def run_blast(self):
"""
BLAST the alleles against the genomes
"""
logging.info('BLASTing alleles against sequence files')
for query_file in self.query_files:
# Create a metadata object to store all the sample-specific information
sample = MetadataObject()
sample.alleles = GenObject()
local_db = os.path.splitext(query_file)[0]
sample.name = os.path.basename(local_db)
# Set the name of the BLAST output file
sample.alleles.blast_report = os.path.join(
self.reportpath, '{seq_id}.tsv'.format(seq_id=sample.name))
# Update the list of metadata objects with this sample
self.runmetadata.samples.append(sample)
self.blast_reports.append(sample.alleles.blast_report)
# Run the appropriate BLAST command: BLASTn for nt; tBLASTn for aa against translated nt
if self.amino_acid:
blast = NcbitblastnCommandline(db=local_db,
query=self.target_file,
num_alignments=100000000,
evalue=0.001,
num_threads=self.cpus,
task='tblastn',
outfmt=self.outfmt,
word_size=3,
out=sample.alleles.blast_report)
else:
blast = NcbiblastnCommandline(db=local_db,
query=self.target_file,
num_alignments=100000000,
evalue=0.001,
num_threads=self.cpus,
task='blastn',
outfmt=self.outfmt,
out=sample.alleles.blast_report)
if not os.path.isfile(sample.alleles.blast_report):
# Run BLAST - supply the record sequence as stdin, so BLAST doesn't look for an input file
try:
blast()
# BLAST can have issues with genomes that have very large contigs. Retry the analysis using only one
# thread
except ApplicationError:
os.remove(sample.alleles.blast_report)
blast = NcbitblastnCommandline(
db=local_db,
query=self.target_file,
num_alignments=100000000,
evalue=0.001,
num_threads=1,
task='tblastn',
outfmt=self.outfmt,
word_size=3,
out=sample.alleles.blast_report)
blast()
def record_extraction(self):
"""
Parse the input FASTA file, and create a dictionary of header: sequence for each entry
"""
for record in SeqIO.parse(self.file, 'fasta'):
metadata = MetadataObject()
metadata.name = record.id
metadata.records = record.seq.upper()
# self.records[record.id] = record.seq.upper()
self.samples.append(metadata)
def file_list(self):
"""
Create metadata objects for every .ab1 file in the supplied sequence path
"""
# Glob and sort a list of all the paths to the .ab1 files
file_list = sorted(glob(os.path.join(self.sequencepath, '*.ab1')),
reverse=True)
for seq_file in file_list:
# P19954_2019FCP-0000034876-4_VI0364_22 _1D06_M13-R17_E11_087.ab1
file_name = os.path.splitext(os.path.basename(seq_file))[0]
# Create a metadata object for each sample
sample = MetadataObject()
sample.name = file_name
sample.filepath = seq_file
self.samples.append(sample)
def helper(self):
"""Helper function for file creation (if desired), manipulation, quality assessment,
and trimming as well as the assembly"""
# Simple assembly without requiring accessory files (SampleSheet.csv, etc).
if self.basicassembly:
self.runmetadata = Basic(inputobject=self)
else:
# Populate the runmetadata object by parsing the SampleSheet.csv, GenerateFASTQRunStatistics.xml, and
# RunInfo.xml files
self.runinfo = os.path.join(self.path, 'RunInfo.xml')
self.runmetadata = runMetadata.Metadata(passed=self)
# Extract the flowcell ID and the instrument name if the RunInfo.xml file was provided
self.runmetadata.parseruninfo()
# Extract PhiX mapping information from the run
phi = phix.PhiX(inputobject=self)
phi.main()
# Populate the lack of bclcall and nohup call into the metadata sheet
for sample in self.runmetadata.samples:
sample.commands = GenObject()
sample.commands.nohupcall = 'NA'
sample.commands.bclcall = 'NA'
# Move/link the FASTQ files to strain-specific working directories
fastqmover.FastqMover(inputobject=self)
# Print the metadata to file
metadataprinter.MetadataPrinter(inputobject=self)
def query_prep(self):
"""
Create metadata objects for each sample
"""
logging.info('Preparing query files')
# Find all the sequence files in the path
fastas = sorted(glob(os.path.join(self.query_path, '*.fasta')))
for fasta in fastas:
name = os.path.splitext(os.path.basename(fasta))[0]
if name != 'combinedtargets':
# Create a metadata object for each sample
metadata = MetadataObject()
metadata.samples = list()
# Populate the metadata object with the required attributes
metadata.name = name
metadata.general = GenObject()
metadata.commands = GenObject()
metadata.alleles = GenObject()
metadata.alleles.outputdirectory = os.path.join(self.query_path, metadata.name)
# Set the name of the BLAST output file
metadata.alleles.blast_report = os.path.join(metadata.alleles.outputdirectory,
'{seq_id}.tsv'.format(seq_id=metadata.name))
try:
os.remove(metadata.alleles.blast_report)
except FileNotFoundError:
pass
make_path(metadata.alleles.outputdirectory)
metadata.general.bestassemblyfile = relative_symlink(src_file=fasta,
output_dir=metadata.alleles.outputdirectory,
export_output=True)
metadata.samples.append(metadata)
self.runmetadata.samples.append(metadata)
def create_args():
arguments = ArgumentParser()
arguments.sequencepath = test_sequences_path
arguments.starttime = time()
arguments.reportpath = os.path.join(arguments.sequencepath, 'reports')
arguments.runmetadata = MetadataObject()
# Create metadata objects for the samples
arguments.runmetadata.samples = Filer.filer(arguments)
return arguments
def excelparse(self):
"""
Parses input excel file, and creates objects with headers as keys, and cell data as values for each row
"""
logging.info('Loading excel file')
# A dictionary to store the parsed excel file in a more readable format
nesteddictionary = dict()
# Use pandas to read in the excel file, and subsequently convert the pandas data frame to a dictionary
# (.to_dict()). Only read the first fourteen columns (parse_cols=range(14)), as later columns are not
# relevant to this script
dictionary = pandas.read_excel(self.file, usecols=range(14)).to_dict()
# Iterate through the dictionary - each header from the excel file
for header in dictionary:
# Sample is the primary key, and value is the value of the cell for that primary key + header combination
for sample, value in dictionary[header].items():
# Update the dictionary with the new data
try:
