def by_genome(x, args):
"""All processing conducted per genome.
Parameters
----------
x : list
[inFile,taxonName]
inFile -- genome sequence file name
taxonName -- taxon name of genome
args : dict
user-provided args
Returns
-------
l2d -- list of lists
for each fragment: [taxonName,scaf,start,end,GC]
"""
taxonName,inFile = x
# status
sys.stderr.write('Processing: "{}"\n'.format(taxonName))
# making genome object
assert '--fr' in args, '"--fr" must be provided in args'
genome = Genome(inFile, taxonName, args['--fr'])
# MFEprimer.py executable
MFEprimerExe = args['--MFE']
# sequenced read template location: amplicons
if genome.primerFile is not None:
# in-silico PCR
assert '--rtr' in args, '"--rtr" must be in args'
genome.callMFEprimer(rtr=args['--rtr'], MFEprimerExe=MFEprimerExe)
# filtering overlapping in-silico amplicons
genome.filterOverlaps()
# simulating fragments
simFO = SimFrags(fld=args['--fld'], flr=args['--flr'], rtl=args['--rtl'])
nFragsMade = 0
fragList = dict()
## if no amplicons
if genome.nAmplicons == 0:
pass
## if using coverage
elif args['--nf'].endswith('X') or args['--nf'].endswith('x'):
coverage = float(args['--nf'].rstrip('xX'))
fragLenCov = genome.length * coverage
fragLenTotal = 0
while 1:
(scaf,fragStart,fragLen,fragGC) = simFO.simFrag(genome)
try:
type(fragList[scaf])
except KeyError:
fragList[scaf] = []
if fragStart == "NA":
break
elif fragLenTotal > fragLenCov:
break
fragLenTotal += fragLen
nFragsMade += 1
fragList[scaf].append([fragStart, fragLen, fragGC])
## if using fixed number of fragments
else:
for i in xrange(int(args['--nf'])):
(scaf,fragStart,fragLen,fragGC) = simFO.simFrag(genome)
try:
type(fragList[scaf])
except KeyError:
fragList[scaf] = []
if fragStart == "NA":
break
nFragsMade += 1
fragList[scaf].append([fragStart, fragLen, fragGC])
# status
sys.stderr.write(' Genome name: {}\n'.format(genome.taxonName))
sys.stderr.write(' Genome length (bp): {}\n'.format(genome.length))
if args['--nf']:
msg = ' Number of amplicons: {}\n'
sys.stderr.write(msg.format(genome.nAmplicons))
msg = ' Number of fragments simulated: {}\n'
sys.stderr.write(msg.format(nFragsMade))
return [genome.taxonName, fragList]
