def test_sistr(variables):
metadata = MetadataObject()
method.runmetadata.samples = list()
fasta = os.path.join(variables.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()
# Set the destination folder
outputdir = os.path.join(variables.sequencepath, metadata.name)
make_path(outputdir)
# Add the output directory to the metadata
metadata.general.outputdirectory = outputdir
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 == 'SAL_BA2732AA'
variable_update()
def basic(self):
# Grab any .fastq files in the path
fastqfiles = glob(os.path.join(self.path, '*.fastq*'))
# Extract the base name of the globbed name + path provided
fastqnames = map(lambda x: os.path.split(x)[1], filer(fastqfiles))
# Iterate through the names of the fastq files
for fastqname in sorted(fastqnames):
# Set the name
metadata = MetadataObject()
metadata.name = fastqname
# Set the destination folder
outputdir = os.path.join(self.path, fastqname)
# Make the destination folder
make_path(outputdir)
# Get the fastq files specific to the fastqname
specificfastq = glob(
os.path.join(self.path, '{}*.fastq*'.format(fastqname)))
# Link the files to the output folder
try:
# Link the .gz files to :self.path/:filename
list(
map(
lambda x: os.symlink(
'../{}'.format(os.path.basename(x)), '{}/{}'.
format(outputdir, os.path.basename(x))),
specificfastq))
# Except os errors
except OSError as exception:
# If there is an exception other than the file exists, raise it
if exception.errno != errno.EEXIST:
raise
# Initialise the general and run categories
metadata.general = GenObject()
metadata.run = GenObject()
# Populate the .fastqfiles category of :self.metadata
metadata.general.fastqfiles = [
fastq for fastq in sorted(
glob(
os.path.join(outputdir, '{}*.fastq*'.format(
metadata.name)))) if 'trimmed' not in fastq
and 'normalised' not in fastq and 'corrected' not in fastq
and 'paired' not in fastq and 'unpaired' not in fastq
]
# Add the output directory to the metadata
metadata.general.outputdirectory = outputdir
metadata.general.logout = os.path.join(
self.path, metadata.name,
'{}_log_out.txt'.format(metadata.name))
metadata.general.logerr = os.path.join(
self.path, metadata.name,
'{}_log_err.txt'.format(metadata.name))
# Append the metadata to the list of samples
self.samples.append(metadata)
# Grab metadata from previous runs
previousmetadata = metadataReader.MetadataReader(self)
# Update self.samples (if required)
if previousmetadata.samples:
self.samples = previousmetadata.samples
# Run the read length method
self.readlength()
def createobject(self):
# Grab any .fastq files in the path
fastqfiles = glob(os.path.join(self.path, '*.fastq*'))
# Extract the base name of the globbed name + path provided
fastqnames = map(lambda x: os.path.split(x)[1], filer(fastqfiles))
# Iterate through the names of the fastq files
for fastqname in sorted(fastqnames):
# Set the name
metadata = MetadataObject()
metadata.name = fastqname
# Set the destination folder
outputdir = os.path.join(self.path, fastqname)
# Make the destination folder
make_path(outputdir)
# Get the fastq files specific to the fastqname
specificfastq = glob(
os.path.join(self.path, '{}*.fastq*'.format(fastqname)))
# Make relative symlinks to the files in :self.path
try:
for fastq in specificfastq:
# Get the basename of the file
fastqfile = os.path.split(fastq)[-1]
# Set the destination fastq path as the base name plus the destination folder
destinationfastq = os.path.join(outputdir, fastqfile)
# Symlink the files
os.symlink('../{}'.format(fastqfile), destinationfastq)
# Except os errors
except OSError as exception:
# If there is an exception other than the file exists, raise it
if exception.errno != errno.EEXIST:
raise
# Initialise the general and run categories
metadata.general = GenObject()
metadata.run = GenObject()
# Populate the .fastqfiles category of :self.metadata
metadata.general.fastqfiles = [
fastq for fastq in glob(
os.path.join(outputdir, '{}*.fastq*'.format(fastqname)))
if 'trimmed' not in fastq
]
# Add the output directory to the metadata
metadata.general.outputdirectory = outputdir
metadata.run.outputdirectory = outputdir
metadata.general.bestassemblyfile = True
metadata.general.trimmedcorrectedfastqfiles = metadata.general.fastqfiles
metadata.general.logout = os.path.join(
metadata.general.outputdirectory, 'logout')
metadata.general.logerr = os.path.join(
metadata.general.outputdirectory, 'logerr')
# Initialise an attribute to store commands
metadata.commands = GenObject()
# Append the metadata to the list of samples
self.samples.append(metadata)
def estimateabundance(self):
"""
Estimate the abundance of taxonomic groups
"""
printtime('Estimating abundance of taxonomic groups', self.start)
# Create and start threads
for i in range(self.cpus):
# Send the threads to the appropriate destination function
threads = Thread(target=self.estimate, args=())
# Set the daemon to true - something to do with thread management
threads.setDaemon(True)
# Start the threading
threads.start()
for sample in self.runmetadata.samples:
try:
if sample.general.combined != 'NA':
# Set the name of the abundance report
sample.general.abundance = sample.general.combined.split(
'.')[0] + '_abundance.csv'
# if not hasattr(sample, 'commands'):
if not sample.commands.datastore:
sample.commands = GenObject()
# Define system calls
sample.commands.target = self.targetcall
sample.commands.classify = self.classifycall
sample.commands.abundancecall = \
'cd {} && ./estimate_abundance.sh -D {} -F {} > {}'.format(self.clarkpath,
self.databasepath,
sample.general.classification,
sample.general.abundance)
self.abundancequeue.put(sample)
