Restructured code and renamed project

.gitignore

@@ -1,5 +1,21 @@
-# Created by https://www.toptal.com/developers/gitignore/api/python,visualstudiocode
-# Edit at https://www.toptal.com/developers/gitignore?templates=python,visualstudiocode
+# File created using '.gitignore Generator' for Visual Studio Code: https://bit.ly/vscode-gig
+# Created by https://www.toptal.com/developers/gitignore/api/visualstudiocode,linux,python
+# Edit at https://www.toptal.com/developers/gitignore?templates=visualstudiocode,linux,python
+
+### Linux ###
+*~
+
+# temporary files which can be created if a process still has a handle open of a deleted file
+.fuse_hidden*
+
+# KDE directory preferences
+.directory
+
+# Linux trash folder which might appear on any partition or disk
+.Trash-*
+
+# .nfs files are created when an open file is removed but is still being accessed
+.nfs*
 
 ### Python ###
 # Byte-compiled / optimized / DLL files
@@ -192,4 +208,7 @@ pyrightconfig.json
 .history
 .ionide
 
-# End of https://www.toptal.com/developers/gitignore/api/python,visualstudiocode
+# End of https://www.toptal.com/developers/gitignore/api/visualstudiocode,linux,python
+
+# Custom rules (everything added below won't be overriden by 'Generate .gitignore File' if you use 'Update' option)
+

.vscode/launch.json

@@ -8,11 +8,12 @@
             "name": "Run Fasta Filter",
             "type": "python",
             "request": "launch",
-            "program": "fasta_filter.py",
+            "program": "${workspaceFolder}/filterfasta/filterfasta.py",
             "args": [
                 "reference_standards.fas",
                 "reference_standards_filtered.fas",
-                "-c", "rt"
+                "-c",
+                "rt"
             ],
             "console": "integratedTerminal",
             "justMyCode": true

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "python.formatting.provider": "black"
+}

fasta_filter.py

@@ -1,65 +0,0 @@
-#!/usr/bin/env python3
-
-import os
-from Bio import SeqIO
-import argparse
-
-
-def main(args):
-    kept_records = []
-    for s_record in SeqIO.parse(args.input, "fasta"):
-        if args.property != "all" and not (
-                    args.contains in getattr(s_record, args.property)
-                ):
-            kept_records.append(s_record)
-        elif args.property == "all" and not (
-            args.contains in s_record.id
-            or args.contains in s_record.name
-                or args.contains in s_record.description):
-            kept_records.append(s_record)
-    SeqIO.write(
-        kept_records,
-        os.path.abspath(args.output),
-        "fasta"
-    )
-
-
-if __name__ == "__main__":
-    argparser = argparse.ArgumentParser(
-        "Removes sequences where id contains certain string.")
-    argparser.add_argument(
-        "input",
-        type=str,
-        metavar="i",
-        help="The input fasta file."
-    )
-
-    argparser.add_argument(
-        "output",
-        type=str,
-        metavar="o",
-        help="The output file path."
-    )
-
-    argparser.add_argument(
-        "-c",
-        "--contains",
-        type=str,
-        default=None,
-        required=False,
-        help="The string to search for."
-    )
-
-    argparser.add_argument(
-        "-p",
-        "--property",
-        type=str,
-        default="all",
-        required=False,
-        help="""
-        The part of the fasta file to look through. Valid options are: id,
-        name, description, or all.
-        """
-    )
-
-    main(argparser.parse_args())

filterfasta/filterfasta.py

@@ -0,0 +1,66 @@
+#!/usr/bin/env python3
+
+import os
+from Bio import SeqIO
+import argparse
+
+
+def filter(input: str, a_property: str, contains: str):
+    kept_records = []
+    for s_record in SeqIO.parse(input, "fasta"):
+        if a_property != "all" and not (contains in getattr(s_record, a_property)):
+            kept_records.append(s_record)
+        elif a_property == "all" and not (
+            contains in s_record.id
+            or contains in s_record.name
+            or contains in s_record.description
+        ):
+            kept_records.append(s_record)
+    return kept_records
+
+
+def write_to_fasta(kept_records, output: str):
+    SeqIO.write(kept_records, os.path.abspath(output), "fasta")
+
+
+def run(args):
+    kept = filter(args.input, args.property, args.contains)
+    write_to_fasta(kept, args.output)
+
+
+def main():
+    argparser = argparse.ArgumentParser(
+        "Removes sequences where id contains certain string."
+    )
+    argparser.add_argument("input", type=str, metavar="i", help="The input fasta file.")
+
+    argparser.add_argument(
+        "output", type=str, metavar="o", help="The output file path."
+    )
+
+    argparser.add_argument(
+        "-c",
+        "--contains",
+        type=str,
+        default=None,
+        required=False,
+        help="The string to search for.",
+    )
+
+    argparser.add_argument(
+        "-p",
+        "--property",
+        type=str,
+        default="all",
+        required=False,
+        help="""
+        The part of the fasta file to look through. Valid options are: 'id',
+        'name', 'description', or 'all'.
+        """,
+    )
+    args = argparser.parse_args()
+    run(args)
+
+
+if __name__ == "__main__":
+    main()

tox.ini

@@ -0,0 +1,3 @@
+[flake8]
+max-line-length = 88
+extend-ignore = E203