nesteddictionary[sample].update({header: value})
# Create the nested dictionary if it hasn't been created yet
except KeyError:
nesteddictionary[sample] = dict()
nesteddictionary[sample].update({header: value})
# Create objects for each of the samples, rather than using a nested dictionary. It may have been possible to
# skip the creation of the nested dictionary, and create the objects from the original dictionary, but there
# seemed to be too many possible places for something to go wrong
for line in nesteddictionary:
# Create an object for each sample
metadata = MetadataObject()
# Set the name of the metadata to be the primary key for the sample from the excel file
metadata.name = line
# Find the headers and values for every sample
for header, value in nesteddictionary[line].items():
# Try/except for value.encode() - some of the value are type int, so they cannot be encoded
try:
# Create each attribute - use the header (in lowercase, and spaces removed) as the attribute name,
# and the value as the attribute value
setattr(metadata,
str(header).replace(' ', '').lower(), str(value))
except TypeError:
setattr(metadata,
str(header).replace(' ', '').lower(), value)
# Append the object to the list of objects
self.metadata.append(metadata)
def ultimatum(args):
SetupLogging(debug=args.debug)
# Create metadata objects for the samples
args.runmetadata = MetadataObject()
args.runmetadata.samples = Filer.filer(args)
finder = Ultimatum(metadataobject=args.runmetadata.samples,
sequencepath=args.sequencepath,
reportpath=os.path.join(args.sequencepath, 'reports'),
primerfile=args.primerfile,
primer_format=args.primer_format,
mismatches=args.mismatches,
export_amplicons=args.export_amplicons)
finder.main()
def __init__(self, path, amino_acid):
if path.startswith('~'):
self.path = os.path.abspath(os.path.expanduser(os.path.join(path)))
else:
self.path = os.path.abspath(os.path.join(path))
self.allele_path = os.path.join(self.path, 'alleles')
self.aa_allele_path = os.path.join(self.path, 'aa_alleles')
self.profile_path = os.path.join(self.path, 'profile')
self.aa_profile_path = os.path.join(self.path, 'aa_profile')
make_path(self.profile_path)
self.profile_file = os.path.join(self.profile_path, 'profile.txt')
self.aa_profile_file = os.path.join(self.aa_profile_path, 'aa_profile.txt')
self.query_path = os.path.join(self.path, 'query')
self.report_path = os.path.join(self.path, 'reports')
self.aa_report_path = os.path.join(self.path, 'aa_reports')
make_path(self.report_path)
make_path(self.aa_report_path)
novel_alleles = glob(os.path.join(self.report_path, '*.fasta'))
for novel_allele in novel_alleles:
os.remove(novel_allele)
self.aa_notes_path = os.path.join(self.path, 'aa_notes')
make_path(self.aa_notes_path)
self.aa_profile_notes = os.path.join(self.aa_notes_path, 'aa_profile_notes.tsv')
self.amino_acid = amino_acid
if not self.amino_acid:
self.combined_targets = os.path.join(self.allele_path, 'combinedtargets.fasta')
else:
self.combined_targets = os.path.join(self.aa_allele_path, 'combinedtargets.fasta')
self.gene_names = list()
self.runmetadata = MetadataObject()
self.runmetadata.samples = list()
self.cpus = multiprocessing.cpu_count() - 1
self.profile_report = os.path.join(self.report_path, 'profiles.tsv')
self.aa_profile_report = os.path.join(self.aa_report_path, 'aa_profiles.tsv')
try:
os.remove(self.profile_report)
except FileNotFoundError:
pass
# Fields used for custom outfmt 6 BLAST output:
self.fieldnames = ['query_id', 'subject_id', 'identical', 'mismatches', 'gaps',
'evalue', 'bit_score', 'query_length', 'subject_length', 'alignment_length',
'query_start', 'query_end', 'subject_start', 'subject_end',
'query_sequence', 'subject_sequence']
self.extended_fieldnames = self.fieldnames.copy()
self.extended_fieldnames.insert(14, 'percent_match')
self.outfmt = '6 qseqid sseqid nident mismatch gaps evalue bitscore qlen slen length ' \
'qstart qend sstart send qseq sseq'
# A string of the header to use for formatting the profile file, and the report headers
self.data = str()
self.aa_allele_dict = dict()
self.aa_nt_allele_link_dict = dict()
def __init__(self, inputobject):
# Define variables based on supplied arguments
self.start = inputobject.start
self.path = inputobject.path
self.sequencepath = inputobject.sequencepath
self.datapath = inputobject.datapath
self.reportpath = inputobject.reportpath
# Use the argument for the number of threads to use, or default to the number of cpus in the system
self.cpus = inputobject.cpus
# Set the cutoff to be a percent
self.cutoff = inputobject.cutoff
# Initialise a variable to hold the sample objects
self.runmetadata = inputobject.runmetadata if inputobject.runmetadata else MetadataObject(
)
# Initialise queues
self.loadqueue = Queue()
self.listqueue = Queue()
self.filterqueue = Queue()
self.devnull = open(os.devnull, 'wb')
def legacy(args):
# Prep the args object to be used in the legacy script
SetupLogging(debug=args.debug)
args.reportpath = os.path.join(args.sequencepath, 'reports')
args.runmetadata = MetadataObject()
# Create metadata objects for the samples
args.runmetadata.samples = Filer.filer(args)
if args.analysistype == 'vtyper':
# Perform vtx typing
vtyper = Vtyper(inputobject=args,
analysistype='vtyper_legacy',
mismatches=args.mismatches)
vtyper.vtyper()
else:
epcr = Custom(inputobject=args,
analysistype='custom_epcr',
primerfile=args.primerfile,
ampliconsize=args.maxampliconsize,
mismatches=args.mismatches,
primer_format=args.primer_format,
export_amplicons=args.export_amplicons)
epcr.main()
def identity(args):
SetupLogging(debug=args.debug)
# Create metadata objects for the samples
args.runmetadata = MetadataObject()
args.runmetadata.samples = Filer.filer(args)
if args.analysistype == 'vtyper':
epcr = VtyperIP(metadataobject=args.runmetadata.samples,
analysistype=args.analysistype,
reportpath=os.path.join(args.sequencepath, 'reports'))
epcr.vtyper()
else:
epcr = CustomIP(metadataobject=args.runmetadata.samples,
sequencepath=args.sequencepath,
reportpath=os.path.join(args.sequencepath, 'reports'),
primerfile=args.primerfile,
min_amplicon_size=args.minampliconsize,
max_amplicon_size=args.maxampliconsize,