except KeyError:
pass
self.abundancequeue.join()
def metaparse(self, sample, quastoutputdirectory):
import functools
# Tuples of strings to replace when parsing the results file
repls = ('>=', 'Over'), ('000 Bp', 'kbp'), ('#', 'Num'), \
("'", ''), ('(', ''), (')', ''), (' ', ''), ('>', 'Less'), ('Gc%', 'GC%')
# Initialise the results dictionary
quast = dict()
# The results file is gage_report.tsv if that file exists, otherwise it is report.tsv
resfile = "{0:s}/gage_report.tsv".format(quastoutputdirectory) \
if os.path.isfile("{0:s}/gage_report.tsv".format(quastoutputdirectory)) \
else "{0:s}/report.tsv".format(quastoutputdirectory)
with open(resfile) as report:
for line in report:
# Use headings in report as keys for the GenObject supplied from generator and replace incrementally
# with reduce and lambda function below
k, v = [
functools.reduce(lambda a, kv: a.replace(*kv), repls,
s.title())
for s in line.rstrip().split('\t')
]
quast[k] = v
# Create the quast metadata object
sample.quast = GenObject(quast)
sample.quast.outputdirectory = quastoutputdirectory
sample.quast.kmers = self.kmers
def __init__(self, inputobject):
self.metadata = inputobject.runmetadata.samples
self.cpus = inputobject.cpus
try:
self.threads = int(self.cpus / len(
self.metadata)) if self.cpus / len(self.metadata) > 1 else 1
except TypeError:
self.threads = self.cpus
# self.devnull = open(os.devnull, 'wb')
self.qcqueue = Queue(maxsize=self.cpus)
self.trimqueue = Queue(maxsize=self.cpus)
self.correctqueue = Queue(maxsize=self.cpus)
self.start = inputobject.starttime
try:
self.forwardlength = inputobject.forwardlength
self.reverselength = inputobject.reverselength
except AttributeError:
self.forwardlength = 'full'
self.reverselength = 'full'
self.numreads = inputobject.numreads
self.logfile = inputobject.logfile
self.path = inputobject.path
self.analysistype = 'quality'
self.reffilepath = inputobject.reffilepath
# Initialise the quality attribute in the metadata object
for sample in self.metadata:
setattr(sample, self.analysistype, GenObject())
def __init__(self, passed):
"""Initialise variables"""
self.path = passed.path
self.runinfo = passed.runinfo
self.flowcell = "NA"
self.instrument = "NA"
self.samples = list()
self.ids = list()
self.date = str()
self.totalreads = 0
self.runid = str()
self.runnumber = str()
self.commit = passed.commit
# Create and start to populate the header object
self.header = GenObject()
# If a custom sample sheet has been provided, use it
if passed.customsamplesheet:
self.samplesheet = passed.customsamplesheet
assert os.path.isfile(self.samplesheet), u'Could not find CustomSampleSheet as entered: {0!r:s}'\
.format(self.samplesheet)
else:
self.samplesheet = os.path.join(self.path, "SampleSheet.csv")
# Extract data from SampleSheet.csv
self.parsesamplesheet()
def parse_qaml(self):
"""
Parse the GenomeQAML report, and populate metadata objects
"""
printtime('Parsing GenomeQAML outputs', self.start)
# A dictionary to store the parsed excel file in a more readable format
nesteddictionary = dict()
# Use pandas to read in the CSV file, and convert the pandas data frame to a dictionary (.to_dict())
dictionary = pandas.read_csv(self.qaml_report).to_dict()
# Iterate through the dictionary - each header from the CSV 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})
# Get the results into the metadata object
for sample in self.metadata:
# Initialise the plasmid extractor genobject
setattr(sample, self.analysistype, GenObject())
# Initialise the list of all plasmids
sample[self.analysistype].prediction = str()
# Iterate through the dictionary of results
for line in nesteddictionary:
# Extract the sample name from the dictionary
name = nesteddictionary[line]['Sample']
# Ensure that the names match
if name == sample.name:
# Append the plasmid name extracted from the dictionary to the list of plasmids
sample[self.analysistype].prediction = nesteddictionary[
line]['Predicted_Class']
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(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(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(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(self)
# Print the metadata to file
metadataprinter.MetadataPrinter(self)
def primers(self):
"""Setup and create threads for ePCR"""
# Create the threads for the ePCR analysis
for sample in self.metadata:
if sample.general.bestassemblyfile != 'NA':
threads = Thread(target=self.epcr, args=())
threads.setDaemon(True)
threads.start()
for sample in self.metadata:
if sample.general.bestassemblyfile != 'NA':
setattr(sample, self.analysistype, GenObject())
# Get the primers ready
try:
sample[self.analysistype].primers = glob(os.path.join(self.reffilepath,
self.analysistype,
sample.general.referencegenus,
'primers',
'*.txt'))[0]
# Find the name of the probe file
sample[self.analysistype].probes = glob(os.path.join(self.reffilepath,
self.analysistype,
sample.general.referencegenus,
'probes',
'*.fa'))[0]
# Create the BLAST database of the probes (if necessary)
self.makeblastdb(sample[self.analysistype].probes)
# Initialise a list to store the names of the targets
sample[self.analysistype].targets = list()
# Open the primer file, and read the names of the targets into a list
with open(sample[self.analysistype].primers, 'r') as primerfile:
for line in primerfile:
sample[self.analysistype].targets.append(line.split('\t')[0])
# Organisms without primer/probe files will fail. Populate metadata with 'NA' values
except IndexError:
sample[self.analysistype].primers = 'NA'
sample[self.analysistype].probes = 'NA'
# Only try to process organisms with primer files
if sample[self.analysistype].primers != 'NA':
