From 79f3adddea77ad61699e57e4a3903858ca8d5fdc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?=
 <apcamargo@users.noreply.github.com>
Date: Mon, 23 Dec 2024 18:29:44 -0800
Subject: [PATCH] Test with help dialogue

---
 recipes/pdb2fasta/build.sh        |  2 +-
 recipes/pdb2fasta/meta.yaml       |  2 +-
 recipes/pdb2fasta/pdb2fasta.patch | 34 ++++++++++++++++++++++++++++++-
 3 files changed, 35 insertions(+), 3 deletions(-)

diff --git a/recipes/pdb2fasta/build.sh b/recipes/pdb2fasta/build.sh
index 6c43b17ac63ef..6dfee62b849e2 100644
--- a/recipes/pdb2fasta/build.sh
+++ b/recipes/pdb2fasta/build.sh
@@ -1,5 +1,5 @@
 #!/bin/bash -euo
 
 mkdir -p ${PREFIX}/bin
-${CC} ${CFLAGS} pdb2fasta.c -o pdb2fasta
+${CC} -O2 pdb2fasta.c -o pdb2fasta
 mv pdb2fasta ${PREFIX}/bin
diff --git a/recipes/pdb2fasta/meta.yaml b/recipes/pdb2fasta/meta.yaml
index c6eb6eb29d547..f1a27eb513069 100644
--- a/recipes/pdb2fasta/meta.yaml
+++ b/recipes/pdb2fasta/meta.yaml
@@ -22,7 +22,7 @@ requirements:
 
 test:
   commands:
-    - pdb2fasta
+    - pdb2fasta --help
 
 about:
   home: "https://github.com/kad-ecoli/pdb2fasta"
diff --git a/recipes/pdb2fasta/pdb2fasta.patch b/recipes/pdb2fasta/pdb2fasta.patch
index e97d2f625cabd..d0cf696829648 100644
--- a/recipes/pdb2fasta/pdb2fasta.patch
+++ b/recipes/pdb2fasta/pdb2fasta.patch
@@ -1,8 +1,40 @@
 diff --git a/pdb2fasta.c b/pdb2fasta.c
-index 9642d03..f197f1f 100644
+index 9642d03..9e8eef1 100644
 --- a/pdb2fasta.c
 +++ b/pdb2fasta.c
 @@ -1,3 +1,4 @@
 +#include<stdlib.h>
  #include<stdio.h>
  #include<string.h>
+
+@@ -99,14 +100,24 @@ char *pdb2fasta(char *pdb_file){
+ }
+
+ int main(int argc, char** argv){
+-    if (argc<2){
+-        printf("pdb2fasta pdb.pdb > seq.fasta\n");
+-        printf("    convert PDB file pdb.pdb to FASTA sequence file seq.fasta\n");
++    if (argc < 2){
++        printf("Usage: pdb2fasta pdb.pdb > seq.fasta\n");
++        printf("    Convert PDB file pdb.pdb to FASTA sequence file seq.fasta\n");
+         return argc;
+     }
+-
+-    int i;
+-    for (i=1;i<argc;i++){
++
++    if (argc == 2 && strcmp(argv[1], "--help") == 0) {
++        printf("Usage: pdb2fasta [options] pdb.pdb\n");
++        printf("Options:\n");
++        printf("  --help    Display this help dialogue and exit\n");
++        printf("\nDescription:\n");
++        printf("  Convert a PDB file to a FASTA sequence format. Output is printed to stdout.\n");
++        printf("  Example:\n");
++        printf("    pdb2fasta pdb.pdb > seq.fasta\n");
++        return 0;
++    }
++
++    for (int i=1; i<argc; i++){
+         char *pdb_file=argv[i];
+         printf("%s",pdb2fasta(pdb_file));
+     }