def rmlst():
"""Performs the necessary analyses on strains using armi targets"""
global targetpath, seqdict
# Set the analysis type
analysistype = "rMLST"
# Set the profile name
profiletype = "rMLSTprofile"
# Set the path of the analysistype data
currenttargetpath = "%s%s" % (targetpath, analysistype)
# Set the allele and profile path variables
rmlstpath = currenttargetpath + "/alleles"
rmlstprofilepath = currenttargetpath + "/profile"
# Find the .json version of the profile file
profilefile = glob("%s/*.json" % rmlstprofilepath)
# If there is no .json file, use the .txt profile file instead. Note that this file must be edited (by removing
# any columns after the last gene)
if not profilefile:
profilefile = glob("%s/*.txt" % rmlstprofilepath)[0]
else:
profilefile = profilefile[0]
# Because the combined database of alleles is so large (~143 MB), it is filtered with uSearch prior to baiting
# this is not done automatically, so the set-up of the bait files is slightly different here
# In order to save time, a precomputed hash file is used
baitfile = glob("%s/bait/*.gz" % rmlstpath)[0]
baittargets(rmlstpath, analysistype)
# Get the target files into a list
targets = glob("%s/*.*fa" % rmlstpath)
# Filter the targets
targets = [target for target in targets if ".fai" not in target and "Concatenated" not in target]
# Add the bait file, the profile file, and a list of the targets to seqdict
for strain in seqdict:
seqdict[strain]["bait"]["fastqFiles"][analysistype] = baitfile
seqdict[strain]["targets"][analysistype] = targets
seqdict[strain][profiletype] = profilefile
# Index the targets
print "\nIndexing %s targets" % analysistype
SMALT.smaltindextargetsprocesses(targets, rmlstpath)
# Bait!
print "Filtering .fastq files with %s targets" % analysistype
baitrprocesses(analysistype)
# Get the MLST profile into a dictionary
print "\nLoading %s profiles" % analysistype
profiledict, genedict = rawMLST.profilR(seqdict, profiletype)
# Use SMALT to perform reference mapping
print '\nPerforming %s reference mapping' % analysistype
SMALT.smaltmappingprocesses(seqdict, analysistype, "SMALT")
# Use samtools to sort bam files
print "\nSorting mapped %s files" % analysistype
bamProcessor.sortingprocesses(seqdict, analysistype)
# Use samtools to index bam files
print '\nIndexing sorted %s files' % analysistype
bamProcessor.bamindexingprocesses(seqdict, analysistype)
# Use pysamstats to parse bam files
print '\nParsing %s results' % analysistype
mlstmatches = bamPysamStats.bamparseprocesses(seqdict, analysistype)
# Determine sequence types
print '\nFinding multilocus sequence types'
sequencetypes = rawMLST.sequenceTyper(mlstmatches, profiledict, genedict)
# Create a report
rawMLST.rMLSTreportMaker(seqdict, sequencetypes, analysistype, reportfolder, path)
def sixteens():
"""Performs the necessary analyses on strains using 16S targets"""
global targetpath, seqdict
# Set the analysis type variable to 16S. This variable is important for retrieving 16S-specific data from seqdict
analysistype = "16S"
# Set the path of the analysistype data
currenttargetpath = "%s%s" % (targetpath, analysistype)
# Create the bait target file (if necessary)
baittargets(currenttargetpath, analysistype)
# In order to save time, during baiting, a precomputed hash file is used
hashfile = glob("%s/bait/*.gz" % currenttargetpath)
# If the hashfile is present, use it
if hashfile:
baitfile = hashfile[0]
# Otherwise, use the concatenated bait file
else:
baitfile = glob("%s/bait/*.fa*" % currenttargetpath)[0]
print "Filtering .fastq files with %s targets" % analysistype
# Get a list of the targets into a variable
sixteensdatabase = glob("%s/*.fa*" % currenttargetpath)
# Filter as above - repeated as the above code is not executed if the bait file is already present
sixteensdatabase = [target for target in sixteensdatabase if ".fai" not in target]
# Populate seqdict with the name and path of the bait file used as well as the database
for foldername in seqdict:
seqdict[foldername]["bait"]["fastqFiles"][analysistype] = baitfile
seqdict[foldername]["targets"][analysistype] = sixteensdatabase
# Run the baiting process
baitrprocesses(analysistype)
# Perform SMALT indexing of targets
print "\nIndexing %s targets" % analysistype
SMALT.smaltindextargetsprocesses(sixteensdatabase, currenttargetpath)
# Perform reference mapping with SMALT
print '\nPerforming %s reference mapping' % analysistype
SMALT.smaltmappingprocesses(seqdict, analysistype, "SMALT")
