From 15586901094d61ada6631658e35bfda597c3eb4d Mon Sep 17 00:00:00 2001
From: ChocoParrot <lachocoparrot@gmail.com>
Date: Tue, 14 Sep 2021 09:27:15 +0800
Subject: [PATCH] [refactor] updated documentation

---
 README.md                                     |  2 +-
 setup.py                                      |  2 +-
 .../help_pages/orffinder-to-gff3.txt          | 35 +++++++++++++++++++
 src/cline_tools/orffinder-to-gff3             |  2 +-
 4 files changed, 38 insertions(+), 3 deletions(-)
 create mode 100644 src/cline_tools/help_pages/orffinder-to-gff3.txt

diff --git a/README.md b/README.md
index 9b840ed..ed4b3e1 100644
--- a/README.md
+++ b/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`.
 
diff --git a/setup.py b/setup.py
index c1872c4..75fcb16 100644
--- a/setup.py
+++ b/setup.py
@@ -7,7 +7,7 @@
 
 setuptools.setup(
     name="orffinder",
-    version="1.5",
+    version="1.6",
     author="ChocoParrot",
     author_email="lachocoparrot@gmail.com",
     description="Open Reading Frame finder natively coded in Python.",
diff --git a/src/cline_tools/help_pages/orffinder-to-gff3.txt b/src/cline_tools/help_pages/orffinder-to-gff3.txt
new file mode 100644
index 0000000..045b52c
--- /dev/null
+++ b/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_"
diff --git a/src/cline_tools/orffinder-to-gff3 b/src/cline_tools/orffinder-to-gff3
index 24b229f..821d846 100644
--- a/src/cline_tools/orffinder-to-gff3
+++ b/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)