# Make the output path
sample[self.analysistype].reportdir = os.path.join(sample.general.outputdirectory,
self.analysistype)
make_path(sample[self.analysistype].reportdir)
# Set the base name of the output file
outfile = sample[self.analysistype].reportdir + sample.name
# Set the hashing and mapping commands
sample.commands.famap = 'famap -b {}.famap {}.fasta'.format(outfile, sample.general.filenoext)
sample.commands.fahash = 'fahash -b {}.hash {}.famap'.format(outfile, outfile)
# re-PCR uses the subtyping primers list to search the contigs file using the following parameters
# -S {hash file} (Perform STS lookup using hash-file), -r + (Enable/disable reverse STS lookup)
# -m 10000 (Set variability for STS size for lookup),
# -n 1 (Set max allowed mismatches per primer for lookup)
# -g 0 (Set max allowed indels per primer for lookup),
# -G (Print alignments in comments), -o {output file}
sample.commands.epcr = 're-PCR -S {}.hash -r + -m 10000 -n 2 -g 0 -G -q -o {}.txt {}' \
.format(outfile, outfile, sample[self.analysistype].primers)
# Add the variables to the queue
self.epcrqueue.put((sample, outfile))
self.epcrqueue.join()
def extract_rmlst_reads(self):
"""
rMLST read extraction. Should be the first thing called after parsing the fastq directory.
"""
for sample in self.metadata:
# Create the object to store the variables
setattr(sample, self.analysistype, GenObject())
# Initialise variables
sample[self.analysistype].snv_count = list()
# Initialise a starting value for the number of unique kmers found in each sample
sample[self.analysistype].unique_kmers = -1
# Set and create the output directory
try:
sample[self.analysistype].outputdir = os.path.join(
sample.run.outputdirectory, self.analysistype)
except KeyError:
sample[self.analysistype].outputdir = os.path.join(
sample.general.outputdirectory, self.analysistype)
make_path(sample[self.analysistype].outputdir)
sample[self.analysistype].logout = os.path.join(
sample[self.analysistype].outputdir, 'logout.txt')
sample[self.analysistype].logerr = os.path.join(
sample[self.analysistype].outputdir, 'logerr.txt')
sample[self.analysistype].baitedfastq = os.path.join(
sample[self.analysistype].outputdir,
'{}_targetMatches.fastq.gz'.format(self.analysistype))
# Create the command to run the baiting - paired inputs and a single, zipped output
sample[self.analysistype].bbdukcmd = 'bbduk.sh ref={} in1={} in2={} threads={} outm={}'\
.format(self.database,
sample.general.trimmedcorrectedfastqfiles[0],
sample.general.trimmedcorrectedfastqfiles[1],
str(self.threads),
sample[self.analysistype].baitedfastq)
# Sometimes bbduk hangs forever, so that needs to be handled. Give it a very generous timeout.
try:
# Run the call, and write any errors to the logfile
command = sample[self.analysistype].bbdukcmd
if self.analyse:
out, err = run_subprocess(command)
else:
out = str()
err = str()
write_to_logfile(command, command, self.logfile,
sample.general.logout, sample.general.logerr,
sample[self.analysistype].logout,
sample[self.analysistype].logerr)
write_to_logfile(out, err, self.logfile, sample.general.logout,
sample.general.logerr,
sample[self.analysistype].logout,
sample[self.analysistype].logerr)
except TimeoutExpired:
print('ERROR: Could not extract rMLST reads from sample {}'.
format(sample.name))
def setup(self):
"""
Set up the metadata object to be passed to Vtyper()
"""
from glob import glob
files = sorted(glob('{}*.fasta'.format(self.sequencepath)))
samples = list()
# Create the metadata for each file
for fasta in files:
# Create a metadata object to store all metadata associated with each strain
metadata = MetadataObject()
metadata.general = GenObject()
metadata.commands = GenObject()
# Set the name
metadata.name = os.path.basename(fasta).split('.')[0]
metadata.general.bestassemblyfile = fasta
metadata.general.stx = True
metadata.general.outputdirectory = self.path
metadata.general.filenoext = fasta.split('.')[0]
metadata.general.fastqfiles = list()
samples.append(metadata)
return samples
def main(self):
"""
Run the necessary methods in the correct order
"""
printtime('Starting {} analysis pipeline'.format(self.analysistype), self.starttime)
# Create the objects to be used in the analyses
objects = Objectprep(self)
objects.objectprep()
self.runmetadata = objects.samples
self.threads = int(self.cpus / len(self.runmetadata.samples)) if self.cpus / len(self.runmetadata.samples) > 1 \
else 1
# Run the genesippr analyses
self.analysistype = 'genesippr'
self.targetpath = os.path.join(self.reffilepath, self.analysistype, '')
Sippr(self, 0.90)
# Create the reports
self.reports = Reports(self)
Reports.reporter(self.reports)
# Run the 16S analyses using the filtered database
self.targetpath = self.reffilepath
# Run the 16S analyses
self.analysistype = 'sixteens_full'
SixteensFull(self, self.commit, self.starttime, self.homepath, 'sixteens_full', 0.985)
# ResFinding
Resistance(self, self.commit, self.starttime, self.homepath, 'resfinder', 0.90, False, True)
# Run the GDCS analysis
self.analysistype = 'GDCS'
self.pipeline = True
self.targetpath = os.path.join(self.targetpath, self.analysistype)
Sippr(self, 0.95)
# Create the reports
Reports.gdcsreporter(self.reports)
# Perform serotyping for samples classified as Escherichia
for sample in self.runmetadata.samples:
if sample.general.bestassemblyfile != 'NA':
sample.mash = GenObject()
try:
sample.mash.closestrefseqgenus = sample.general.closestrefseqgenus
for genus, species in self.taxonomy.items():
if genus == sample.mash.closestrefseqgenus:
sample.mash.closestrefseqspecies = species
except KeyError:
sample.mash.closestrefseqgenus = 'NA'
sample.mash.closestrefseqspecies = 'NA'
else:
sample.mash.closestrefseqgenus = 'NA'
sample.mash.closestrefseqspecies = 'NA'
SeroSippr(self, self.commit, self.starttime, self.homepath, 'serosippr', 0.95, True)
# Print the metadata
printer = MetadataPrinter(self)
printer.printmetadata()
def predictthreads(self):
printtime('Performing gene predictions', self.start)
# Create the threads for the analyses
for sample in self.metadata:
if sample.general.bestassemblyfile != 'NA':
threads = Thread(target=self.predict, args=())
threads.setDaemon(True)
threads.start()
for sample in self.metadata:
# Create the .prodigal attribute
sample.prodigal = GenObject()
if sample.general.bestassemblyfile != 'NA':
self.predictqueue.put(sample)
self.predictqueue.join()
def sistr(self):
"""Perform sistr analyses on Salmonella"""
printtime('Performing sistr analyses', self.start)
for sample in self.metadata:
# Create the analysis-type specific attribute
setattr(sample, self.analysistype, GenObject())
if sample.general.bestassemblyfile != 'NA':
try:
# Only process strains that have been determined to be Salmonella
if sample.general.referencegenus == 'Salmonella':
# Set and create the path of the directory to store the strain-specific reports
sample[self.analysistype].reportdir = os.path.join(
sample.general.outputdirectory, self.analysistype)
# Name of the .json output file
sample[self.analysistype].jsonoutput = os.path.join(
sample[self.analysistype].reportdir,
'{}.json'.format(sample.name))
# Set the sistr system call
sample.commands.sistr = \
'sistr -f json -o {} -t {} -T {} {}'\
.format(sample[self.analysistype].jsonoutput,
self.cpus,
os.path.join(sample[self.analysistype].reportdir, 'tmp'),
sample.general.bestassemblyfile)
#
sample[self.analysistype].logout = os.path.join(
sample[self.analysistype].reportdir, 'logout')
sample[self.analysistype].logerr = os.path.join(
sample[self.analysistype].reportdir, 'logerr')
# Only run the analyses if the output json file does not exist
if not os.path.isfile(
sample[self.analysistype].jsonoutput):
out, err = run_subprocess(sample.commands.sistr)
write_to_logfile(sample.commands.sistr,
sample.commands.sistr,
self.logfile,
sample.general.logout,
sample.general.logerr,
sample[self.analysistype].logout,
sample[self.analysistype].logerr)
write_to_logfile(out, err, self.logfile,
sample.general.logout,
sample.general.logerr,
sample[self.analysistype].logout,
sample[self.analysistype].logerr)
self.queue.task_done()
except (ValueError, KeyError):
pass
self.queue.join()
self.report()
def fasta_records(self):
"""
Use SeqIO to create dictionaries of all records for each FASTA file
"""
for sample in self.metadata:
# Create the analysis-type specific attribute
setattr(sample, self.analysistype, GenObject())
# Create a dictionary of records for each file
try:
record_dict = SeqIO.to_dict(
SeqIO.parse(sample.general.bestassemblyfile, "fasta"))
except FileNotFoundError:
record_dict = dict()
# Set the records dictionary as the attribute for the object
sample[self.analysistype].record_dict = record_dict
def epcrparse(self):
"""
Parse the ePCR text file outputs
"""
printtime('Parsing ePCR results', self.start)
for sample in self.metadata:
if sample.general.bestassemblyfile != 'NA':
if 'stx' in sample.general.datastore:
# Initialise count - this allows for the population of vtyperresults with unique values
uniquecount = 0
# This populates vtyperresults with the verotoxin subtypes
toxinlist = []
if os.path.isfile(sample[self.analysistype].resultsfile):
epcrresults = open(sample[self.analysistype].resultsfile, 'r')
for result in epcrresults:
# Only the lines without a # contain results
if "#" not in result:
uniquecount += 1
# Split on \t
data = result.split('\t')
# The subtyping primer pair is the first entry on lines with results
vttype = data[0].split('_')[0]
# Push the name of the primer pair - stripped of anything after a _ to the dictionary
if vttype not in toxinlist:
toxinlist.append(vttype)
# Create a string of the entries in list1 joined with ";"
toxinstring = ";".join(sorted(toxinlist))
# Save the string to the metadata
sample[self.analysistype].toxinprofile = toxinstring
else:
setattr(sample, self.analysistype, GenObject())
sample[self.analysistype].toxinprofile = 'NA'
else:
setattr(sample, self.analysistype, GenObject())
sample[self.analysistype].toxinprofile = 'NA'
def reader(self):
import os
import json
from accessoryFunctions.accessoryFunctions import GenObject, MetadataObject
for sample in self.metadata:
metadatafile = '{}{}/{}_metadata.json'.format(
self.path, sample.name, sample.name)
if os.path.isfile(metadatafile):
size = os.stat(metadatafile).st_size
if size != 0:
try:
with open(metadatafile) as metadatareport:
jsondata = json.load(metadatareport)
# Create the metadata objects
metadata = MetadataObject()
# Initialise the metadata categories as GenObjects created using the appropriate key
for attr in jsondata:
if not isinstance(jsondata[attr], dict):
setattr(metadata, attr, jsondata[attr])
else:
setattr(metadata, attr,
GenObject(jsondata[attr]))
# As files often need to be reanalysed after being moved, test to see if it possible to use the
# metadata from the previous assembly
jsonfile = '{}/{}_metadata.json'.format(
metadata.general.outputdirectory, sample.name)
try:
# Open the metadata file to write
with open(
jsonfile, 'w'
) as metadatafile: # Change from wb to w since this is text in python3
# Write the json dump of the object dump to the metadata file
json.dump(sample.dump(),
metadatafile,
sort_keys=True,
indent=4,
separators=(',', ': '))
# Set the name
metadata.name = sample.name