primer_format=args.primer_format,
mismatches=args.mismatches,
export_amplicons=args.export_amplicons,
contigbreaks=args.contigbreaks)
epcr.main()
def __init__(self, start, sequencepath, referencefilepath, scriptpath,
debug):
"""
:param start:
:param sequencepath:
:param referencefilepath:
:param scriptpath:
"""
self.debug = debug
SetupLogging(self.debug)
logging.info('Welcome to the CFIA bacterial typing pipeline {}'.format(
__version__))
# Define variables from the arguments - there may be a more streamlined way to do this
self.sequencepath = os.path.join(sequencepath)
self.path = self.sequencepath
self.targetpath = os.path.join(referencefilepath)
self.reffilepath = self.targetpath
# Define the start time
self.starttime = start
self.start = self.starttime
# Use the argument for the number of threads to use, or default to the number of cpus in the system
self.cpus = multiprocessing.cpu_count() - 1
# Assertions to ensure that the provided variables are valid
assert os.path.isdir(self.sequencepath), 'Supplied path location is not a valid directory {0!r:s}'\
.format(self.sequencepath)
self.reportpath = os.path.join(self.sequencepath, 'reports')
assert os.path.isdir(self.targetpath), 'Reference file path is not a valid directory {0!r:s}'\
.format(self.targetpath)
self.commit = __version__
self.homepath = scriptpath
self.analysistype = 'assembly_typing'
self.genus_specific = False
self.logfile = os.path.join(self.sequencepath, 'logfile')
self.pipeline = True
# Initialise the metadata object
self.metadata = list()
self.runmetadata = MetadataObject()
def test_sistr_seqsero():
metadata = MetadataObject()
method.runmetadata.samples = list()
fasta = os.path.join(var.sequencepath, 'NC_003198.fasta')
metadata.name = os.path.split(fasta)[1].split('.')[0]
# Initialise the general and run categories
metadata.general = GenObject()
metadata.run = GenObject()
metadata.general.fastqfiles = list()
metadata.general.trimmedcorrectedfastqfiles = [
os.path.join(var.sequencepath, 'seqsero',
'2014-SEQ-1049_seqsero.fastq.gz')
]
# Set the destination folder
outputdir = os.path.join(var.sequencepath, metadata.name)
make_path(outputdir)
# Add the output directory to the metadata
metadata.general.outputdirectory = outputdir
metadata.general.logout = os.path.join(outputdir, 'out')
metadata.general.logerr = os.path.join(outputdir, 'err')
metadata.run.outputdirectory = outputdir
metadata.general.bestassemblyfile = True
# Initialise an attribute to store commands
metadata.commands = GenObject()
# Assume that all samples are Salmonella
metadata.general.referencegenus = 'Salmonella'
# Set the .fasta file as the best assembly
metadata.general.bestassemblyfile = fasta
method.runmetadata.samples.append(metadata)
method.sistr()
for sample in method.runmetadata.samples:
assert sample.sistr.cgmlst_genome_match == 'ERR586739' or sample.sistr.cgmlst_genome_match == 'SAL_BA2732AA'
method.seqsero()
for sample in method.runmetadata.samples:
assert sample.seqsero.predicted_serotype == '- 9:f,g,t:-'
variable_update()
def variables():
v = MetadataObject()
v.sequencepath = os.path.join(testpath, 'testdata')
v.referencefilepath = os.path.join(v.sequencepath, 'databases')
v.customsamplesheet = os.path.join(v.sequencepath, 'SampleSheet.csv')
v.debug = True
v.numreads = 2
v.kmerrange = '21'
v.preprocess = False
v.basicassembly = True
v.threads = multiprocessing.cpu_count()
v.startingtime = time()
v.commit = b''
v.homepath = scriptpath
return v
def probefinder(self):
"""
Find the longest probe sequences
"""
logging.info('Finding and filtering probe sequences')
for sample in self.samples:
# A list to store the metadata object for each alignment
sample.gene = list()
for align in sample.alignedalleles:
# Create an object to store all the information for each alignment file
metadata = GenObject()
metadata.name = os.path.splitext(os.path.basename(align))[0]
metadata.alignmentfile = align
# Create an alignment object from the alignment file
try:
metadata.alignment = AlignIO.read(align, 'fasta')
except ValueError:
# If a ValueError: Sequences must all be the same length is raised, pad the shorter sequences
# to be the length of the longest sequence
# https://stackoverflow.com/q/32833230
records = SeqIO.parse(align, 'fasta')
# Make a copy, otherwise our generator is exhausted after calculating maxlen
records = list(records)
# Calculate the length of the longest sequence
maxlen = max(len(record.seq) for record in records)
# Pad sequences so that they all have the same length
for record in records:
if len(record.seq) != maxlen:
sequence = str(record.seq).ljust(maxlen, '.')
record.seq = Seq(sequence)
assert all(len(record.seq) == maxlen for record in records)
# Write to file and do alignment
metadata.alignmentfile = '{}_padded.tfa'.format(
os.path.splitext(align)[0])
with open(metadata.alignmentfile, 'w') as padded:
SeqIO.write(records, padded, 'fasta')
# Align the padded sequences
metadata.alignment = AlignIO.read(metadata.alignmentfile,
'fasta')
metadata.summaryalign = AlignInfo.SummaryInfo(
metadata.alignment)
# The dumb consensus is a very simple consensus sequence calculated from the alignment. Default
# parameters of threshold=.7, and ambiguous='X' are used
consensus = metadata.summaryalign.dumb_consensus()
metadata.consensus = str(consensus)
# The position-specific scoring matrix (PSSM) stores the frequency of each based observed at each
# location along the entire consensus sequence
metadata.pssm = metadata.summaryalign.pos_specific_score_matrix(
consensus)
metadata.identity = list()
# Find the prevalence of each base for every location along the sequence
for line in metadata.pssm:
try:
bases = [
line['A'], line['C'], line['G'], line['T'],
line['-']
]
# Calculate the frequency of the most common base - don't count gaps
metadata.identity.append(
float('{:.2f}'.format(
max(bases[:4]) / sum(bases) * 100)))
except KeyError:
bases = [line['A'], line['C'], line['G'], line['T']]
# Calculate the frequency of the most common base - don't count gaps
metadata.identity.append(
float('{:.2f}'.format(
max(bases) / sum(bases) * 100)))
# List to store metadata objects
metadata.windows = list()
