import Fast5File
import sys

def run(parser, args):

	for fast5 in Fast5File.Fast5FileSet(args.files):

		if args.start_time or args.end_time:
			read_start_time = fast5.get_start_time()
			read_end_time = fast5.get_end_time()
			if args.start_time and args.start_time > read_start_time:
				fast5.close()
				continue
			if args.end_time and args.end_time < read_end_time:
				fast5.close()
				continue

		fas = fast5.get_fastas(args.type)
		
		# high quality 2D: means there are more nanopore events on the 
		# complement strand than on the template strand. We also
		# require there to be a 2D base-called sequence from Metrichor.
		if args.high_quality:
			if (fast5.get_complement_events_count() <= \
			   fast5.get_template_events_count()) or not fast5.has_2D():
				fast5.close()
				continue

		# norem quality 2D : means there are less (or equal) nanopore 
		# events on the complement strand than on the template strand. 
		# We also require there to be a 2D base-called sequence from Metrichor.
		if args.normal_quality:
			if (fast5.get_complement_events_count() > \
			   fast5.get_template_events_count()) or not fast5.has_2D():
				fast5.close()
				continue

		for fa in fas:
			if fa is None or \
			len(fa.seq) < args.min_length or \
			len(fa.seq) > args.max_length and \
			args.max_length > 0:			
				continue			

			print fa

		fast5.close()


import Fast5File
import sys

def run(parser, args):

	for fast5 in Fast5File.Fast5FileSet(args.files):

		if args.start_time or args.end_time:
			read_start_time = fast5.get_start_time()
			read_end_time = fast5.get_end_time()
			if args.start_time and args.start_time > read_start_time:
				fast5.close()
				continue
			if args.end_time and args.end_time < read_end_time:
				fast5.close()
				continue

		fas = fast5.get_fastas(args.type)
		
		# high quality 2D: means there are more nanopore events on the 
		# complement strand than on the template strand. We also
		# require there to be a 2D base-called sequence from Metrichor.
		if args.high_quality:
			if (fast5.get_complement_events_count() <= \
			   fast5.get_template_events_count()) or not fast5.has_2D():
				fast5.close()
				continue

		# norem quality 2D : means there are less (or equal) nanopore 
		# events on the complement strand than on the template strand. 
		# We also require there to be a 2D base-called sequence from Metrichor.
		if args.normal_quality:
			if (fast5.get_complement_events_count() > \
			   fast5.get_template_events_count()) or not fast5.has_2D():
				fast5.close()
				continue

		for fa in fas:
			if fa is None or \
			len(fa.seq) < args.min_length or \
			(len(fa.seq) > args.max_length and \
			args.max_length > 0):			
				continue			

			print fa

		fast5.close()


Update fasta.py