本文整理汇总了Python中Bio.SeqFeature.SeqFeature.qualifiers["alignment"]方法的典型用法代码示例。如果您正苦于以下问题：Python SeqFeature.qualifiers["alignment"]方法的具体用法？Python SeqFeature.qualifiers["alignment"]怎么用？Python SeqFeature.qualifiers["alignment"]使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类Bio.SeqFeature.SeqFeature的用法示例。
在下文中一共展示了SeqFeature.qualifiers["alignment"]方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: seqBlastToFeatures
# 需要导入模块: from Bio.SeqFeature import SeqFeature [as 别名]
# 或者: from Bio.SeqFeature.SeqFeature import qualifiers["alignment"] [as 别名]
def seqBlastToFeatures(self, blastDB, blastExe, seqFile, blastType = "blastn",scoreMin = 1e-3, logFile = None):
'''
Blast sequence file against blast database
parse files into records.
This function may not work as well on very large blast comparisons because
it does a full read of the result for the conversion to features.
'''
print ">blast %s %s %s %s" % (self.blastDB, self.blastExe, seqFile, blastType)
blastRecords = self.seqBlast(seqFile, blastType = "blastn", scoreMin = 1e-3, logFile = None)
result = []
index = 0
for r in blastRecords:
recordFeatures = []
for alignment in r.alignments:
name = alignment.title
query = r.query
for hsp in alignment.hsps:
if hsp.expect < scoreMin:
(ts,ss) = hsp.frame
strand = ss
start = hsp.sbjct_start
end = hsp.sbjct_end
location = FeatureLocation(start,end)
feature = SeqFeature(id=query,location=location,strand=strand)
aMatch = hsp.query + "\n" + hsp.match + "\n" + hsp.sbjct
feature.qualifiers["query"] = hsp.query
feature.qualifiers["subject"] = hsp.sbjct
feature.qualifiers["alignment"] = aMatch
recordFeatures.append(feature)
result.append(recordFeatures)
index = index + 1
return result