# Variable to store whether a suitable probe has been found for the current organism + gene pair.
# As the probe sizes are evaluated in descending size, as soon as a probe has been discovered, the
# search for more probes can stop, and subsequent probes will be smaller than the one(s) already found
passing = False
# Create sliding windows of size self.max - self.min from the list of identities for each column
# of the alignment
for i in reversed(range(self.min, self.max + 1)):
if not passing:
windowdata = MetadataObject()
windowdata.size = i
windowdata.max = 0
windowdata.sliding = list()
# Create a counter to store the starting location of the window in the sequence
n = 0
# Create sliding windows from the range of sizes for the list of identities
windows = self.window(metadata.identity, i)
# Go through each window from the collection of sliding windows to determine which window(s)
# has (have) the best results
for window in windows:
# Create another object to store all the data for the window
slidingdata = MetadataObject()
# Only consider the window if every position has a percent identity greater than the cutoff
if min(window) > self.cutoff:
# Populate the object with the necessary variables
slidingdata.location = '{}:{}'.format(n, n + i)
slidingdata.min = min(window)
slidingdata.mean = float('{:.2f}'.format(
numpy.mean(window)))
slidingdata.sequence = str(consensus[n:n + i])
# Create attributes for evaluating windows. A greater/less windowdata.max/windowdata.min
# means a better/less overall percent identity, respectively
windowdata.max = slidingdata.mean if slidingdata.mean >= windowdata.max \
else windowdata.max
windowdata.min = slidingdata.mean if slidingdata.mean <= windowdata.max \
else windowdata.min
# Add the object to the list of objects
windowdata.sliding.append(slidingdata)
passing = True
n += 1
# All the object to the list of objects
metadata.windows.append(windowdata)
# All the object to the list of objects
sample.gene.append(metadata)
def __init__(self, inputobject, extension='fasta', light=False):
# Create an object to mimic the command line arguments necessary for the script
args = MetadataObject()
args.path = inputobject.path
args.sequencepath = inputobject.path
args.databasepath = os.path.join(inputobject.reffilepath, 'clark')
make_path(args.databasepath)
args.clarkpath = os.path.dirname(which('CLARK'))
args.clarkpath += '/../opt/clark/'
args.cutoff = 0.005
args.database = 'bacteria'
args.rank = 'species'
args.filter = False
args.threads = inputobject.cpus
args.runmetadata = inputobject.runmetadata
args.clean_seqs = False
args.reffilepath = inputobject.reffilepath
args.extension = extension
args.light = light
# Run CLARK
CLARK(args, inputobject.commit, inputobject.starttime,
inputobject.homepath)
def __init__(self, args, pipelinecommit, startingtime, scriptpath):
# Initialise variables
self.commit = str(pipelinecommit)
self.start = startingtime
self.homepath = scriptpath
# Define variables based on supplied arguments
self.args = args
self.path = os.path.join(args.path)
assert os.path.isdir(
self.path
), u'Supplied path is not a valid directory {0!r:s}'.format(self.path)
self.sequencepath = os.path.join(args.sequencepath, '')
assert os.path.isdir(self.sequencepath), u'Supplied sequence path is not a valid directory {0!r:s}' \
.format(self.sequencepath)
self.databasepath = os.path.join(args.databasepath, '')
assert os.path.isdir(self.databasepath), u'Supplied database path is not a valid directory {0!r:s}' \
.format(self.databasepath)
# There seems to be an issue with CLARK when running with a very high number of cores. Limit self.cpus to 1
self.cpus = 4
# Set variables from the arguments
self.database = args.database
self.rank = args.rank
self.clarkpath = args.clarkpath
self.cutoff = float(args.cutoff) * 100
# Initialise variables for the analysis
self.targetcall = str()
self.classifycall = str()
self.devnull = open(os.devnull, 'wb')
self.filelist = os.path.join(self.path, 'sampleList.txt')
self.reportlist = os.path.join(self.path, 'reportList.txt')
self.abundancequeue = Queue()
self.datapath = str()
self.reportpath = os.path.join(self.path, 'reports')
self.clean_seqs = args.clean_seqs
self.light = args.light
self.extension = args.extension
if self.clean_seqs:
try:
self.reffilepath = args.reffilepath
except AttributeError:
self.clean_seqs = False
# If run as part of the assembly pipeline, a few modifications are necessary to ensure that the metadata objects
# and variables play nice
try:
if args.runmetadata:
self.runmetadata = args.runmetadata
# Create the name of the final report
self.report = os.path.join(
self.reportpath,
'abundance_{ft}.xlsx'.format(ft=self.extension))
# Only re-run the CLARK analyses if the CLARK report doesn't exist. All files created by CLARK
if not os.path.isfile(self.report):
logging.info(
'Performing CLARK analysis on {ft} files'.format(
ft=self.extension))
if self.extension != 'fastq':
for sample in self.runmetadata.samples:
sample.general.combined = sample.general.bestassemblyfile
# Run the pipeline
self.main()
else:
# Only perform FASTQ analyses if the sample is declared to be a metagenome
metagenome = False
for sample in self.runmetadata.samples:
try:
status = sample.run.Description
except AttributeError:
status = 'unknown'
if status == 'metagenome':
metagenome = True
# If any of the samples are metagenomes, run the CLARK analysis on the raw files
if metagenome:
fileprep.Fileprep(self)
# Run the pipeline
self.main()
# Clean up the files and create/delete attributes to be consistent with pipeline Metadata objects
for sample in self.runmetadata.samples:
# Create a GenObject to store metadata when this script is run as part of the pipeline
clarkextension = 'clark{}'.format(self.extension)
setattr(sample, clarkextension, GenObject())
# Create a folder to store all the CLARK files
sample[clarkextension].outputpath = os.path.join(
sample.general.outputdirectory, 'CLARK')
make_path(sample[clarkextension].outputpath)
