Merge pull request #43 from FOI-Bioinformatics/version_update_v0.4.2

Version update v0.4.2

.gitignore

@@ -3,8 +3,8 @@ build*
 test*
 *.dmp
 .ctbd
-*.db
-*.txt
+#*.db
+#*.txt
 *egg*
 dist*
 logs*

flextaxd/create_databases.py

@@ -84,7 +84,7 @@ def __init__(self,  message,expression=""):
 	parser = argparse.ArgumentParser()
 	basic = parser.add_argument_group('basic', 'Basic commands')
 	basic.add_argument('-o', '--outdir',metavar="", default=".", help="Output directory (same directory as custom_taxonomy_databases dump)")
-	basic.add_argument('-db', '--database',metavar="", type=str, default=".ctdb" , help="Custom taxonomy sqlite3 database file")
+	basic.add_argument('-db', '--database', '--db' ,metavar="", type=str, default=".ctdb" , help="Custom taxonomy sqlite3 database file")
 
 	### Download options, process local directory and potentially download files
 	download_opts = parser.add_argument_group('download_opts', "Download and file handling")
@@ -116,6 +116,10 @@ def __init__(self,  message,expression=""):
 
 	parser.add_argument("--version", action='store_true', help=argparse.SUPPRESS)
 
+	if len(sys.argv)==1:
+		parser.print_help(sys.stderr)
+		sys.exit(1)
+
 	args = parser.parse_args()
 
 	if not os.path.exists(args.database):
@@ -185,7 +189,7 @@ def __init__(self,  message,expression=""):
 		if args.download or args.representative:
 			download = dynamic_import("modules", "DownloadGenomes")
 			download_obj = download(args.processes,outdir=args.outdir,force=args.force_download,download_path=args.genomes_path)
-			new_genome_path, missing = download_obj.run(missing,args.rep_path)
+			new_genome_path, missing = download_obj.run(missing,representative=args.representative,url=args.rep_path)
 			if not new_genome_path:
 				still_missing = missing
 				if len(still_missing) > 0: print("Not able to download: {nr}".format(nr=len(still_missing)))
@@ -209,6 +213,7 @@ def __init__(self,  message,expression=""):
 			limit = 10
 		'''Use the genome -> path dictionary to build database'''
 		if not skip:
+			logger.info("Get genomes from input directory!")
 			genomes = process_directory_obj.get_genome_path_dict()
 		else: genomes=False
 		if args.skip:

flextaxd/custom_taxonomy_databases.py

@@ -20,7 +20,7 @@
 each column (not <tab>|<tab>).
 '''
 
-__version__ = "0.4.1"
+__version__ = "0.4.2"
 __author__ = "David Sundell"
 __credits__ = ["David Sundell"]
 __license__ = "GPLv3"
@@ -147,6 +147,10 @@ def __init__(self,  message,expression=""):
 
     parser.add_argument("--version", action='store_true', help=argparse.SUPPRESS)
 
+    if len(sys.argv)==1:
+        parser.print_help(sys.stderr)
+        sys.exit(1)
+
     args = parser.parse_args()
 
     if args.version:
@@ -187,6 +191,7 @@ def __init__(self,  message,expression=""):
     if args.force:
         force = True
 
+
     ### Run pipeline
 
     '''If database is not given, and input data is not given raise error'''

flextaxd/modules/CreateKrakenDatabase.py

@@ -50,6 +50,8 @@ def __init__(self, database, kraken_database, genome_names, outdir,verbose=False
 		if genome_names:
 			self.genome_names = list(genome_names.keys())   ## List for multiprocessing
 			self.genome_path = genome_names					## genome_id to path dictionary
+		else:
+			logger.error("Genome names are missing")
 		self.accession_to_taxid = self.database.get_genomes(self.database)
 		self.files = []
 		self.params = params

flextaxd/modules/DownloadGenomes.py

@@ -9,7 +9,7 @@
 from modules.functions import download_genomes
 from multiprocessing import Process,Manager,Pool
 from subprocess import Popen,PIPE
-import os
+import os,time
 
 class DownloadGenomes(object):
 	"""DownloadGenomes takes a list of genome names (GCF or GCA) and download (if possible) files from NCBI refseq and or genbank"""
@@ -85,7 +85,7 @@ def download_represenatives(self,genome_path,url="https://data.ace.uq.edu.au/pub
 		logger.debug(" ".join(args))
 		logger.info("Waiting for download process to finish (this may take a while)!")
 		p = Popen(args, stdout=PIPE)
-		(output, err) = p.communicate() 
+		(output, err) = p.communicate()
 		p_status = p.wait()
 		return input_file_name
 
