紫框:pysam.AlignmentFile,最重要的属性为pileup,即绿框 绿框:由PileupColumn组成的迭代器 红框:PileupColumn,最重要的属性为pileups,pileups是由PileupRead组成的列表 橙框:PileupRead,最重要的属性为alignment,alignment即pysam.AlignedSegment 蓝框:AlignedSegment ...
pileup()方法 访问基因组每个碱基的比对情况 iterable = f1.pileup(contig = 'chr1',start = 27056142,stop = 27056261) for line in iterable: print(line) print(line.reference_name) print(line.pos) print(line.nsegments) find_introns()/find_introns_slow()方法 返回字典 {(start, stop): count}...
1 pileup(self, contig=None, start=None, stop=None, region=None, reference=None, end=None, **kwargs) 类似于samtools的pileup操作,返回一个迭代器,每次迭代返回一个位点的PileupColumn对象,该对象的操作在后面进行详细介绍。 pileupcolumn=sam.pileup("chr1",999863,999865,truncate=True)pc=next(pileup...
4. 同时,还可以通过fetch和pileup两种方式来访问,fetch访问区域的alignment,用法如下 >>> for i in bam.fetch('chr1', 10000, 20000): ... print(i.qname) ... print(i.flag) 1. 2. 3. pileup访问基因组每个碱基的比对情况,用法如下 >>> for i in bam.pileup('chr1', 10000, 20000): ......
if not pileupread.is_del and not pileupread.is_refskip: # query position is None if is_del or is_refskip is set. print ('\tbase in read %s = %s' % (pileupread.alignment.query_name, pileupread.alignment.query_sequence[pileupread.query_position])) ...
pileup(self, contig=None, start=None, stop=None, region=None, reference=None, end=None, **kwargs) 类似于samtools的pileup操作，返回一个迭代器，每次迭代返回一个位点的PileupColumn对象,该对象的操作在后面进行详细介绍。get_aligned_pairs(self, matches_only=False, with_seq=False) ...
Without an index, random access viafetch()andpileup()is disabled. 如果需要遍历一个文件的话,那么直接 import pysam samfile = pysam.AlignmentFile("Treat.20M.merged.sam") lineCount = 0 for read in samfile: print(read) lineCount = lineCount + 1 ...
pileup访问基因组每个碱基的比对情况,用法如下 从形式上看,两种方法差不多,但是其返回值为不同Class的对象,可以根据API来访问具体的属性和方法。 除了访问操作,也可以调用samtools的功能,因为pysam是对samtools的封装,所以samtools的子命令在该模块中,可以通过函数形式来调用,用法如下 ...
pileups: if not pileupread.is_del and not pileupread.is_refskip: # query position is None if is_del or is_refskip is set. print ('\tbase in read %s = %s' % (pileupread.alignment.query_name, pileupread.alignment.query_sequence[pileupread.query_position])) samfile.close() The...
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