if sample.general.bestassemblyfile != 'NA':
# Move the files to the CLARK folder
try:
move(
sample.general.abundance,
os.path.join(
sample[clarkextension].outputpath,
os.path.basename(
sample.general.abundance)))
move(
sample.general.classification,
os.path.join(
sample[clarkextension].outputpath,
os.path.basename(
sample.general.classification)))
except (AttributeError, FileNotFoundError):
pass
# Set the CLARK-specific attributes
try:
sample[
clarkextension].abundance = sample.general.abundance
sample[
clarkextension].classification = sample.general.classification
sample[
clarkextension].combined = sample.general.combined
except AttributeError:
pass
if self.extension == 'fastq':
# Remove the combined .fastq files
try:
if type(sample[clarkextension].combined
) is list:
os.remove(
sample[clarkextension].combined)
except (OSError, AttributeError):
pass
# Remove the text files lists of files and reports created by CLARK
try:
map(
lambda x: os.remove(os.path.join(self.path, x)
),
['reportList.txt', 'sampleList.txt'])
except OSError:
pass
else:
self.runmetadata = MetadataObject()
self.report = os.path.join(self.reportpath, 'abundance.xlsx')
# Create the objects
self.objectprep()
self.main()
except AttributeError:
self.runmetadata = MetadataObject()
self.report = os.path.join(self.reportpath, 'abundance.xlsx')
# Create the objects
self.objectprep()
# Set the run description to 'metagenome' in order to process the samples
for sample in self.runmetadata.samples:
sample.run.Description = 'metagenome'
self.main()
# Optionally filter the .fastq reads based on taxonomic assignment
if args.filter:
filtermetagenome.PipelineInit(self)
# Print the metadata to file
metadataprinter.MetadataPrinter(self)
class RunAssemble(object):
def main(self):
"""
Run the methods in the correct order
"""
# Start the assembly
self.helper()
# Create the quality object
self.create_quality_object()
# Run the quality analyses
self.quality()
# Perform assembly
self.assemble()
# Perform genus-agnostic typing
self.agnostictyping()
# Perform typing
self.typing()
# Compress or remove all large, temporary files created by the pipeline
if not self.debug:
compress.Compress(self)
metadataprinter.MetadataPrinter(inputobject=self)
def helper(self):
"""Helper function for file creation (if desired), manipulation, quality assessment,
and trimming as well as the assembly"""
# Simple assembly without requiring accessory files (SampleSheet.csv, etc).
if self.basicassembly:
self.runmetadata = Basic(inputobject=self)
else:
# Populate the runmetadata object by parsing the SampleSheet.csv, GenerateFASTQRunStatistics.xml, and
# RunInfo.xml files
self.runinfo = os.path.join(self.path, 'RunInfo.xml')
self.runmetadata = runMetadata.Metadata(passed=self)
# Extract the flowcell ID and the instrument name if the RunInfo.xml file was provided
self.runmetadata.parseruninfo()
# Extract PhiX mapping information from the run
phi = phix.PhiX(inputobject=self)
phi.main()
# Populate the lack of bclcall and nohup call into the metadata sheet
for sample in self.runmetadata.samples:
sample.commands = GenObject()
sample.commands.nohupcall = 'NA'
sample.commands.bclcall = 'NA'
# Move/link the FASTQ files to strain-specific working directories
fastqmover.FastqMover(inputobject=self)
# Print the metadata to file
metadataprinter.MetadataPrinter(inputobject=self)
def create_quality_object(self):
"""
Create the quality object
"""
self.qualityobject = quality.Quality(inputobject=self)
def quality(self):
"""
Creates quality objects and runs quality assessments and quality processes on the
supplied sequences
"""
# Validate that the FASTQ files are in the proper format, and that there are no issues e.g. different numbers
# of forward and reverse reads, read length longer than quality score length, proper extension
if not self.debug:
self.fastq_validate()
# Run FastQC on the unprocessed fastq files
self.fastqc_raw()
# Perform quality trimming and FastQC on the trimmed files
self.quality_trim()
# Run FastQC on the trimmed files
self.fastqc_trimmed()
# Perform error correcting on the reads
self.error_correct()
# Detect contamination in the reads
self.contamination_detection()
# Run FastQC on the processed fastq files
self.fastqc_trimmedcorrected()
# Exit if only pre-processing of data is requested
metadataprinter.MetadataPrinter(inputobject=self)
if self.preprocess:
logging.info('Pre-processing complete')
quit()
def fastq_validate(self):
"""
Attempt to detect and fix issues with the FASTQ files
"""
self.qualityobject.validate_fastq()
metadataprinter.MetadataPrinter(inputobject=self)
def fastqc_raw(self):
"""
Run FastQC on the unprocessed FASTQ files
"""
self.qualityobject.fastqcthreader(level='Raw')
metadataprinter.MetadataPrinter(inputobject=self)
def quality_trim(self):
"""
Perform quality trimming and FastQC on the trimmed files
"""
self.qualityobject.trimquality()
metadataprinter.MetadataPrinter(inputobject=self)
def fastqc_trimmed(self):
"""
Run FastQC on the quality trimmed FASTQ files
"""
self.qualityobject.fastqcthreader(level='Trimmed')
metadataprinter.MetadataPrinter(inputobject=self)
def error_correct(self):
"""
Perform error correcting on the reads
"""
self.qualityobject.error_correction()
metadataprinter.MetadataPrinter(inputobject=self)
def contamination_detection(self):
"""
Calculate the levels of contamination in the reads
"""
self.qualityobject.contamination_finder(report_path=self.reportpath,
debug=self.debug)
metadataprinter.MetadataPrinter(inputobject=self)
def fastqc_trimmedcorrected(self):
"""
Run FastQC on the processed fastq files
"""
self.qualityobject.fastqcthreader(level='trimmedcorrected')
metadataprinter.MetadataPrinter(inputobject=self)
def assemble(self):
"""
Assemble genomes and perform some basic quality analyses
"""
# Assemble genomes
self.assemble_genomes()
# Calculate assembly metrics on raw assemblies
self.evaluate_assemblies()
# ORF detection
self.prodigal()
# CLARK analyses
self.clark()
def assemble_genomes(self):
"""
Use skesa to assemble genomes