self.samples.append(metadata)
except IOError:
self.samples.append(sample)
except ValueError:
self.samples.append(sample)
else:
self.samples.append(sample)
def error(sample, message):
"""
Check to see if the run GenObject exists. If so, update the run.Description to reflect the error
:param sample: metadata sample object
:param message: error message to add to the sample.run.Description attribute
"""
# Set the .fastqfiles attribute to 'NA' to remove this strain from the analyses
sample.general.fastqfiles = ['NA']
# Ensure that the run attribute exists
if GenObject.isattr(sample, 'run'):
# If the Description attribute exists, overwrite it, otherwise create and populate it
if GenObject.isattr(sample.run, 'status'):
sample.run.status = message
else:
setattr(sample.run, 'status', message)
# Otherwise create and populate the attribute
else:
setattr(sample, 'run', GenObject())
sample.run.Description = message
def vtyper(self):
"""Setup and create threads for ePCR"""
printtime('Running ePCR', self.start)
# Create the threads for the BLAST analysis
for sample in self.metadata:
if sample.general.bestassemblyfile != 'NA':
threads = Thread(target=self.epcr, args=())
threads.setDaemon(True)
threads.start()
# Create the system calls for famap, fahash, and ePCR
for sample in self.metadata:
if sample.general.bestassemblyfile != 'NA':
if 'stx' in sample.general.datastore:
setattr(sample, self.analysistype, GenObject())
# Get the primers ready
if self.reffilepath:
sample[self.analysistype].primers = '{}{}/vtx_subtyping_primers.txt'\
.format(self.reffilepath, self.analysistype)
else:
sample[self.analysistype].primers = self.primerfile
# Make the output path
sample[self.analysistype].reportdir = '{}/{}/'.format(sample.general.outputdirectory,
self.analysistype)
make_path(sample[self.analysistype].reportdir)
outfile = sample[self.analysistype].reportdir + sample.name
# Set the hashing and mapping commands
sample.commands.famap = 'famap -b {}.famap {}.fasta'.format(outfile, sample.general.filenoext)
sample.commands.fahash = 'fahash -b {}.hash {}.famap'.format(outfile, outfile)
# re-PCR uses the subtyping primers list to search the contigs file using the following parameters
# -S {hash file} (Perform STS lookup using hash-file),
# -r + (Enable/disable reverse STS lookup)
# -m 10000 (Set variability for STS size for lookup),
# -n 1 (Set max allowed mismatches per primer for lookup)
# -g 0 (Set max allowed indels per primer for lookup),
# -G (Print alignments in comments),
# -q quiet
# -o {output file},
sample.commands.epcr = 're-PCR -S {}.hash -r + -m 10000 -n 1 -g 0 -G -q -o {}.txt {}'\
.format(outfile, outfile, sample[self.analysistype].primers)
sample[self.analysistype].resultsfile = '{}.txt'.format(outfile)
self.epcrqueue.put((sample, outfile))
self.epcrqueue.join()
self.epcrparse()
def runner(self):
"""
Run the necessary methods in the correct order
"""
printtime('Starting {} analysis pipeline'.format(self.analysistype),
self.starttime,
output=self.portallog)
if not self.pipeline:
# If the metadata has been passed from the method script, self.pipeline must still be false in order to
# get Sippr() to function correctly, but the metadata shouldn't be recreated
try:
eq = vars(self.runmetadata)['samples']
except KeyError:
# Create the objects to be used in the analyses
objects = Objectprep(self)
objects.objectprep()
self.runmetadata = objects.samples
else:
for sample in self.runmetadata.samples:
setattr(sample, self.analysistype, GenObject())
sample.run.outputdirectory = sample.general.outputdirectory
self.threads = int(self.cpus / len(self.runmetadata.samples)) \
if self.cpus / len(self.runmetadata.samples) > 1 \
else 1
# Use a custom sippr method to use the full reference database as bait, and run mirabait against the FASTQ
# reads - do not perform reference mapping yet
SixteenSBait(self, self.cutoff)
# Subsample 1000 reads from the FASTQ files
self.subsample()
# Convert the subsampled FASTQ files to FASTA format
self.fasta()
# Create BLAST databases if required
self.makeblastdb()
# Run BLAST analyses of the subsampled FASTA files against the NCBI 16S reference database
self.blast()
# Parse the BLAST results
self.blastparse()
# Feed the BLAST results into a modified sippr method to perform reference mapping using the calculated
# genus of the sample as the mapping file
SixteenSSipper(self, self.cutoff)
# Create reports
self.reporter()
def sketching(self):
printtime('Indexing assemblies for mash analysis', self.starttime)
# Create the threads for the analysis
for sample in self.metadata:
if sample.general.bestassemblyfile != 'NA':
threads = Thread(target=self.sketch, args=())
threads.setDaemon(True)
threads.start()
# Populate threads for each gene, genome combination
for sample in self.metadata:
# Create the analysis type-specific GenObject
setattr(sample, self.analysistype, GenObject())
if sample.general.bestassemblyfile != 'NA':
# Set attributes
sample[self.analysistype].reportdir = os.path.join(
sample.general.outputdirectory, self.analysistype)
sample[self.analysistype].targetpath = os.path.join(
self.referencefilepath, self.analysistype)
sample[self.analysistype].refseqsketch = \
sample[self.analysistype].targetpath + '/RefSeqSketchesDefaults.msh'
sample[self.analysistype].sketchfilenoext = '{}/{}'.format(
sample[self.analysistype].reportdir, sample.name)
sample[self.analysistype].sketchfile = sample[
self.analysistype].sketchfilenoext + '.msh'
# Make the mash output directory if necessary
make_path(sample[self.analysistype].reportdir)
# Create a file containing the path/name of the filtered, corrected fastq files
sample[self.
