remove main

main.py

-#!/usr/bin/env python3
-
-import sys
-import os
-import shutil
-import click
-from datetime import datetime
-from subprocess import CalledProcessError
-
-from Bio import SeqIO
-
-from nested.core.nester import Nester
-from nested.core.generator import Generator
-from nested.output.sketcher import Sketcher
-
-def setup():
-	if not os.path.exists('data'):
-		os.makedirs('data')
-
-	if not os.path.exists('generated_data'):
-		os.makedirs('generated_data')
-
-	if not os.path.exists('tmp'):
-		os.makedirs('tmp')
-
-def cleanup():
-	shutil.rmtree('tmp/')
-
-@click.command()
-@click.option('--input_fasta', '-i', type=str, help='Input fasta file.')
-@click.option('--sketch_only', '-s', is_flag=True, help='If true, nesting is not computed. Genes are sketched only from existing gff files.')
-@click.option('--generate_from_fasta', '-g', type=str, help='Generate nested elements for source_db.')
-@click.option('--baselength', '-gb', type=int, help='Baselength for generated elements.')
-@click.option('--number_of_iterations', '-gi', type=int, help='Number of iterations in generating.')
-@click.option('--filter_string', '-gf', type=str, help='Filter string in generating.')
-@click.option('--number_of_elements', '-ge', type=int, help='Number of generated elements.')
-def main(input_fasta, sketch_only, generate_from_fasta, baselength, number_of_iterations, filter_string, number_of_elements):
-	number_of_errors = 0
-	start_time = datetime.now()
-	setup()
-	sketcher = Sketcher()
-
-	if input_fasta:
-		sequences = list(SeqIO.parse(open(input_fasta), 'fasta'))
-		for sequence in sequences:
-			sequence.id = sequence.id.replace('/', '--')
-			seq_start_time = datetime.now()
-			print('Processing {}...'.format(sequence.id), end='\r')
-			try:						
-				if not sketch_only:
-					nester = Nester(sequence)
-					sketcher.create_gff(nester.nested_element)
-				sketcher.sketch(sequence.id)
-				seq_end_time = datetime.now()
-				print('Processing {}: done [{}]'.format(sequence.id, seq_end_time - seq_start_time))	
-			except KeyboardInterrupt:
-				raise
-			except CalledProcessError:
-				number_of_errors += 1
-				print('Processing {}: SUBPROCESS ERROR'.format(sequence.id))		
-			except:
-				number_of_errors += 1
-				print('Processing {}: UNEXPECTED ERROR:'.format(sequence.id), sys.exc_info()[0])		
-	elif generate_from_fasta:
-		generator = Generator(generate_from_fasta)
-		params = {}
-		if baselength: params['baselength'] = baselength
-		if number_of_iterations: params['number_of_iterations'] = number_of_iterations
-		if filter_string: params['filter_string'] = filter_string		
-		if number_of_elements: params['number_of_elements'] = number_of_elements
-		generator.generate_random_nested_elements(**params)
-		generator.save_elements_to_fasta('generated_data/generated.fa')
-		for element in generator.elements:
-			sketcher.create_gff(element, 'generated_data')
-			sketcher.sketch(element.id, 'generated_data')
-
-
-	cleanup()
-	endTime = datetime.now()
-	print('Total time: {}'.format(endTime - start_time))
-	print('Number of errors: {}'.format(number_of_errors))
-
-if __name__ == '__main__':
-	main()

nested/cli/nester.py

@@ -15,7 +15,7 @@ from nested.output.sketcher import Sketcher
 @click.option('--sketch_only', '-s', is_flag=True, help='If true, nesting is not computed. Genes are sketched only from existing gff files.')
 @click.option('--data_folder', '-d', type=str, help='Output data folder.')
 #TODO DATA_FOLDER
-def main(input_fasta, sketch_only):
+def main(input_fasta, sketch_only, data_folder):
     number_of_errors = 0
     start_time = datetime.now()
     sequences = list(SeqIO.parse(open(input_fasta), 'fasta'))

nested/config/config.py

@@ -16,7 +16,7 @@ ltr_finder_args += ['-s', ltr_finder_tRNAdb_path]
 gt_sketch_path = 'gt'
 gt_sketch_args = ['sketch']
 gt_sketch_args += ['-width', '1400']
-gt_sketch_args += ['-style', '/home/radovan/git/nested/gt.style']
+gt_sketch_args += ['-style', '/home/radovan/git/nested/nested/config/gt.style']
 
 blastx_args = {
     'db': '/home/radovan/lexa/blastDB/data/gydb_proteins.fa',