@@ -114,52 +114,65 @@ def download_files(self,files):
 		Returns
 			list - list of files not downloaded
 		'''
-		logger.info("Downloading {files} files".format(files=len(files)))
-		if len(files) < self.processes:
-			self.processes = len(files)
-		self.download_map = self._split(files,self.processes)
-		logger.info("Using {np} parallel processes to download files".format(np=self.processes))
-
-		'''function to run download of genomes in paralell'''
-		jobs = []
-		manager = Manager()
-		added = manager.Queue()
-		fpath = manager.Queue()
-		missing = manager.Queue()
-		for i in range(self.processes):
-			p = Process(target=download_genomes, args=(self.download_map[i],added,fpath,missing,self.force))
-			p.daemon=True
-			p.start()
-			jobs.append(p)
-		for job in jobs:
-			job.join()
-		self.added = added.qsize()
-		if not any(proc.is_alive() for proc in jobs):
-			logger.info('All download processes completed')
-		elif len(added.qsize()) % 100 == 0:
-			print("{n} downloaded".format(added.qsize()),end="\r")
-
-		count = 0
-		while True:
-			if added.qsize() == 0: ## Check if no genome was succesfully downlaoded if no break
-				logger.info("None of listed genomes could be downloaded! Files not downloaded will be printed to {outdir}/FlexTaxD.missing".format(outdir=self.outdir.rstrip("/")))
-				self.write_missing(files)
-				break
-			l = len(self.genome_names)
-			gen = added.get()
-			if gen:
-				self.genome_names += gen
-				self.genome_path[gen] = fpath.get()
-				if l == len(self.genome_names):
+		try:
+			logger.info("Downloading {files} files".format(files=len(files)))
+			if len(files) < self.processes:
+				self.processes = len(files)
+			self.download_map = self._split(files,self.processes)
+			logger.info("Using {np} parallel processes to download files".format(np=self.processes))
+
+			'''function to run download of genomes in paralell'''
+			jobs = []
+			manager = Manager()
+			added = manager.Queue()
+			fpath = manager.Queue()
+			missing = manager.Queue()
+			for i in range(self.processes):
+				p = Process(target=download_genomes, args=(self.download_map[i],added,fpath,missing,self.force))
+				p.daemon=True
+				p.start()
+				jobs.append(p)
+			for job in jobs:
+				job.join()
+			self.added = added.qsize()
+			if not any(proc.is_alive() for proc in jobs):
+				logger.info('All download processes completed')
+			elif len(added.qsize()) % 100 == 0:
+				print("{n} downloaded".format(added.qsize()),end="\r")
+
+			count = 0
+			while True:
+				if self.added == 0: ## Check if no genome was succesfully downlaoded if no break
+					logger.info("None of listed genomes could be downloaded! Files not downloaded will be printed to {outdir}/FlexTaxD.missing".format(outdir=self.outdir.rstrip("/")))
+					self.write_missing(files)
 					break
-			else:
-				self.not_downloaded += missing.get()
-				count+=1
-		if len(self.not_downloaded) > 0:
-			self.write_missing(self.not_downloaded)
+				l = len(self.genome_names)
+				gen = added.get()
+				if gen:
+					self.genome_names += gen
+					self.genome_path[gen] = fpath.get()
+					if l == len(self.genome_names):
+						break
+				else:
+					self.not_downloaded += missing.get()
+					count+=1
+				if added.qsize():
+					break
+			if len(self.not_downloaded) > 0:
+				self.write_missing(self.not_downloaded)
+		except KeyboardInterrupt:
+			logger.info("Program was interrupted by user: cleaning up subprocesses!")
+		finally: ## Make sure all sub-processes are ended even if program is forced to quit
+			if any(proc.is_alive() for proc in jobs):
+				for p in jobs:
+					print(p)
+					p.kill()
+			time.sleep(1)
+			if any(proc.is_alive() for proc in jobs):
+				logger.error("Could not stop all subprocesses check your process manager and end them manually!")
 		return self.not_downloaded
 
-	def run(self, files, representatives=False):
+	def run(self, files, representative=False,url=""):
 		'''Download list of GCF and or GCA files from NCBI or download represenative genomes
 
 		Parameters
@@ -169,12 +182,14 @@ def run(self, files, representatives=False):
 		Returns
 			list - list of files not downloaded
 		'''
-		if representatives:
-			tarfile = self.download_represenatives(genome_path=self.download_path, url=representatives)
+		if representative:
+			logger.info("Download GTDB Representative genomes")
+			tarfile = self.download_represenatives(genome_path=self.download_path, url=url)
 			folder_path = self.parse_representatives(tarfile)
 			'''Process the downloaded folder'''
 			return folder_path,[]
 		else:
 			if len(files) > 0:
+				logger.info("Download missing genomes")
 				not_downloaded = self.download_files(files)
 				return False,not_downloaded

flextaxd/modules/ModifyTree.py

@@ -68,6 +68,8 @@ def __init__(self, database=".taxonomydb", mod_database=False, mod_file=False, c
 		self.ncbi_order = True
 		self.mod_genomes =False
 
