灰框:pysam.FastaFile(),因为在bam文件里是没有保存ref的碱基,所以需要重新读取fasta 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...
PileupRead对象内置方法 1 获得pysam.Alignment对象 importpysam samfile=pysam.AlignmentFile("test.bam","rb")#核查索引samfile.check_index()#返回true 2 AlignmentFile对象内置方法 计算目标区域内比对上的reads数目 count(self,contig=None, start=None, stop=None, region=None, until_eof=False, read_callbac...
Closed PileupRead() indel property and deletions #31 ronammar opened this issue Aug 6, 2014· 11 comments Assignees CommentsCopy link Quote reply ronammar commented Aug 6, 2014 I'm observing instances where .indel = 0 and .is_del = 1. The base upstream of the deletion, is ...
如果输入的文件没有 index 将无法使用fetch()和pileup(); 如果是写文件: 给了template,header 拷贝来源的 AlignmentFile (template 必须是AlignmentFile). 若给了header ,header 就有这个多层字典构建 默认'r'mode 下,会检查头文件(check_header = True)和染色体名称的定义(check_sq = True). ...
pos, pileupcolumn.n)) for pileupread in pileupcolumn.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_...
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) ...
.. autoclass:: pysam.PileupColumn :members: .. autoclass:: pysam.PileupRead :members: .. autoclass:: pysam.IndexedReads :members: Tabix files :class:`~pysam.TabixFile`opens tabular files that have been indexed withtabix_. .. autoclass:: pysam.TabixFile :members: ...
-l (小写 L) 可以添加只给出匹配文件的文件名。 -e 是搜索过程中使用的模式 除了这些, --exclude,...
BAM_FDUP set; "nofilter" applies no filter to returned reads; "samtools": filter & read processing as in _csamtools_ pileup. This requires afastafile. For complete details see the pysam documentation. -d, --padPad pileup-based stats so a record is emitted for ...
Pysam[1]是一个 Python 模块，它打包了高通量测序库htslib[2]的 C-API，可用于读写基因组相关文件，...