def support(inputDir, gapTable, outputDir, extras):
ret = []
command = Template(
"Support.py ${inputm4} ${gapTable} ${outFile} ${debug} ${extras}")
mappingFiles = glob.glob(os.path.join(inputDir, "mapping/*.m4"))
if len(mappingFiles) == 0:
logging.warning("No mapping files found!")
return ret
for inputm4 in mappingFiles:
baseName = inputm4[inputm4.rindex('/') + 1:inputm4.rindex(".m4")]
outFile = os.path.join(outputDir, baseName + ".gml")
if os.path.isfile(outFile):
logging.warning("Overwriting %s" % outFile)
myCommand = command.substitute( {"inputm4": inputm4,\
"gapTable": gapTable,\
"outFile": outFile,\
"debug": DEBUG,\
"extras":extras} )
ret.append( Command(myCommand,\
baseName+".support",\
os.path.join(outputDir,baseName+".out"),\
os.path.join(outputDir,baseName+".err")) )
return ret
def extraction(outputDir, protocol, extras):
command = Template("Extraction.py ${protocol} ${debug} ${extras}")
myCommand = command.substitute({"protocol": protocol, \
"debug":DEBUG, \
"extras":extras})
return Command(myCommand, "extraction", \
os.path.join(outputDir,"extraction.out"), \
os.path.join(outputDir,"extraction.err"))
def assembly(inputDir, gapInfoFn, extras):
gapInfo = GapInfoFile(gapInfoFn)
command = Template("Assembly.py ${inputDir} ${size} ${debug} ${extras}")
ret = []
allInputs = glob.glob(os.path.join(inputDir,"ref*"))
if len(allInputs) == 0:
logging.warning("No gaps to be assembled were found in %s! Have you run 'extraction' yet?" % inputDir)
sys.exit(1)
for inputDir in allInputs:
#get The predicted size if exists
mySize = ""
gapName = inputDir.split('/')[-1]
if gapName.count('.') > 0:
g = gapName.split('_')
if len(g) == 1:
ref,cnam = g[0].split('.')
cn = int(cnam[:-2])
if cnam.endswith('e5'):
ca = cn-1
cb = cn
elif cnam.endswith('e3'):
ca = cn
cb = cn+1
else:
logging.error("Single End Extension is misFormatted for %s" % inputDir)
exit(1)
size = gapInfo["%s_%d_%d" % (ref, ca, cb)].length
mySize = "-p %d" % (size)
elif len(g) == 2:
ref,ca = g[0].split('.')
ref,cb = g[1].split('.')
#Hackey Shack. - effect of sorting node names
# to prevent redundancies during graph building
ca = int(ca[:-2])
cb = int(cb[:-2])
j = [ca,cb]
j.sort()
ca, cb = j
size = gapInfo["%s_%d_%d" % (ref, ca, cb)].length
mySize = "-p %d" % (size)
else:
logging.error("Couldn't recreate gapName from refDir for %s" % inputDir)
exit(1)
myCommand = command.substitute({"inputDir":inputDir,\
"size":mySize,\
"debug":DEBUG,\
"extras":extras})
ret.append(Command(myCommand,
os.path.join(inputDir.split('/')[-1],"assembly"), \
os.path.join(inputDir,"assembly.out"), \
os.path.join(inputDir,"assembly.err")) )
return ret
def collection(inputDir, protocol, extras):
command = Template("Collection.py ${protocol} ${extras}")
myCommand = command.substitute({"protocol": protocol.protocolName,
"extras": extras})
return Command(myCommand, \
os.path.join(inputDir,"collectingOutput"), \
os.path.join(inputDir,"output.out"), \
os.path.join(inputDir,"output.err"))
def setup(scaffoldName, scaffoldQualName, gapInfoName, extras):
"""
Generate all the information we need from the input scaffolding
"""
#Error
if scaffoldQualName is None:
scaffoldQualName = ""
command = Template("Setup.py ${scaf} -g ${gap} -i ${debug} ${extras}")\
.substitute( \
{"scaf":scaffoldName, \
"scafQual":scaffoldQualName, \
"gap":gapInfoName, \
"debug":DEBUG, \
"extras":extras})
baseName = os.path.dirname(scaffoldName)
ret = Command(command, "setup", os.path.join(baseName,"setup.out"), \
os.path.join(baseName,"setup.err"))
return ret
def mapping(jobDirs, outDir, reference, referenceSa, parameters, extras):
"""
Input:
- a list of fasta inputs
- an output directory
- a reference - (should be contigs.. see scaffoldIntakeSetup
- a pacbio indexed reference
Task:
- map each fasta to reference