analysistype].filelist = '{}/{}_fastqfiles.txt'.format(
sample[self.analysistype].reportdir, sample.name)
with open(sample[self.analysistype].filelist, 'w') as filelist:
filelist.write('\n'.join(
sample.general.trimmedcorrectedfastqfiles))
# Create the system call
sample.commands.sketch = 'mash sketch -m 2 -p {} -l {} -o {}' \
.format(self.cpus, sample[self.analysistype].filelist, sample[self.analysistype].sketchfilenoext)
# Add each sample to the threads
self.sketchqueue.put(sample)
# Join the threads
self.sketchqueue.join()
self.mashing()
def sketching(self):
printtime('Indexing files for {} analysis'.format(self.analysistype), self.starttime)
# Create the threads for the analysis
for i in range(self.cpus):
threads = Thread(target=self.sketch, args=())
threads.setDaemon(True)
threads.start()
# Populate threads for each gene, genome combination
for sample in self.metadata:
# Create the analysis type-specific GenObject
setattr(sample, self.analysistype, GenObject())
# Set attributes
sample[self.analysistype].reportdir = os.path.join(sample.general.outputdirectory, self.analysistype)
make_path(sample[self.analysistype].reportdir)
sample[self.analysistype].targetpath = self.referencefilepath if not self.pipeline else os.path.join(
self.referencefilepath, self.analysistype)
sample[self.analysistype].refseqsketch = os.path.join(sample[self.analysistype].targetpath,
'RefSeqSketchesDefaults.msh')
sample[self.analysistype].sketchfilenoext = os.path.join(sample[self.analysistype].reportdir, sample.name)
sample[self.analysistype].sketchfile = sample[self.analysistype].sketchfilenoext + '.msh'
# Make the mash output directory if necessary
make_path(sample[self.analysistype].reportdir)
# Create a file containing the path/name of the filtered, corrected fastq files
sample[self.analysistype].filelist = os.path.join(sample[self.analysistype].reportdir,
'{}_fastqfiles.txt'.format(sample.name))
with open(sample[self.analysistype].filelist, 'w') as filelist:
filelist.write('\n'.join(sample.general.trimmedcorrectedfastqfiles))
# Create the system call
sample.commands.sketch = 'mash sketch -m 2 -p {} -l {} -o {}' \
.format(self.cpus, sample[self.analysistype].filelist, sample[self.analysistype].sketchfilenoext)
# Add each sample to the threads
try:
self.sketchqueue.put(sample)
except (KeyboardInterrupt, SystemExit):
printtime('Received keyboard interrupt, quitting threads', self.starttime)
quit()
# Join the threads
self.sketchqueue.join()
self.mashing()
def targets(self):
"""
Create the GenObject for the analysis type, create the hash file for baiting (if necessary)
"""
for sample in self.runmetadata:
if sample.general.bestassemblyfile != 'NA':
setattr(sample, self.analysistype, GenObject())
sample[self.analysistype].runanalysis = True
sample[self.analysistype].targetpath = self.targetpath
baitpath = os.path.join(self.targetpath, 'bait')
sample[self.analysistype].baitfile = glob(
os.path.join(baitpath, '*.fa'))[0]
sample[self.analysistype].outputdir = os.path.join(
sample.run.outputdirectory, self.analysistype)
sample[self.analysistype].logout = os.path.join(
sample[self.analysistype].outputdir, 'logout.txt')
sample[self.analysistype].logerr = os.path.join(
sample[self.analysistype].outputdir, 'logerr.txt')
sample[self.analysistype].baitedfastq = os.path.join(
sample[self.analysistype].outputdir,
'{}_targetMatches.fastq'.format(self.analysistype))
sample[self.analysistype].complete = False
def versions(self):
for sample in self.metadata:
# Initialise the attribute
sample.software = GenObject()
# Populate the versions of the software used
ss = sample.software
ss.python = self.python
ss.arch = self.arch
ss.blast = self.blast
ss.bowtie2 = self.bowversion
ss.samtools = self.samversion
ss.qualimap = self.qualimap
ss.mash = self.mash
ss.prodigal = self.prodigal
ss.pipeline = self.commit
ss.spades = self.spades
ss.bbmap = self.bbmap
ss.fastqc = self.fastqc
ss.blc2fastq = self.bcl2fastq
ss.perl = self.perl
ss.biopython = self.biopython
ss.java = self.java
arguments = parser.parse_args()
# Define the start time
arguments.starttime = time.time()
# Find the files
fastas = sorted(glob(os.path.join(arguments.sequencepath, '*.fa*')))
# Create a metadata object
arguments.runmetadata = MetadataObject()
arguments.runmetadata.samples = list()
for fasta in fastas:
metadata = MetadataObject()
metadata.name = os.path.split(fasta)[1].split('.')[0]
# Initialise the general and run categories
metadata.general = GenObject()
metadata.run = GenObject()
# Set the destination folder
outputdir = os.path.join(arguments.sequencepath, metadata.name)
make_path(outputdir)
# Add the output directory to the metadata
metadata.general.outputdirectory = outputdir
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
arguments.runmetadata.samples.append(metadata)
def contamination_finder(self,
input_path=None,
report_path=None,
portal_log=None):
"""
Helper function to get confindr integrated into the assembly pipeline
