fixed permission check for non-existing output folder

nested/cli/nester.py

 #!/usr/bin/env python3
 
+import os
 import sys
 import click
 import glob
@@ -19,15 +20,16 @@ from nested.core.sequence_thread import SequenceThread
 @click.option('--sketch', '-s', is_flag=True, default=False, help='Sketch output.')
 @click.option('--format', '-f', default='genome_browser', help='Format for GFF.')
 @click.option('--output_fasta_offset', '-o', default=0, help='Number of bases around the element included in output fasta files.')
-@click.option('--output_folder', '-d', default="", type=click.Path(writable=True, resolve_path=True), help='Output data folder.')
+@click.option('--output_folder', '-d', default="", type=click.Path(writable=True), help='Output data folder.')
 @click.option('--initial_threshold', '-t', type=int, default=500, help='Initial threshold value.')
 @click.option('--threshold_multiplier', '-m', type=float, default=1, help='Threshold multiplier.')
 @click.option('--threads', '-n', type=int, default=1, help='Number of threads')
 def main(input_fasta, sketch, format, output_fasta_offset, output_folder, initial_threshold, threshold_multiplier, threads):    
+    check_permissions(output_folder, os.W_OK | os.X_OK)
     number_of_errors = [0]
     start_time = datetime.now()
     sequences = list(SeqIO.parse(open(input_fasta), 'fasta'))
-    sketcher = Sketcher()
+    sketcher = Sketcher()  
     futuress = []
     with futures.ThreadPoolExecutor(threads) as executor:
         for sequence in sequences:
@@ -64,6 +66,16 @@ def process_sequence(sequence, sketcher, sketch, format, output_fasta_offset, ou
         errors[0] += 1
         print('Processing {}: UNEXPECTED ERROR:'.format(sequence.id[:strlen]), sys.exc_info()[0])
 
+def check_permissions(path, permissions):
+    path = os.getcwd() if len(path) == 0 else path
+    if not os.path.exists('{}/data'.format(path)):
+        try:
+            os.makedirs('{}/data'.format(path))
+        except PermissionError:
+            raise click.BadParameter("Path \"{}\" is not writable.".format(path), param=path, param_hint='\"--output_folder\" / \"-d\"')
+        except Exception:
+            return        
+
 def cleanup():
     for file in glob.glob("*ltrs.fa"):
         os.remove(file)

nested/output/sketcher.py

@@ -16,7 +16,7 @@ class Sketcher(object):
         self._gff_path = ''
 
     def create_gff(self, nested_element, dirpath, output_fasta_offset=0, format='default'):
-        path = os.path.join(dirpath, DEFAULT_DIRPATH)        
+        path = os.path.join(dirpath, DEFAULT_DIRPATH)
         self._gff_maker.create_gff(nested_element, path, output_fasta_offset, format)
 
     def create_solo_ltr_gff(self, solo_ltrs, dirpath):