def __init__(self,opts=None):
"""
"""
PicardBase.__init__(self, opts=opts)
self.tempout = os.path.join(opts.outdir,'rgPicardValidate.out')
self.temptab = os.path.join(opts.outdir,'rgPicardValidate.xls')
self.sortedfile = os.path.join(self.opts.outdir,'rgcleansam.sorted')
def __init__(self,opts=None,cl=[],tidy=False):
"""
"""
PicardBase.__init__(self,opts=opts)
self.tidy = tidy
self.isPDF = 'InsertSizeHist.pdf'
self.pdfpath = os.path.join(self.opts.outdir,self.isPDF)
def __init__(self,opts=None,tidy=True):
"""
"""
PicardBase.__init__(self,opts=opts)
self.tidy = tidy
self.metricstxt = 'rgPicardMarkDupsout.txt'
self.metricstab = os.path.join(self.opts.outdir,self.metricstxt)
self.inputext = opts.inputext
def __init__(self, opts=None, tidy=True):
"""
"""
PicardBase.__init__(self, opts=opts)
self.tidy = tidy
self.metricstxt = 'rgPicardMarkDupsout.txt'
self.metricstab = os.path.join(self.opts.outdir, self.metricstxt)
self.inputext = opts.inputext
def __init__(self, opts=None):
"""
"""
PicardBase.__init__(self, opts=opts)
# Opts.adapters needs to be one string. If it's None, it must be coerced to empty str.
opts.adapters = opts.adapters or ""
self.tempout = os.path.join(self.opts.outdir, "picardAlignSumMetrics_out.txt")
# Picard only accepts reference files that have a 'fasta' extension name
if not self.opts.refseq.endswith("fasta"):
new_filename = "%s.fasta" % self.opts.refseq
destination = os.path.join(self.opts.outdir, new_filename)
shutil.copy(os.path.abspath(self.opts.refseq), destination)
self.opts.refseq = destination
def __init__(self, opts=None):
"""
"""
PicardBase.__init__(self, opts=opts)
self.fakefasta = os.path.join(self.opts.outdir, "%s_fake.fasta" % os.path.split(self.opts.refseq)[-1])
try:
os.symlink(self.opts.refseq, self.fakefasta)
except:
s = "## unable to symlink %s to %s - different devices? May need to replace with shutil.copy"
info = s
print >>sys.stderr, s
exit(1)
self.title = self.opts.title.translate(self.trantab)
def __init__(self, opts=None):
"""
"""
PicardBase.__init__(self, opts=opts)
# Opts.adapters needs to be one string. If it's None, it must be coerced to empty str.
opts.adapters = opts.adapters or ''
self.tempout = os.path.join(self.opts.outdir,
'picardAlignSumMetrics_out.txt')
# Picard only accepts reference files that have a 'fasta' extension name
if not self.opts.refseq.endswith('fasta'):
new_filename = '%s.fasta' % self.opts.refseq
destination = os.path.join(self.opts.outdir, new_filename)
shutil.copy(os.path.abspath(self.opts.refseq), destination)
self.opts.refseq = destination
def __init__(self, opts=None):
"""
"""
PicardBase.__init__(self, opts=opts)
self.fakefasta = os.path.join(
self.opts.outdir,
'%s_fake.fasta' % os.path.split(self.opts.refseq)[-1])
try:
os.symlink(self.opts.refseq, self.fakefasta)
except:
s = '## unable to symlink %s to %s - different devices? May need to replace with shutil.copy'
info = s
print >> sys.stderr, s
exit(1)
self.title = self.opts.title.translate(self.trantab)
def __init__(self, opts=None):
PicardBase.__init__(self,opts=opts)
def __init__(self, opts=None):
PicardBase.__init__(self, opts=opts)
self.baitf = os.path.join(self.opts.outdir, 'rgPicardHsMetrics.bait')
self.targetf = os.path.join(self.opts.outdir,
'rgPicardHsMetrics.target')
def __init__(self,opts=None):
"""
"""
PicardBase.__init__(self, opts=opts)
self.outtxt = 'estlibcompout.txt'
def __init__(self, opts=None):
PicardBase.__init__(self,opts=opts)
self.baitf = os.path.join(self.opts.outdir,'rgPicardHsMetrics.bait')
self.targetf = os.path.join(self.opts.outdir,'rgPicardHsMetrics.target')