"""
if portal_log is not None:
printtime('Calculating contamination in reads',
self.start,
output=portal_log)
else:
printtime('Calculating contamination in reads', self.start)
if input_path is not None:
input_dir = input_path
else:
input_dir = self.path
if report_path is not None:
reportpath = report_path
else:
reportpath = os.path.join(input_dir, 'confindr')
report = os.path.join(reportpath, 'confindr_report.csv')
if not os.path.isfile(report):
# Create an object to store attributes to pass to confinder
args = MetadataObject
args.input_directory = input_dir
args.output_name = reportpath
args.databases = os.path.join(self.reffilepath, 'ConFindr',
'databases')
args.forward_id = '_R1'
args.reverse_id = '_R2'
args.threads = self.cpus
args.kmer_size = 31
args.number_subsamples = 3
args.subsample_depth = 20
args.kmer_cutoff = 2
try:
shutil.rmtree(args.output_name)
except IOError:
pass
make_path(reportpath)
# Open the output report file.
with open(os.path.join(report), 'w') as f:
f.write(
'Strain,Genus,NumContamSNVs,NumUniqueKmers,ContamStatus\n')
for sample in self.metadata:
if len(sample.general.trimmedcorrectedfastqfiles) == 2:
confindr.find_contamination(
sample.general.trimmedcorrectedfastqfiles, args)
elif len(sample.general.trimmedcorrectedfastqfiles) == 1:
confindr.find_contamination_unpaired(
args, sample.general.trimmedcorrectedfastqfiles[0])
if portal_log:
printtime('Contamination detection complete!',
self.start,
output=portal_log)
else:
printtime('Contamination detection complete!', self.start)
# Load the confindr report into a dictionary using pandas
# https://stackoverflow.com/questions/33620982/reading-csv-file-as-dictionary-using-pandas
confindr_results = pandas.read_csv(report, index_col=0).T.to_dict()
# Find the results for each of the samples
for sample in self.metadata:
# Create a GenObject to store the results
sample.confindr = GenObject()
# Iterate through the dictionary to find the outputs for each sample
for line in confindr_results:
# If the current line corresponds to the sample of interest
if sample.name in line:
# Set the values using the appropriate keys as the attributes
sample.confindr.genus = confindr_results[line]['Genus']
sample.confindr.num_contaminated_snvs = confindr_results[
line]['NumContamSNVs']
sample.confindr.unique_kmers = confindr_results[line][
'NumUniqueKmers']
try:
sample.confindr.cross_contamination = confindr_results[
line]['CrossContamination']
except KeyError:
sample.confindr.cross_contamination = str()
sample.confindr.contam_status = confindr_results[line][
'ContamStatus']
if sample.confindr.contam_status is True:
sample.confindr.contam_status = 'Contaminated'
elif sample.confindr.contam_status is False:
sample.confindr.contam_status = 'Clean'
# Re-write the output to be consistent with the rest of the pipeline
with open(os.path.join(reportpath, 'confindr_report.csv'), 'w') as csv:
data = 'Strain,Genus,NumContamSNVs,NumUniqueKmers,ContamStatus\n'
for sample in self.metadata:
data += '{str},{genus},{numcontamsnv},{numuniqkmer},{status}\n'.format(
str=sample.name,
genus=sample.confindr.genus,
numcontamsnv=sample.confindr.num_contaminated_snvs,
numuniqkmer=sample.confindr.unique_kmers,
status=sample.confindr.contam_status)
csv.write(data)
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 = 1
# 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
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
self.extension = self.runmetadata.extension
# Create the name of the final report
self.report = os.path.join(
self.reportpath,
'{}'.format('abundance{}.xlsx'.format(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):
printtime(
'Performing CLARK analysis on {} files'.format(
self.extension), self.start)
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 KeyError:
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:
if sample.general.bestassemblyfile != 'NA':
# 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)
# 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 (KeyError, 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 KeyError:
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, KeyError):
pass
# Remove all the attributes from .general
map(lambda x: delattr(sample.general, x),
['abundance', 'classification', 'combined'])
# 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()
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)
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/questions/32833230/biopython-alignio-valueerror-says-strings-must-be-same-length
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 createfastq(self):
"""Uses bcl2fastq to create .fastq files from a MiSeqRun"""
# Initialise samplecount
samplecount = 0
# If the fastq destination folder is not provided, make the default value of :path/:miseqfoldername
self.fastqdestination = self.fastqdestination if self.fastqdestination else self.path + self.miseqfoldername