"""
assembly = skesa.Skesa(inputobject=self)
assembly.main()
metadataprinter.MetadataPrinter(inputobject=self)
def evaluate_assemblies(self):
"""
Evaluate assemblies with Quast
"""
qual = evaluate.AssemblyEvaluation(inputobject=self)
qual.main()
metadataprinter.MetadataPrinter(inputobject=self)
def prodigal(self):
"""
Use prodigal to detect open reading frames in the assemblies
"""
prodigal.Prodigal(self)
metadataprinter.MetadataPrinter(self)
def clark(self):
"""
Run CLARK metagenome analyses on the raw reads and assemblies if the system has adequate resources
"""
# Run CLARK typing on the .fastq and .fasta files
automateCLARK.PipelineInit(inputobject=self,
extension='fasta',
light=True)
automateCLARK.PipelineInit(inputobject=self,
extension='fastq',
light=True)
def agnostictyping(self):
"""
Perform typing that does not require the genus of the organism to be known
"""
# Run mash
self.mash()
# Run rMLST on assemblies
self.rmlst_assembled()
# Create reports summarising the run and sample qualities
self.quality_report()
# Run the 16S analyses
self.sixteens()
# Find genes of interest
self.genesippr()
# Resistance finding - raw reads
self.ressippr()
# Resistance finding - assemblies
self.resfinder()
# Run MOB-suite
self.mob_suite()
# Prophage detection
self.prophages()
# Univec contamination search
self.univec()
# Virulence
self.virulence()
# cgMLST
self.cgmlst()
def mash(self):
"""
Run mash to determine closest refseq genome
"""
mash.Mash(inputobject=self, analysistype='mash')
metadataprinter.MetadataPrinter(inputobject=self)
def rmlst_assembled(self):
"""
Run rMLST analyses on assemblies
"""
if not os.path.isfile(os.path.join(self.reportpath, 'rmlst.csv')):
rmlst = BLAST(args=self, analysistype='rmlst', cutoff=100)
rmlst.seekr()
else:
parse = ReportParse(args=self, analysistype='rmlst')
parse.report_parse()
metadataprinter.MetadataPrinter(inputobject=self)
def quality_report(self):
"""
Create reports summarising the run and sample quality outputs
"""
qual_report = reporter.Reporter(self)
qual_report.run_quality_reporter()
qual_report.sample_quality_report()
def sixteens(self):
"""
Run the 16S analyses
"""
SixteensFull(args=self,
pipelinecommit=self.commit,
startingtime=self.starttime,
scriptpath=self.homepath,
analysistype='sixteens_full',
cutoff=0.95)
metadataprinter.MetadataPrinter(inputobject=self)
def genesippr(self):
"""
Find genes of interest
"""
GeneSippr(args=self,
pipelinecommit=self.commit,
startingtime=self.starttime,
scriptpath=self.homepath,
analysistype='genesippr',
cutoff=0.95,
pipeline=False,
revbait=False)
metadataprinter.MetadataPrinter(inputobject=self)
def mob_suite(self):
"""
"""
mob = MobRecon(metadata=self.runmetadata.samples,
analysistype='mobrecon',
databasepath=self.reffilepath,
threads=self.cpus,
logfile=self.logfile,
reportpath=self.reportpath)
mob.mob_recon()
metadataprinter.MetadataPrinter(inputobject=self)
def ressippr(self):
"""
Resistance finding - raw reads
"""
res = Resistance(args=self,
pipelinecommit=self.commit,
startingtime=self.starttime,
scriptpath=self.homepath,
analysistype='resfinder',
cutoff=0.7,
pipeline=False,
revbait=True)
res.main()
metadataprinter.MetadataPrinter(inputobject=self)
def resfinder(self):
"""
Resistance finding - assemblies
"""
resfinder = BLAST(args=self, analysistype='resfinder_assembled')
resfinder.seekr()
metadataprinter.MetadataPrinter(inputobject=self)
def prophages(self, cutoff=90):
"""
Prophage detection
:param cutoff: cutoff value to be used in the analyses
"""
prophages = Prophages(args=self,
analysistype='prophages',
cutoff=cutoff,
unique=True)
if not os.path.isfile(os.path.join(self.reportpath, 'prophages.csv')):
prophages.seekr()
metadataprinter.MetadataPrinter(inputobject=self)
def univec(self):
"""
Univec contamination search
"""
if not os.path.isfile(os.path.join(self.reportpath, 'univec.csv')):
univec = Univec(args=self,
analysistype='univec',
cutoff=80,
unique=True)
univec.seekr()
metadataprinter.MetadataPrinter(inputobject=self)
def virulence(self):
"""
Virulence gene detection
"""
vir = Virulence(args=self,
pipelinecommit=self.commit,
startingtime=self.starttime,
scriptpath=self.homepath,
analysistype='virulence',
cutoff=0.9,
pipeline=False,
revbait=True)
if not os.path.isfile(os.path.join(self.reportpath, 'virulence.csv')):
vir.reporter()
metadataprinter.MetadataPrinter(inputobject=self)
def cgmlst(self):
"""
Run rMLST analyses on raw reads
"""
if not os.path.isfile(os.path.join(self.reportpath, 'cgmlst.csv')):
cgmlst = KMAMLST(args=self,
pipeline=True,
analysistype='cgmlst',
cutoff=98,
kma_kwargs=' -cge -and')
cgmlst.main()
else:
parse = ReportParse(args=self, analysistype='cgmlst')
parse.report_parse()
metadataprinter.MetadataPrinter(inputobject=self)
def typing(self):
"""
Perform analyses that use genera-specific databases
"""
# Run modules and print metadata to file
# MLST on assemblies
self.mlst_assembled()
# Assembly-based serotyping
self.ec_typer()
# Serotyping
self.serosippr()
# SeqSero
self.seqsero()
# Assembly-based vtyper
self.legacy_vtyper()
# Raw read verotoxin typing
self.verotoxin()
# Sistr
self.sistr()
# Calculate the presence/absence of GDCS
self.run_gdcs()
# Create a final summary report
self.run_report()
def mlst_assembled(self):
"""
Run rMLST analyses on assemblies
"""
if not os.path.isfile(os.path.join(self.reportpath, 'mlst.csv')):
mlst = BLAST(args=self,
analysistype='mlst',
cutoff=100,
genus_specific=True)
mlst.seekr()
else:
parse = ReportParse(args=self, analysistype='mlst')
parse.report_parse()
metadataprinter.MetadataPrinter(inputobject=self)
def ec_typer(self):
"""
Assembly-based serotyping
"""
ec = ECTyper(metadata=self.runmetadata,
report_path=self.reportpath,
assembly_path=os.path.join(self.path, 'raw_assemblies'),
threads=self.cpus,
logfile=self.logfile)
ec.main()
metadataprinter.MetadataPrinter(inputobject=self)
def serosippr(self):
"""
Serotyping analyses
"""
Serotype(args=self,
pipelinecommit=self.commit,
startingtime=self.starttime,
scriptpath=self.homepath,
