +1,13 @@
+blast_DBs/
+cdd_rps_db/
+hmmscan_DBs/
+taxdump/
+.DS_Store
+**/.DS_Store
+mmseqs_DBs/
+pfam_32_db/
+
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

dummy_template.sbt

@@ -0,0 +1,90 @@
+Submit-block ::= {
+  contact {
+    contact {
+      name name {
+        last "Taker",
+        first "Cenote",
+        middle "",
+        initials "",
+        suffix "",
+        title ""
+      },
+      affil std {
+        affil "Cenote",
+        div "Taker 2",
+        city "Cenote",
+        sub "DC",
+        country "USA",
+        street "1000 Circle St.",
+        email "cenote@donotsubmit.net",
+        postal-code "31111"
+      }
+    }
+  },
+  cit {
+    authors {
+      names std {
+        {
+          name name {
+            last "Taker",
+            first "Cenote",
+            middle "",
+            initials "",
+            suffix "",
+            title ""
+          }
+        }
+      },
+      affil std {
+        affil "Cenote",
+        div "Taker 2",
+        city "Cenote",
+        sub "DC",
+        country "USA",
+        street "1000 Circle St.",
+        postal-code "31111"
+      }
+    }
+  },
+  subtype new
+}
+Seqdesc ::= pub {
+  pub {
+    gen {
+      cit "unpublished",
+      authors {
+        names std {
+          {
+            name name {
+              last "Taker",
+              first "Cenote",
+              middle "",
+              initials "",
+              suffix "",
+              title ""
+            }
+          }
+        }
+      },
+      title "Cenote-Taker 2 dummy template file. Do NOT submit"
+    }
+  }
+}
+Seqdesc ::= user {
+  type str "Submission",
+  data {
+    {
+      label str "AdditionalComment",
+      data str "ALT EMAIL:cenote@donotsubmit.net"
+    }
+  }
+}
+Seqdesc ::= user {
+  type str "Submission",
+  data {
+    {
+      label str "AdditionalComment",
+      data str "Submission Title:None"
+    }
+  }
+}

pyproject.toml

@@ -0,0 +1,38 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "cenotetaker3"
+version = "3.0.0"
+authors = [
+  { name="Mike Tisza", email="michael.tisza@gmail.com" },
+]
+description = "Discover and annotate the virome."
+readme = "README.md"
+requires-python = ">=3.6"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+]
+dependencies = [
+    "numpy",    
+    "biopython",
+]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+"cenotetaker3" = ["*.sbt", "*.sh"]
+
+[tool.setuptools]
+script-files = ["src/cenote/cenote_main.sh", "src/cenote/dummy_template.sbt"]
+
+[project.scripts]  
+cenotetaker3 = "cenote:cenotetaker3"
+
+[project.urls]
+"Homepage" = "https://github.com/cmmr/Cenote-Taker3"
+"Bug Tracker" = "https://github.com/cmmr/Cenote-Taker3/issues"

src/cenote/__init__.py

@@ -0,0 +1 @@
+from .cenotetaker3 import cenotetaker3