Python inputGD示例

示例#1

文件： make_calls_gencons.py 项目： JBEI/MiSeqValPipeline

 def make_call(self,seq):
   if self.pct_cov < 1.0: return "Incomplete"
   if self.mean_cov < 5.0: return "Low coverage"
   if not self.variants and not self.dips: return "Pass"
   
   result = runGD(inputGD(self.name, self.variants+self.dips, seq))
   if not result['score'] == '-1': return "Fixable:%s,%s" % (result['primer1'],result['primer2'])
   if self.variants: return 'Errors'
   return 'Dips'

示例#2

    def make_call(self, seq):
        if self.pct_cov < 1.0: return "Incomplete"
        if self.mean_cov < 5.0: return "Low coverage"
        if not self.variants and not self.dips: return "Pass"

        result = runGD(inputGD(self.name, self.variants + self.dips, seq))
        if not result['score'] == '-1':
            return "Fixable:%s,%s" % (result['primer1'], result['primer2'])
        if self.variants: return 'Errors'
        return 'Dips'

示例#3

文件： make_calls_gatk.py 项目： eoberortner/JGI-MiSeq

 def make_call(self,seq):
     if self.pct_cov < 1.0: return "Incomplete"
     
     ## changed from 5.0 to 100.0
     ## CHANGE: 08/25/15    -- Ernst Oberortner
     ## changed threshold from 5.0 to 100.0
     ## old: 
     ## if self.mean_cov < 5.0: return "Low coverage"
     ## new:
     if self.mean_cov < 100.0: return "Low coverage"
     if not self.variants and not self.dips: return "Pass"
     
     result = runGD(inputGD(self.name, self.variants+self.dips, seq))
     if not result['score'] == '-1': return "Fixable:%s,%s" % (result['primer1'],result['primer2'])
     if self.variants: return 'Errors'
     return 'Dips'

示例#4

文件： make_calls_gatk.py 项目： raj347/JGI-MiSeq

    def make_call(self, seq):
        if self.pct_cov < 1.0: return "Incomplete"

        ## changed from 5.0 to 100.0
        ## CHANGE: 08/25/15    -- Ernst Oberortner
        ## changed threshold from 5.0 to 100.0
        ## old:
        ## if self.mean_cov < 5.0: return "Low coverage"
        ## new:
        if self.mean_cov < 100.0: return "Low coverage"
        if not self.variants and not self.dips: return "Pass"

        result = runGD(inputGD(self.name, self.variants + self.dips, seq))
        if not result['score'] == '-1':
            return "Fixable:%s,%s" % (result['primer1'], result['primer2'])
        if self.variants: return 'Errors'
        return 'Dips'