analysistype='serosippr',
cutoff=0.90,
pipeline=True)
metadataprinter.MetadataPrinter(inputobject=self)
def seqsero(self):
"""
Run SeqSero2 on Salmonella samples
"""
seqsero = SeqSero(self)
seqsero.main()
metadataprinter.MetadataPrinter(inputobject=self)
def legacy_vtyper(self):
"""
Legacy vtyper - uses ePCR
"""
legacy_vtyper = LegacyVtyper(inputobject=self,
analysistype='legacy_vtyper',
mismatches=2)
legacy_vtyper.vtyper()
metadataprinter.MetadataPrinter(inputobject=self)
def verotoxin(self):
"""
Raw read verotoxin typing
"""
vero = Verotoxin(args=self,
pipeline=True,
analysistype='verotoxin',
cutoff=90)
vero.main()
def sistr(self):
"""
Sistr
"""
sistr_obj = sistr.Sistr(inputobject=self, analysistype='sistr')
sistr_obj.main()
metadataprinter.MetadataPrinter(inputobject=self)
def run_gdcs(self):
"""
Determine the presence of genomically-dispersed conserved sequences (genes from MLST, rMLST, and cgMLST
analyses)
"""
# Run the GDCS analysis
gdcs = GDCS(inputobject=self)
gdcs.main()
metadataprinter.MetadataPrinter(inputobject=self)
def run_report(self):
"""
Create the final combinedMetadata report
"""
run_report = reporter.Reporter(self)
# Create the standard and legacy reports
run_report.metadata_reporter()
run_report.legacy_reporter()
# Clean the large attributes from the metadata objects
run_report.clean_object()
def __init__(self, args):
"""
Initialises the variables required for this class
:param args: list of arguments passed to the script
"""
self.debug = args.debug
SetupLogging(self.debug)
logging.info(
'Welcome to the CFIA OLC Workflow for Bacterial Assembly and Typing (COWBAT) version {version}'
.format(version=__version__))
# Define variables from the arguments - there may be a more streamlined way to do this
self.args = args
if args.sequencepath.startswith('~'):
self.path = os.path.abspath(
os.path.expanduser(os.path.join(args.sequencepath)))
else:
self.path = os.path.abspath(os.path.join(args.sequencepath))
self.sequencepath = self.path
if args.referencefilepath.startswith('~'):
self.reffilepath = os.path.expanduser(
os.path.abspath(os.path.join(args.referencefilepath)))
else:
self.reffilepath = os.path.abspath(
os.path.join(args.referencefilepath))
self.numreads = args.numreads
self.preprocess = args.preprocess
# Define the start time
self.starttime = args.startingtime
if args.customsamplesheet:
if args.customsamplesheet.startswith('~'):
self.customsamplesheet = os.path.expanduser(
os.path.abspath(os.path.join(self.customsamplesheet)))
else:
self.customsamplesheet = os.path.abspath(
os.path.join(args.customsamplesheet))
else:
self.customsamplesheet = args.customsamplesheet
if self.customsamplesheet:
assert os.path.isfile(self.customsamplesheet), 'Cannot find custom sample sheet as specified {css}' \
.format(css=self.customsamplesheet)
self.basicassembly = args.basicassembly
if not self.customsamplesheet and not os.path.isfile(
os.path.join(self.path, 'SampleSheet.csv')):
self.basicassembly = True
logging.warning(
'Could not find a sample sheet. Performing basic assembly (no run metadata captured)'
)
# Use the argument for the number of threads to use, or default to the number of cpus in the system
self.cpus = args.threads if args.threads else multiprocessing.cpu_count(
) - 1
# Assertions to ensure that the provided variables are valid
make_path(self.path)
assert os.path.isdir(
self.path
), 'Supplied path location is not a valid directory {0!r:s}'.format(
self.path)
self.reportpath = os.path.join(self.path, 'reports')
make_path(self.reportpath)
assert os.path.isdir(self.reffilepath), 'Reference file path is not a valid directory {0!r:s}' \
.format(self.reffilepath)
self.commit = __version__
self.homepath = args.homepath
self.logfile = os.path.join(self.path, 'logfile')
self.runinfo = str()
self.pipeline = True
self.qualityobject = MetadataObject()
# Initialise the metadata object
self.runmetadata = MetadataObject()
def __init__(self, args):
"""
Initialises the variables required for this class
:param args: list of arguments passed to the script
"""
self.debug = args.debug
SetupLogging(self.debug)
logging.info(
'Welcome to the CFIA OLC Workflow for Bacterial Assembly and Typing (COWBAT) version {version}'
.format(version=__version__))
# Define variables from the arguments - there may be a more streamlined way to do this
self.args = args
if args.sequencepath.startswith('~'):
self.path = os.path.abspath(
os.path.expanduser(os.path.join(args.sequencepath)))
else:
self.path = os.path.abspath(os.path.join(args.sequencepath))
self.sequencepath = self.path
if args.referencefilepath.startswith('~'):
self.reffilepath = os.path.expanduser(
os.path.abspath(os.path.join(args.referencefilepath)))
else:
self.reffilepath = os.path.abspath(
os.path.join(args.referencefilepath))
self.numreads = args.numreads
self.preprocess = args.preprocess
# Define the start time
self.starttime = args.startingtime
if args.customsamplesheet:
if args.customsamplesheet.startswith('~'):
self.customsamplesheet = os.path.expanduser(
os.path.abspath(os.path.join(self.customsamplesheet)))
else:
self.customsamplesheet = os.path.abspath(
os.path.join(args.customsamplesheet))
else:
self.customsamplesheet = args.customsamplesheet
if self.customsamplesheet:
assert os.path.isfile(self.customsamplesheet), 'Cannot find custom sample sheet as specified {css}' \
.format(css=self.customsamplesheet)
self.basicassembly = args.basicassembly
if not self.customsamplesheet and not os.path.isfile(
os.path.join(self.path, 'SampleSheet.csv')):
self.basicassembly = True
logging.warning(
'Could not find a sample sheet. Performing basic assembly (no run metadata captured)'
)
# Use the argument for the number of threads to use, or default to the number of cpus in the system
self.cpus = args.threads if args.threads else multiprocessing.cpu_count(
) - 1
# Assertions to ensure that the provided variables are valid
make_path(self.path)
assert os.path.isdir(
self.path
), 'Supplied path location is not a valid directory {0!r:s}'.format(
