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')