[refactor] updated documentation

README.md

@@ -18,7 +18,7 @@ Finds the open reading frame (6-frame scan) on a given 5' to 3' nucleotide.
 `pip3 install orffinder`
 
 ### Terminal Usage
-Two command-line executable commands are available: `orffinder-to-gtf` `orffinder-to-sequence`.
+Three command-line executable commands are available: `orffinder-to-gtf` `orffinder-to-sequence` and `orffinder-to-gff3`.
 
 Documentation for these commands can be retrieved by specifying `<command> -h`.
 

setup.py

@@ -7,7 +7,7 @@
 
 setuptools.setup(
     name="orffinder",
-    version="1.5",
+    version="1.6",
     author="ChocoParrot",
     author_email="[email protected]",
     description="Open Reading Frame finder natively coded in Python.",

src/cline_tools/help_pages/orffinder-to-gff3.txt

@@ -0,0 +1,35 @@
+USAGE
+  orffinder-to-gff3 [-in input] [-infmt format] [-out output] [-outfmt format] [-orf_size int]
+      [-remove_nested boolean] [-trim_trailing boolean] [-max_orfs_per_sequence int]
+      [-attr_name string]
+
+DESCRIPTION
+      ORFFinder Python v1.5
+
+PARAMETERS
+[-h]
+Shows this interface.
+
+[-in (string)]:
+Input nucleotide sequence to extract ORFs from.
+
+[-infmt (string)]:
+Can be "fasta", "genbank", or any other Biopython supported format. Default: "fasta"
+
+[-out (string)]
+Optional output file. If not specified, will output to stdout.
+
+[-orf_size (integer)]
+Minimum size (in nucleotides) of ORF. Default: 75
+
+[-remove_nested (boolean)]
+Remove ORFs that are completely nested in another ORF. Default: False
+
+[-trim_trailing (boolean)]
+Remove ORFs that have a start codon but no stop codon at the edges of the sequence. Default: False
+
+[-max_orfs_per_sequence (integer)]
+Maximum number of ORFs to return per sequence, sorted by length. Default: -1 (no limit)
+
+[-attr_name (string)]
+Attribute ID name in GTF file. Suffixed by ORF index number. Default: "ORF_"

src/cline_tools/orffinder-to-gff3

@@ -18,7 +18,7 @@ try:
             classed_arguments[argument[1:]] = arguments[i + 1]
 
     if "h" in classed_arguments.keys():
-        help_output = open("help_pages/orffinder-to-gtf.txt", "r").read()
+        help_output = open("help_pages/orffinder-to-gff3.txt", "r").read()
         print(help_output)
         os._exit(1)