# Make the path
make_path(self.fastqdestination)
# Initialise variables for storing index information
index = ''
indexlength = int()
# bcl2fastq requires an older version of the sample sheet, this recreates the required version
# Create the new sample sheet
with open('{}/SampleSheet_modified.csv'.format(self.fastqdestination),
"w") as modifiedsamplesheet:
# Write the required headings to the file
modifiedsamplesheet.write(
"FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator,SampleProject\n"
)
for strain in self.samples:
# Create a combined index of index1-index2
try:
strain.run.modifiedindex = '{}-{}'.format(
strain.run.index, strain.run.index2)
indexlength = 16
index = 'I8,I8'
except KeyError:
strain.run.modifiedindex = strain.run.index
indexlength = 6
index = 'I6'
# The list of items to print to each line of the modified sample sheet
printlist = [
self.flowcell, '1', strain.name,
str(strain.run.SampleNumber), strain.run.modifiedindex,
strain.run.Description, 'N', 'NA',
strain.run.InvestigatorName, self.projectname
]
modifiedsamplesheet.write('{}\n'.format(",".join(printlist)))
samplecount += 1
# Set :forward/reverse length to :header.forward/reverse length if the argument is not provided, or it's 'full',
# otherwise use the supplied argument
self.forwardlength = self.metadata.header.forwardlength if self.forwardlength.lower()\
== 'full' else self.forwardlength
# Set :reverselength to :header.reverselength
self.reverselength = self.metadata.header.reverselength if self.reverselength.lower() \
== 'full' else self.reverselength
# As the number of cycles required is the number of forward reads + the index(8) + the second index(8)
# Also set the basemask variable as required
if self.reverselength != '0':
self.readsneeded = int(self.forwardlength) + int(
self.reverselength) + indexlength
basemask = "Y{}n*,{},Y{}n*".format(self.forwardlength, index,
self.reverselength)
nohup = "nohup make -j 16 > nohup.out"
else:
# + 1
self.readsneeded = int(self.forwardlength) + indexlength
basemask = "Y{}n*,{},n*".format(self.forwardlength, index)
nohup = "nohup make -j 16 r1 > nohup.out"
# Handle plurality appropriately
samples = 'samples' if samplecount > 1 else 'sample'
number = 'are' if samplecount > 1 else 'is'
printtime(
'There {} {} {} in this run. '
'Running fastq creating module with the following parameters:\n'
'MiSeqPath: {},\n'
'MiSeqFolder: {},\n'
'Fastq destination: {},\n'
'SampleSheet: {}'.format(
number, samplecount, samples, self.miseqpath, self.miseqfolder,
self.fastqdestination,
'{}/SampleSheet_modified.csv'.format(self.fastqdestination)),
self.start)
# Count the number of completed cycles in the run of interest
cycles = glob('{}Data/Intensities/BaseCalls/L001/C*'.format(
self.miseqfolder))
while len(cycles) < self.readsneeded:
printtime(
'Currently at {} cycles. Waiting until the MiSeq reaches cycle {}'
.format(len(cycles), self.readsneeded), self.start)
sleep(1800)
cycles = glob('{}Data/Intensities/BaseCalls/L001/C*'.format(
self.miseqfolder))
# configureBClToFastq requires :self.miseqfolder//Data/Intensities/BaseCalls/config.xml in order to work
# When you download runs from BaseSpace, this file is not provided. There is an empty config.xml file that
# can be populated with run-specific values and moved to the appropriate folder
if not os.path.isfile('{}Data/Intensities/BaseCalls/config.xml'.format(
self.miseqfolder)):
self.configfilepopulator()
# Define the bcl2fastq system call
bclcall = "configureBclToFastq.pl --input-dir {}Data/Intensities/BaseCalls " \
"--output-dir {} --force --sample-sheet {}/SampleSheet_modified.csv " \
"--mismatches 1 --no-eamss --fastq-cluster-count 0 --compression none --use-bases-mask {}"\
.format(self.miseqfolder, self.fastqdestination, self.fastqdestination, basemask)
# Define the nohup system call
nohupcall = "cd {} && {}".format(self.fastqdestination, nohup)
# fnull = open(os.devnull, 'wb')
if not os.path.isdir("{}/Project_{}".format(self.fastqdestination,
self.projectname)):
# Call configureBclToFastq.pl
printtime('Running bcl2fastq', self.start)
# Run the commands
threadlock = threading.Lock()
outstr = ''
outerr = ''
out, err = run_subprocess(bclcall)
outstr += out
outerr += out
out, err = run_subprocess(nohupcall)
outstr += out
outerr += out
# call(bclcall, shell=True, stdout=fnull, stderr=fnull)
# call(nohupcall, shell=True, stdout=fnull, stderr=fnull)
threadlock.acquire()
write_to_logfile(bclcall, bclcall, self.logfile)
write_to_logfile(nohupcall, nohupcall, self.logfile)
write_to_logfile(outstr, outerr, self.logfile)
threadlock.release()
# Populate the metadata
for sample in self.metadata.samples:
sample.commands = GenObject()
sample.commands.nohup = nohupcall
sample.commands.bcl = bclcall
sample.run.forwardlength = self.forwardlength
sample.run.reverselength = self.reverselength
# Copy the fastq files to a central folder so they can be processed
self.fastqmover()