[re/factor] v1.5

setup.py

@@ -7,7 +7,7 @@
 
 setuptools.setup(
     name="orffinder",
-    version="1.4",
+    version="1.5",
     author="ChocoParrot",
     author_email="[email protected]",
     description="ORFFinder API.",
@@ -23,7 +23,7 @@
         "Operating System :: OS Independent",
     ),
     install_requires=[
-        "biopython==1.79"
+        "biopython>=1.79"
     ],
     scripts=[
         "src/cline_tools/orffinder-to-gtf",

src/cline_tools/orffinder-to-gff3.py

@@ -0,0 +1,63 @@
+#!/usr/bin/env python
+
+import sys
+import os
+from Bio import SeqIO
+from orffinder import orffinder
+
+arguments = sys.argv + [""]
+classed_arguments = {"orf_size": "75", "max_orfs_per_sequence": "-1", "remove_nested": "False", "trim_trailing": "False", "infmt": "fasta", "attr_name": "ORF_"}
+
+try:
+    for i in range(len(arguments)):
+
+        argument = arguments[i]
+
+        if argument.startswith("-"):
+
+            classed_arguments[argument[1:]] = arguments[i + 1]
+
+    if "h" in classed_arguments.keys():
+        help_output = open("help_pages/orffinder-to-gtf.txt", "r").read()
+        print(help_output)
+        os._exit(1)
+
+    sequences = SeqIO.parse(classed_arguments["in"], classed_arguments["infmt"])
+
+    orf_size = int(classed_arguments["orf_size"])
+    remove_nested = classed_arguments["remove_nested"] == "True"
+    trim_trailing = classed_arguments["trim_trailing"] == "True"
+    attr_name = classed_arguments["attr_name"]
+    max_orfs_per_sequence = int(classed_arguments["max_orfs_per_sequence"])
+
+    output = [["##gff-version 3"]]
+    index = int()
+
+    for sequence in sequences:
+
+        seqname = sequence.description
+        orfs = orffinder.getORFs(sequence, minimum_length=orf_size, trim_trailing=trim_trailing, remove_nested=remove_nested)
+
+        local_index = int()
+        for orf in orfs:
+
+            index += 1
+            local_index += 1
+            output.append([seqname, "ORFFinder Python", "ORF", str(orf["start"]), str(orf["end"]), ".", orf["sense"], str(orf["frame"] - 1), "orf_id=" + attr_name + str(index) + ";"])
+
+            if local_index >= max_orfs_per_sequence and max_orfs_per_sequence != -1:
+                break
+
+
+    full_output = "\n".join(["\t".join(x) for x in output])
+
+    if "out" not in classed_arguments.keys():
+
+        print(full_output)
+
+    else:
+
+        open(classed_arguments["out"], "w+").write(full_output)
+
+except:
+    print("USAGE\n  orffinder-to-gff3 [-in input] [-infmt format] [-out output] [-orf_size int]\n    [-remove_nested boolean] [-trim_trailing boolean] [-max_orfs_per_sequence int]\n    [-attr_name string]\n\nDESCRIPTION\n  ORFFinder Python v1.5\n\nUse '-help' to print detailed descriptions of command line arguments\n========================================================================")