self.path)
self.reportpath = os.path.join(self.path, 'reports')
make_path(self.reportpath)
assert os.path.isdir(self.reffilepath), 'Reference file path is not a valid directory {0!r:s}' \
.format(self.reffilepath)
self.commit = __version__
self.homepath = args.homepath
self.logfile = os.path.join(self.path, 'logfile')
self.runinfo = str()
self.pipeline = True
self.qualityobject = MetadataObject()
# Initialise the metadata object
self.runmetadata = MetadataObject()
def __init__(self, path, fasta_path, records, amino_acid):
if path.startswith('~'):
self.path = os.path.abspath(os.path.expanduser(os.path.join(path)))
else:
self.path = os.path.abspath(os.path.join(path))
if fasta_path.startswith('~'):
self.fasta_path = os.path.abspath(
os.path.expanduser(os.path.join(fasta_path)))
else:
self.fasta_path = os.path.abspath(os.path.join(fasta_path))
self.working_path = os.path.join(self.path, 'strain_profiles')
self.sequencepath = os.path.join(self.working_path, 'query')
make_path(self.sequencepath)
target_files = [
fasta
for fasta in sorted(glob(os.path.join(self.fasta_path, '*.fasta')))
if os.path.basename(fasta) != 'combinedtargets.fasta'
or os.path.basename(fasta) != 'custom.tfa'
]
self.query_files = list()
# Create symlinks of the target files in the local path
for target in target_files:
try:
query_file = os.path.join(
self.sequencepath,
os.path.basename(target).replace('.tfa', '.fasta'))
self.query_files.append(query_file)
os.symlink(target, query_file)
except FileExistsError:
pass
self.targetpath = os.path.join(self.working_path, 'targets')
make_path(self.targetpath)
self.profilepath = os.path.join(self.working_path, 'sequence_profile')
make_path(self.profilepath)
self.profile_file = os.path.join(self.profilepath, 'profile.txt')
self.target_file = os.path.join(self.targetpath,
'combinedtargets.fasta')
shutil.copyfile(src=os.path.join(os.path.join(self.path, 'alleles'),
'combinedtargets.fasta'),
dst=self.target_file)
self.reportpath = os.path.join(self.working_path, 'reports')
make_path(self.reportpath)
self.strain_profile_path = os.path.join(self.working_path,
'strain_profiles')
make_path(self.strain_profile_path)
self.profile_report = os.path.join(self.strain_profile_path,
'profiles.tsv')
self.cpus = multiprocessing.cpu_count() - 1
self.starttime = time()
self.start = self.starttime
self.runmetadata = MetadataObject()
self.runmetadata.samples = list()
self.records = records
# Create an object for performing BLAST analyses
if amino_acid:
self.amino_acid = amino_acid
else:
self.amino_acid = None
if amino_acid:
self.program = 'tblastn'
else:
self.program = 'blastn'
# Fields used for custom outfmt 6 BLAST output:
self.fieldnames = [
'query_id', 'subject_id', 'identical', 'mismatches', 'gaps',
'evalue', 'bit_score', 'query_length', 'subject_length',
'alignment_length', 'query_start', 'query_end', 'subject_start',
'subject_end', 'query_sequence', 'subject_sequence'
]
self.extended_fieldnames = self.fieldnames.copy()
self.extended_fieldnames.insert(14, 'percent_match')
self.outfmt = '6 qseqid sseqid nident mismatch gaps evalue bitscore qlen slen length ' \
'qstart qend sstart send qseq sseq'
self.blast_reports = list()
self.profile_dict = dict()
self.profile_data = dict()
self.profile_set = list()
self.sequence_profile = dict()
self.profile_matches = dict()
self.new_profiles = list()
# A string of the header to use for formatting the profile file, and the report headers
genes = '\t'.join(sorted(self.records))
self.data = 'ST\t{genes}\n'.format(genes=genes.rstrip())
self.gene_names = list()
def __init__(self):
# Get the current commit of the pipeline from git
# Extract the path of the current script from the full path + file name
homepath = os.path.split(os.path.abspath(__file__))[0]
# Find the commit of the script by running a command to change to the directory containing the script and
# run a git command to return the short version of the commit hash
commit = subprocess.Popen(
'cd {} && git tag | tail -n 1'.format(homepath),
shell=True,
stdout=subprocess.PIPE).communicate()[0].rstrip()
# Parser for arguments
parser = ArgumentParser(
description='Filter reads based on taxonomic assignment')
parser.add_argument('-v',
'--version',
action='version',
version='%(prog)s commit {}'.format(commit))
parser.add_argument('path', help='Specify path')
parser.add_argument(
'-t',
'--threads',
help=
'Number of threads. Default is the number of cpus in the system'
)
parser.add_argument('-s',
'--sequencepath',
required=True,
help='Path of .fastq(.gz) files to process.')
parser.add_argument(
'-d',
'--datapath',
required=True,
help=
'Path of .csv files created by CLARK with read ID, length, and assignment.'
)
parser.add_argument(
'-c',
'--cutoff',
default=0.01,
help=
'Cutoff value for deciding which taxIDs to use when sorting .fastq files. '
'Defaults to 1 percent. Please note that you must use a decimal format: enter 0.05'
' to get a 5 percent cutoff value')
parser.add_argument(
'-x',
'--taxids',
help='NOT IMPLEMENTED: CSV of desired taxIDs from each sample. '
)
# Get the arguments into an object
args = parser.parse_args()
self.start = time()
# Define variables based on supplied arguments
self.path = os.path.join(args.path)
assert os.path.isdir(
self.path
), 'Supplied path is not a valid directory {path}'.format(
path=self.path)
self.sequencepath = os.path.join(args.sequencepath)
assert os.path.isdir(self.sequencepath), 'Sequence location supplied is not a valid directory {seq_path}' \
.format(seq_path=self.sequencepath)
self.datapath = os.path.join(args.datapath)
self.reportpath = os.path.join(self.path, 'reports')
# Use the argument for the number of threads to use, or default to the number of cpus in the system
self.cpus = args.threads if args.threads else multiprocessing.cpu_count(
)
# Set the cutoff to be a percent
self.cutoff = args.cutoff * 100
# Run the pipeline
self.runmetadata = MetadataObject()
genome = FilterGenome(self)
genome.objectprep()
logging.info('Filtering complete')