コード例 #1
0
ファイル: __init__.py プロジェクト: Illumina/hap.py
 def collect(self, vcfname, tag):
     """ Return a data frame with features collected from the given VCF, tagged by given type """
     if tag not in ["TP", "FN"]:
         return extractStrelkaSNVFeatures(vcfname, tag, self.chr_depth)
     else:
         features = ["CHROM", "POS", "REF", "ALT", "I.editDistance", "S.2.GT"]
         return GenericFeatures.collectFeatures(vcfname, tag, features, processor=StrelkaAdmixSNVFeatures.processValue)
コード例 #2
0
ファイル: __init__.py プロジェクト: Illumina/hap.py
 def collect(self, vcfname, tag):
     """ Return a data frame with features collected from the given VCF, tagged by given type """
     if tag not in ["TP", "FN"]:
         return extractStrelkaSNVFeatures(vcfname, tag, self.chr_depth)
     else:
         features = ["CHROM", "POS", "REF", "ALT", "QUAL",
                     "I.T_ALT_RATE", "I.DP_normal", "I.DP_tumor", "I.tag", "I.count"]
     return GenericFeatures.collectFeatures(vcfname, tag, features, processor=StrelkaAdmixSNVFeatures.processValue)
コード例 #3
0
ファイル: __init__.py プロジェクト: zzygyx9119/hap.py
 def collect(self, vcfname, tag):
     """ Return a data frame with features collected from the given VCF, tagged by given type """
     if tag not in ["TP", "FN"]:
         return extractStrelkaSNVFeatures(vcfname, tag, self.chr_depth)
     else:
         features = [
             "CHROM", "POS", "REF", "ALT", "I.editDistance", "S.2.GT"
         ]
         return GenericFeatures.collectFeatures(
             vcfname,
             tag,
             features,
             processor=StrelkaAdmixSNVFeatures.processValue)
コード例 #4
0
ファイル: __init__.py プロジェクト: zzygyx9119/hap.py
 def collect(self, vcfname, tag):
     """ Return a data frame with features collected from the given VCF, tagged by given type """
     if tag not in ["TP", "FN"]:
         return extractStrelkaSNVFeatures(vcfname, tag, self.chr_depth)
     else:
         features = [
             "CHROM", "POS", "REF", "ALT", "QUAL", "I.T_ALT_RATE",
             "I.DP_normal", "I.DP_tumor", "I.tag", "I.count"
         ]
     return GenericFeatures.collectFeatures(
         vcfname,
         tag,
         features,
         processor=StrelkaAdmixSNVFeatures.processValue)