[refactor] minor changes to the directory

Chokyotager · Oct 24, 2021 · 424c520 · 424c520
1 parent 4e1a8ec
commit 424c520
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Showing 3 changed files with 9 additions and 3 deletions.
diff --git a/src/cline_tools/orffinder-to-gff3 b/src/cline_tools/orffinder-to-gff3
@@ -8,6 +8,8 @@ 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_"}
 
+dir_path = os.path.dirname(os.path.realpath(__file__))
+
 try:
     for i in range(len(arguments)):
 
@@ -18,7 +20,7 @@ try:
             classed_arguments[argument[1:]] = arguments[i + 1]
 
     if "h" in classed_arguments.keys():
-        help_output = open("help_pages/orffinder-to-gff3.txt", "r").read()
+        help_output = open(dir_path + "/help_pages/orffinder-to-gff3.txt", "r").read()
         print(help_output)
         os._exit(1)
 

diff --git a/src/cline_tools/orffinder-to-gtf b/src/cline_tools/orffinder-to-gtf
@@ -8,6 +8,8 @@ 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_"}
 
+dir_path = os.path.dirname(os.path.realpath(__file__))
+
 try:
     for i in range(len(arguments)):
 
@@ -18,7 +20,7 @@ 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(dir_path + "/help_pages/orffinder-to-gtf.txt", "r").read()
         print(help_output)
         os._exit(1)
 

diff --git a/src/cline_tools/orffinder-to-sequence b/src/cline_tools/orffinder-to-sequence
@@ -9,6 +9,8 @@ from orffinder import orffinder
 arguments = sys.argv + [""]
 classed_arguments = {"orf_size": "75", "outtype": "nucleotide", "max_orfs_per_sequence": "-1", "remove_nested": "False", "trim_trailing": "False", "infmt": "fasta", "attr_name": "ORF_", "outfmt": "fasta"}
 
+dir_path = os.path.dirname(os.path.realpath(__file__))
+
 try:
     for i in range(len(arguments)):
 
@@ -19,7 +21,7 @@ try:
             classed_arguments[argument[1:]] = arguments[i + 1]
 
     if "h" in classed_arguments.keys():
-        help_output = open("help_pages/orffinder-to-sequence.txt", "r").read()
+        help_output = open(dir_path + "/help_pages/orffinder-to-sequence.txt", "r").read()
         print(help_output)
         os._exit(1)