added ram tracker (35c664d9) · Commits · Matej Lexa / nested

README.md

+9 −0

Original line number	Original line	Diff line number	Diff line
	@@ -138,6 +138,7 @@ Options:
	-s, --sketch_only If true, nesting is not computed. Genes are sketched		-s, --sketch_only If true, nesting is not computed. Genes are sketched
	only from existing gff files.		only from existing gff files.
	-d, --data_folder TEXT Output data folder.		-d, --data_folder TEXT Output data folder.
			-dt --discovery-tool TEXT Used discovery tool. Default is LTR-finder.
	--help Show this message and exit.		--help Show this message and exit.
	```		```

	@@ -159,3 +160,11 @@ Options:
	-d, --data_folder TEXT Output data folder.		-d, --data_folder TEXT Output data folder.
	--help Show this message and exit.		--help Show this message and exit.
	```		```

			## Adding new LTR discovery tool

			* Implement run() method in new TE class based on core/TE_template.py

			* Add new value to core/DiscoveryTool.py including any aliases, make sure the numeric value is different from already implemented tools and that it is the same for all of your aliases. (used in calling nester ``-dt <value you set>``)

			* Import your newly implemented class in utils/DependencyResolver.py and add it to ``valueToClassDict`` attribute. (key is numeric value you set in core/DiscoveryTool.py)

nested/cli/nester.py

+5 −0

Original line number	Original line	Diff line number	Diff line
	@@ -4,6 +4,7 @@ import os
	import sys		import sys
	import click		import click
	import glob		import glob
			import tracemalloc
	from concurrent import futures		from concurrent import futures
	from datetime import datetime		from datetime import datetime
	from subprocess import CalledProcessError		from subprocess import CalledProcessError
	@@ -31,6 +32,7 @@ from nested.utils.dependency_resolver import DependencyResolver
	def main(input_fasta, sketch, format, output_fasta_offset, output_folder, initial_threshold,		def main(input_fasta, sketch, format, output_fasta_offset, output_folder, initial_threshold,
	threshold_multiplier, threads, discovery_tool):		threshold_multiplier, threads, discovery_tool):
	check_permissions(output_folder, os.W_OK \| os.X_OK)		check_permissions(output_folder, os.W_OK \| os.X_OK)
			tracemalloc.start()
	number_of_errors = [0]		number_of_errors = [0]
	start_time = datetime.now()		start_time = datetime.now()
	sequences = list(SeqIO.parse(open(input_fasta), 'fasta'))		sequences = list(SeqIO.parse(open(input_fasta), 'fasta'))
	@@ -43,8 +45,11 @@ def main(input_fasta, sketch, format, output_fasta_offset, output_folder, initia
	sketch, format, output_fasta_offset, output_folder,		sketch, format, output_fasta_offset, output_folder,
	initial_threshold, threshold_multiplier, number_of_errors,		initial_threshold, threshold_multiplier, number_of_errors,
	dependencyResolver))		dependencyResolver))
			print("max RAM usage: " + str(tracemalloc.get_traced_memory()[1] / 10**6) + " MB")
	futures.wait(futuress)		futures.wait(futuress)
	end_time = datetime.now()		end_time = datetime.now()
			print("max RAM usage: " + str(tracemalloc.get_traced_memory()[1] / 10**6) + " MB")
			tracemalloc.stop()
	print('Total time: {}'.format(end_time - start_time))		print('Total time: {}'.format(end_time - start_time))
	print('Number of errors: {}'.format(number_of_errors[0]))		print('Number of errors: {}'.format(number_of_errors[0]))

nested/core/te_template.py

0 → 100644

+64 −0

Original line number	Original line	Diff line number	Diff line
			#!/usr/bin/env python3

			import os
			import subprocess
			import re

			from Bio import SeqIO
			from Bio.SeqRecord import SeqRecord

			from nested.config.config import config, args_dict_to_list


			class TE(object):
			"""Class representing TE. Every location is in format [from, to].

			Attributes:
			ppt (list): location of ppt
			pbs (list): location of pbs
			location (list): position of TE in gene
			ltr_left_location (list): location of left ltr
			ltr_right_location (list): location of right ltr
			tsr_left (list): location of left tsr
			tsr_right (list): location of right tsr
			features (dict): dictionary of features assigned to TE (i.e. list of domains on the optimal path in graph)
			score (float): evaluated score of TE
			"""

			def __init__(self, ppt=[0, 0], pbs=[0, 0], location=[0, 0],
			ltr_left_location=[0, 0], ltr_right_location=[0, 0],
			tsr_left=[0, 0], tsr_right=[0, 0], features={}, score=None):
			self.ppt = ppt
			self.pbs = pbs
			self.location = location
			self.ltr_left_location = ltr_left_location
			self.ltr_right_location = ltr_right_location
			self.tsr_left = tsr_left
			self.tsr_right = tsr_right
			self.features = features
			self.score = score

			def __str__(self):
			lines = ['{{location = {},'.format(self.location),
			' left ltr = {},'.format(self.ltr_left_location),
			' right ltr = {},'.format(self.ltr_right_location),
			' left tsr = {},'.format(self.tsr_left),
			' right tsr = {},'.format(self.tsr_right),
			' ppt = {},'.format(self.ppt),
			' pbs = {},'.format(self.pbs),
			# ' features = {},'.format(self.features),
			' score = {}}}'.format(self.score)]
			return '\n'.join(lines)

			@staticmethod
			def run(seqid, sequence):
			"""Run discovery tool of choice on sequence and return list of transposons

			Arguments:
			seqid (str): sequence id
			sequence (Bio.Seq.Seq): sequence

			Returns:
			list[TE]: list of found ltr pairs as a TE class
			"""

nested/utils/dependency_resolver.py

+3 −3

Original line number	Original line	Diff line number	Diff line
	@@ -6,11 +6,11 @@ from nested.core.discovery_tool import DiscoveryTool

	class DependencyResolver():		class DependencyResolver():
	def __init__(self, tool_name):		def __init__(self, tool_name):
			self.valueToClassDict = {1: TE, 2: TE_harvest}
	self.discovery_tool = self.resolve_discovery_tool(tool_name)		self.discovery_tool = self.resolve_discovery_tool(tool_name)

	def resolve_discovery_tool(self, tool_name):		def resolve_discovery_tool(self, tool_name):
	valueToClassDict = {1: TE, 2: TE_harvest}
	value = 1		value = 1
	if (tool_name in DiscoveryTool.__members__):		if (tool_name in DiscoveryTool.__members__):
	value = DiscoveryTool[tool_name].value		value = DiscoveryTool[tool_name].value
	return valueToClassDict[value]		return self.valueToClassDict[value]
	No newline at end of file