# Use samtools to sort the bam files
print "\nSorting mapped %s files" % analysistype
bamProcessor.sortingprocesses(seqdict, analysistype)
# Use samtools to index the sorted bam files
print '\nIndexing sorted %s files' % analysistype
bamProcessor.bamindexingprocesses(seqdict, analysistype)
# Use pysamstats to parse the sorted, indexed bam files
print '\nParsing %s results' % analysistype
generadict, generalist = bamPysamStats.bamparseprocesses(seqdict, analysistype)
# Create reports of the results
sixteensreportmaker(generadict, analysistype)
# Return the computed genera
return generadict, generalist
def mlst(organismdict, organismlist):
"""
Performs the necessary analyses on strains using genus-specific MLST targets
:param organismdict: dictionary of the 16S results
:param organismlist: list of all the genera in the current analysis
"""
global targetpath, seqdict
# Set the analysis type
analysistype = "MLST"
profiletype = "MLSTprofile"
# MLST targets are stored in targetpath/Organism/<genus>/MLST/alleles
currenttargetpath = "%sOrganism" % targetpath
# Print this out before the loop
print '\nIndexing %s target files' % analysistype
for strain in organismdict:
# If there is not an MLST scheme installed for a particular organism, then the script will crash when it tries
# to find the necessary files, as they are not present. Allow index errors to pass
try:
# Using the organismdict entry (genus) generated in the 16S analysis, set the allele and profile paths
# NB: This will come up multiple times with this script, but I only allowed a small amount of freedom in
# the placement of folders. Usually, there are strict folder hierarchies, which must be followed
mlstpath = glob("%s/%s/*MLST*" % (currenttargetpath, organismdict[strain].keys()[0]))[0] + "/alleles"
profilepath = glob("%s/%s/*MLST*" % (currenttargetpath, organismdict[strain].keys()[0]))[0] + "/profile"
# Try to find the precomputed .json profile file
profilefile = glob("%s/*.json" % profilepath)
# If it does not exist, find the .txt profile file. As the script requires a small amount of formatting on
# the profile file prior to analysis, I forced a changed in file extension to hopefully ensure that this
# formatting has been performed
if not profilefile:
profilefile = glob("%s/*.txt" % profilepath)[0]
else:
profilefile = profilefile[0]
# Create the bait target file (if necessary)
baittargets(currenttargetpath, analysistype)
# If a precomputed hash file is present in the bait folder, use it to save on processing time
hashfile = glob("%s/bait/*.gz" % mlstpath)
if hashfile:
baitfile = hashfile[0]
# Otherwise, use the .fasta bait file created above
else:
baitfile = glob("%s/bait/*.fa*" % mlstpath)[0]
# Set the bait type variable using the genus of the strain and the analysis type
baittype = "%s_MLST" % organismdict[strain].keys()[0]
# Store the baittype variable in seqdict
seqdict[strain]["bait"]["fastqFiles"][baittype] = baitfile
# Get the targets into a list
targets = glob("%s/*.*fa" % mlstpath)
# Remove faidx processed files
targets = [target for target in targets if ".fai" not in target]
# Store the target list, and the profile file in seqdict
seqdict[strain]["targets"][analysistype] = targets
seqdict[strain]["MLSTprofile"] = profilefile
# Index the SMALT targets
SMALT.smaltindextargetsprocesses(targets, mlstpath)
except IndexError:
pass
# Bait!
print "Filtering .fastq files with %s targets" % analysistype
baitrprocesses(analysistype)
# Get the MLST profile into a dictionary
print "\nLoading %s profiles" % analysistype
profiledict, genedict = rawMLST.profilR(seqdict, profiletype)
print '\nPerforming %s reference mapping' % analysistype
# Perform SMALT reference mapping
SMALT.smaltmappingprocesses(seqdict, analysistype, "SMALT")
print "\nSorting mapped %s files" % analysistype
# Use samtools to sort reference mapped bam files
bamProcessor.sortingprocesses(seqdict, analysistype)
print '\nIndexing sorted %s files' % analysistype
# Use samtools to index sorted reference mapped bam files
bamProcessor.bamindexingprocesses(seqdict, analysistype)
print '\nParsing %s results' % analysistype
# Use pysamstats to parse indexed sorted reference mapped bam files
mlstmatches = bamPysamStats.bamparseprocesses(seqdict, analysistype)
print '\nFinding multilocus sequence types'
# Determine sequence types
sequencetypes = rawMLST.sequenceTyper(mlstmatches, profiledict, genedict)
# Create a report
rawMLST.MLSTreportMaker(seqdict, sequencetypes, analysistype, reportfolder, organismdict, organismlist, path)