.vscode/launch.json

@@ -8,16 +8,15 @@
             "name": "Splitter Single Gene with Translation",
             "type": "python",
             "request": "launch",
-            "program": "${workspaceFolder}/splitmsa/splitmsa.py",
+            "program": "${workspaceFolder}/msa_splitter.py",
             "args": [
                 "${workspaceFolder}/tests/resources/test_msa-shortened.fa",
-                "--gene-list",
-                "${workspaceFolder}/tests/resources/gene_list.csv",
+                "--gene-list", "${workspaceFolder}/tests/resources/gene_list.csv",
                 "-C",
-                "-E",
-                "DEBUG",
+                "-E", "DEBUG",
                 "--do-translate",
                 "--gen-cut-stop-codon"
+
             ],
             "console": "integratedTerminal",
             "justMyCode": true

Jenkinsfile

@@ -12,11 +12,6 @@ pipeline {
                 sh "python -m build"
             }
         }
-        stage("test") {
-            steps {
-                sh "pip install dist/*.whl"
-            }
-        }
         stage("publish") {
             when {
                 branch '**/master'

environment.yml

@@ -6,4 +6,3 @@ dependencies:
   - pytest=7.2.2
   - twine=4.0.2
   - biopython=1.81
-  - python=3.9

requirements.txt

@@ -0,0 +1 @@
+Bio==1.5.6

setup.cfg

@@ -1,11 +1,11 @@
 [metadata]
 name = splitmsa
-version = 0.0.2
+version = 0.0.1
 
 [options]
 packages = splitmsa
 install_requires =
-    biopython ==1.81; python_version == "3.9"
+    Bio
 
 [options.entry_points]
 console_scripts =

splitmsa/splitmsa.py

@@ -247,67 +247,6 @@ def output_as_csv(gene: str, problems: list[list[str]], output_path: str):
         writer.writerows(problems)
 
 
-def run(args):
-    msa_records = list(read_msa_file(args.input))
-    info(f"MSA records read complete. Found {len(msa_records)} records.")
-    genes = []
-    if args.gene_list:
-        genes = read_genes_from_csv(args.gene_list)
-        info(f"Gene list read from {args.gene_list} resulted in {len(genes)} " "genes.")
-    else:
-        if args.gene_name and args.start and args.end:
-            genes.append([args.gene_name, args.start, args.end])
-            info(
-                f"Extracting {args.gene_name} starting at {args.start} to "
-                f"{args.end}."
-            )
-        else:
-            raise Exception(
-                "Need either a gene list by --gene-list or a start and end "
-                "via --start, and --end respectively."
-            )
-    for gene_name, start, end in genes:
-        info(f"Started on gene {gene_name} ({start} - {end})")
-        (
-            nt_sequence_records,
-            nt_no_stop_sequence_records,
-            aa_sequence_records,
-            aa_no_stop_sequence_records,
-            problems,
-        ) = trim(
-            start,
-            end,
-            args.gen_cut_stop_codon,
-            args.do_translate,
-            msa_records,
-            correction_range=args.correction_range,
-        )
-        if len(problems) > 0:
-            warning(
-                f"There were {len(problems)} problems " f"during trimming {gene_name}!"
-            )
-        if args.catalogue_problems:
-            output_as_csv(
-                gene_name,
-                problems,
-                os.path.join(args.output_dir, f"{gene_name} - problems.csv"),
-            )
-        write_to_file(
-            args.output_dir,
-            gene_name,
-            start,
-            end,
-            args.full_suffix,
-            args.ns_suffix,
-            args.aa_suffix,
-            nt_sequence_records,
-            nt_no_stop_sequence_records,
-            aa_sequence_records,
-            aa_no_stop_sequence_records,
-        )
-        info(f"Completed gene {gene_name} ({start} - {end})")
-
-
 def main():
     parser = argparse.ArgumentParser(
         prog="splitmsa",
@@ -452,9 +391,69 @@ def main():
     )
 
     args = parser.parse_args()
+
     logging.basicConfig(level=args.log_level.upper())
-    run(args)
+
+    msa_records = list(read_msa_file(args.input))
+    info(f"MSA records read complete. Found {len(msa_records)} records.")
+    genes = []
+    if args.gene_list:
+        genes = read_genes_from_csv(args.gene_list)
+        info(f"Gene list read from {args.gene_list} resulted in {len(genes)} " "genes.")
+    else:
+        if args.gene_name and args.start and args.end:
+            genes.append([args.gene_name, args.start, args.end])
+            info(
+                f"Extracting {args.gene_name} starting at {args.start} to "
+                f"{args.end}."
+            )
+        else:
+            raise Exception(
+                "Need either a gene list by --gene-list or a start and end "
+                "via --start, and --end respectively."
+            )
+    for gene_name, start, end in genes:
+        info(f"Started on gene {gene_name} ({start} - {end})")
+        (
+            nt_sequence_records,
+            nt_no_stop_sequence_records,
+            aa_sequence_records,
+            aa_no_stop_sequence_records,
+            problems,
+        ) = trim(
+            start,
+            end,
+            args.gen_cut_stop_codon,
+            args.do_translate,
+            msa_records,
+            correction_range=args.correction_range,
+        )
+        if len(problems) > 0:
+            warning(
+                f"There were {len(problems)} problems " f"during trimming {gene_name}!"
+            )
+        if args.catalogue_problems:
+            output_as_csv(
+                gene_name,
+                problems,
+                os.path.join(args.output_dir, f"{gene_name} - problems.csv"),
+            )
+        write_to_file(
+            args.output_dir,
+            gene_name,
+            start,
+            end,
+            args.full_suffix,
+            args.ns_suffix,
+            args.aa_suffix,
+            nt_sequence_records,
+            nt_no_stop_sequence_records,
+            aa_sequence_records,
+            aa_no_stop_sequence_records,
+        )
+        info(f"Completed gene {gene_name} ({start} - {end})")
 
 
 if __name__ == "__main__":
+
     main()