Commit 30ca8d1f authored by Ivan Vanát's avatar Ivan Vanát
Browse files

fixed permission check for non-existing output folder

parent 5a8784f3

nested/cli/nester.py

+14 −2
Original line number Diff line number Diff line 
#!/usr/bin/env python3



import os

import sys

import click

import glob
@@ -19,11 +20,12 @@ 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'))
@@ -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

+1 −1

File changed.

Contains only whitespace changes.