+		self.fast_clean = True
+
 		### Connect to or create database
 		self.taxonomydb = ModifyFunctions(database,verbose=verbose)
 		self.rank= self.taxonomydb.get_rank(col=2)
@@ -398,7 +400,7 @@ def clean_database(self, ncbi=False):
 		self.all_nodes = set(self.taxonomydb.get_nodes(col=1).keys())
 		'''Add parents to all nodes that may not have annotations'''
 		logger.info("Retrieve all parents of annotated nodes")
-		self.annotated_nodes |= self.taxonomydb.get_parents(self.annotated_nodes,find_all=True)
+		self.annotated_nodes |= self.taxonomydb.get_parents(self.annotated_nodes,find_all=True,ncbi=ncbi)
 		logger.info("Parents added: {an}".format(an=len(self.annotated_nodes)-an))
 		if ncbi:
 			logger.info("Keep main nodes of the NCBI taxonomy (parents on level 3 and above)")
@@ -415,7 +417,12 @@ def clean_database(self, ncbi=False):
 		logger.debug("Nodes remaining {nnodes}".format(nnodes=len(self.annotated_nodes)))
 		logger.info("Clean annotations related to removed nodes")
 		if len(self.clean_links) < len(self.all_links) and len(self.clean_links) > 0:
-			self.taxonomydb.fast_delete_links(self.clean_links)
+			logger.info("Cleaning {nlinks} links".format(nlinks=len(self.clean_links)))
+			if self.fast_clean:
+				self.taxonomydb.fast_delete_links(self.clean_links)
+			else:
+				logger.info("Cleaning tree (this will take a long time for large trees)")
+				self.taxonomydb.delete_links(self.clean_links)
 		if len(self.clean_nodes) < len(self.all_nodes) and len(self.clean_nodes) > 0:
 			self.taxonomydb.delete_nodes(self.clean_nodes)
 			if not ncbi:

flextaxd/modules/NewickTree.py

@@ -147,11 +147,13 @@ def print(self,type="newick"):
 		exists = importlib.find_loader('Bio')
 		if not exists:
 			raise VisualisationError("Visualisations other than newick requires biopython package (conda install biopython)!")
-
 		from Bio import Phylo
 		self.phylo = Phylo.read(StringIO(self.newickTree), "newick")
 		if type == "newick_vis":
 			Phylo.draw_ascii(self.phylo)
+		exists = importlib.find_loader('matplotlib')
+		if not exists:
+			raise VisualisationError("Visualisations using newick tree requires the matplotlib package (conda install matplotlib)!")
 		import matplotlib.pylab as pylab
 		if type == "tree":
 			Phylo.draw(self.phylo)

flextaxd/modules/ReadTaxonomy.py

@@ -109,6 +109,7 @@ def read_nodes(self, treefile=False):
 		with self.zopen(treefile, "r") as _treefile:
 			headers = _treefile.readline().strip().split(self.sep)
 			if "parent" not in headers or "child" not in headers:
+				logger.debug("Headers:  {h} separator [{sep}]".format(h=headers,sep=self.sep))
 				raise InputError("Your input tree file does not contain the headers to specify child and parent!")
 			if headers[0] == "parent":
 				swap = True

flextaxd/modules/ReadTaxonomyNCBI.py

@@ -6,6 +6,7 @@
 
 from .ReadTaxonomy import ReadTaxonomy
 from gzip import open as zopen
+import zlib
 import os
 import logging
 logger = logging.getLogger(__name__)
@@ -98,18 +99,30 @@ def parse_genomeid2taxid(self, genomes_path,annotation_file):
 		if not annotation_file.endswith("accession2taxid.gz"):
 			raise TypeError("The supplied annotation file does not seem to be the ncbi nucl_gb.accession2taxid.gz")
 		annotated_genome = set()
-		with zopen(annotation_file,"r") as f:
-			headers = f.readline().split(b"\t")
-			for row in f:
-				if row.strip() != "": ## If there are trailing empty lines in the file
-					refseqid,taxid = row.split(b"\t")[1:3]
-					try:
-						genebankid = self.refseqid_to_GCF[refseqid]
-						self.database.add_genome(genome=genebankid,_id=taxid.decode("utf-8"))
-						annotated_genome.add(refseqid)
-					except:
-						pass
-			self.database.commit()
+		try:
+			with zopen(annotation_file,"r") as f:
+				headers = f.readline().split(b"\t")
+				for row in f:
+					if row.strip() != "": ## If there are trailing empty lines in the file
+						if len(row.split(b"\t")) > 2:
+							try:
+								refseqid,taxid = row.split(b"\t")[1:3]
+							except:
+								logger.info(row)
+								logger.info(row.split(b"\t"))
+								if len(annotated_genome) > 0:
+									logger.info("Potential error in last row?")
+								else:
+									logger.info("Error on first line in annotation file, check format!")
+							try:
+								genebankid = self.refseqid_to_GCF[refseqid]
+								self.database.add_genome(genome=genebankid,_id=taxid.decode("utf-8"))
+								annotated_genome.add(refseqid)
+							except KeyError:
+								pass
+				self.database.commit()
+		except zlib.error as e:
+			logger.info("Error in annotation file {e}".format(e=e))
 		missing = set(self.refseqid_to_GCF.keys()) - annotated_genome
 		missing = [self.refseqid_to_GCF[m] for m in missing] ## Translate to GCF ids
 		if logging.root.level <=20: ## Equal to --verbose