Output:
- m4 alignments of the input sequence
"""
logFormat = "%(asctime)s [%(levelname)s] %(message)s"
level = "DEBUG" if DEBUG != "" else "INFO"
logging.basicConfig(stream=sys.stderr, level=level, format=logFormat)
logging.info("Running blasr")
mappingTemplate = Template(
"blasr ${fasta} ${ref} ${sa} -m 4 --out ${outFile} ${parameters} ")
tailTemplate = Template(
"m4pie.py ${outFile} ${fasta} ${ref} --nproc ${nproc} -i ${extras}")
ret = []
#sa safety
if os.path.exists(referenceSa):
referenceSa = "--sa " + referenceSa
else:
logging.critical(
"Specified reference.sa %s does not exists. Mapping will be slower"
% (referenceSa))
referenceSa = ""
for fasta in jobDirs:
name = fasta[fasta.rindex('/') + 1:]
if not os.path.exists(fasta):
logging.error("%s doesn't exist." % fasta)
exit(1)
outFile = os.path.join(outDir, name + ".m4")
if os.path.isfile(outFile):
logging.warning(
"Output File %s already exists and will be overwritten." %
(outFile))
#Build Blasr Command
nprocRe = re.compile("-nproc (\d+)")
np = nprocRe.findall(parameters + extras)
if len(np) == 0:
np = '1'
else:
np = np[-1]
cmd = mappingTemplate.substitute({
"fasta": fasta,
"ref": reference,
"sa": referenceSa,
"outFile": outFile,
"parameters": parameters,
"extras": extras
})
cmd2 = tailTemplate.substitute({
"fasta": fasta,
"ref": reference,
"outFile": outFile,
"nproc": np,
"extras": extras
})
fullCmd = cmd + "\n" + cmd2
#Build Command to send to CommandRunner
jobname = name + ".mapping"
stdout = os.path.join(outDir, name + ".out")
stderr = os.path.join(outDir, name + ".err")
ret.append(Command(fullCmd, jobname, stdout, stderr))
return ret
def assembly(inputDir, gapInfoFn, extras):
gapInfo = GapInfoFile(gapInfoFn)
command = Template("Assembly.py ${inputDir} ${size} ${debug} ${extras}")
ret = []
allInputs = glob.glob(os.path.join(inputDir, "ref*"))
if len(allInputs) == 0:
logging.warning(
"No gaps to be assembled were found in %s! Have you run 'extraction' yet?"
% inputDir)
sys.exit(1)
for inputDir in allInputs:
# subdirectories of the assembly/ directory each correspond to a single
# gap, and are named based on the sequences surrounding the gap, in the
# following format:
# [contig1].[ca]e[3|5]_[contig2].[cb]e[3|5]
# where contig1/2 are ref names (e.g., "ref12345")
# I have no idea what ca/cb are. it would be pretty cool if that was
# commented, or at least named more than a two-letter variable.
# e3/5 is the end of the contig that is adjacent to the gap
#get The predicted size if exists
mySize = ""
# gapName = inputDir.split('/')[-1]
# print >> sys.stderr, gapName
# if gapName.count('.') > 0:
# g = gapName.split('_')
# if len(g) == 1:
# ref,cnam = g[0].split('.')
# cn = int(cnam[:-2])
# if cnam.endswith('e5'):
# ca = cn-1
# cb = cn
# elif cnam.endswith('e3'):
# ca = cn
# cb = cn+1
# else:
# logging.error("Single End Extension is misFormatted for %s" % inputDir)
# exit(1)
# size = gapInfo["%s_%d_%d" % (ref, ca, cb)].length
# mySize = "-p %d" % (size)
# elif len(g) == 2:
# splits_a, splits_b = g[0].split('.'), g[1].split('.')
# if len(splits_a) == 2 and len(splits_b) == 2:
# ref,ca = splits_a
# ref,cb = splits_b
# #Hackey Shack. - effect of sorting node names
# # to prevent redundancies during graph building
# ca = int(ca[:-2])
# cb = int(cb[:-2])
# j = [ca,cb]
# j.sort()
# ca, cb = j
# size = gapInfo["%s_%d_%d" % (ref, ca, cb)].length
# mySize = "-p %d" % (size)
# else:
# logging.error("Couldn't recreate gapName from refDir for %s" % inputDir)
# exit(1)
myCommand = command.substitute({"inputDir":inputDir,\
"size":mySize,\
"debug":DEBUG,\
"extras":extras})
ret.append(Command(myCommand,
os.path.join(inputDir.split('/')[-1],"assembly"), \
os.path.join(inputDir,"assembly.out"), \
os.path.join(inputDir,"assembly.err")) )
return ret