Metadata-Version: 1.1
Name: mappy
Version: 2.6
Summary: Minimap2 python binding
Home-page: https://github.com/lh3/minimap2
Author: Heng Li
Author-email: lh3@me.com
License: MIT
Description-Content-Type: UNKNOWN
Description: ==============================
        Mappy: Minimap2 Python Binding
        ==============================
        
        Mappy provides a convenient interface to `minimap2
        <https://github.com/lh3/minimap2>`_, a fast and accurate C program to align
        genomic and transcribe nucleotide sequences.
        
        Installation
        ------------
        
        Mappy depends on `zlib <http://zlib.net>`_. It can be installed with `pip
        <https://en.wikipedia.org/wiki/Pip_(package_manager)>`_:
        
        .. code:: shell
        
        	pip install --user mappy
        
        or from the minimap2 github repo (`Cython <http://cython.org>`_ required):
        
        .. code:: shell
        
        	git clone https://github.com/lh3/minimap2
        	cd minimap2
        	python setup.py install
        
        Usage
        -----
        
        The following Python script demonstrates the key functionality of mappy:
        
        .. code:: python
        
        	import mappy as mp
        	a = mp.Aligner("test/MT-human.fa")  # load or build index
        	if not a: raise Exception("ERROR: failed to load/build index")
        	for name, seq, qual in mp.fastx_read("test/MT-orang.fa"): # read a fasta/q sequence
        		for hit in a.map(seq): # traverse alignments
        			print("{}\t{}\t{}\t{}".format(hit.ctg, hit.r_st, hit.r_en, hit.cigar_str))
        
        APIs
        ----
        
        Mappy implements two classes and one global function.
        
        Class mappy.Aligner
        ~~~~~~~~~~~~~~~~~~~
        
        .. code:: python
        
        	mappy.Aligner(fn_idx_in, preset=None, ...)
        
        This constructor accepts the following arguments:
        
        * **fn_idx_in**: index or sequence file name. Minimap2 automatically tests the
          file type. If a sequence file is provided, minimap2 builds an index. The
          sequence file can be optionally gzip'd.
        
        * **preset**: minimap2 preset. Currently, minimap2 supports the following
          presets: **sr** for single-end short reads; **map-pb** for PacBio
          read-to-reference mapping; **map-ont** for Oxford Nanopore read mapping;
          **splice** for long-read spliced alignment; **asm5** for assembly-to-assembly
          alignment; **asm10** for full genome alignment of closely related species. Note
          that the Python module does not support all-vs-all read overlapping.
        
        * **k**: k-mer length, no larger than 28
        
        * **w**: minimizer window size, no larger than 255
        
        * **min_cnt**: mininum number of minimizers on a chain
        
        * **min_chain_score**: minimum chaing score
        
        * **bw**: chaining and alignment band width
        
        * **best_n**: max number of alignments to return
        
        * **n_threads**: number of indexing threads; 3 by default
        
        * **fn_idx_out**: name of file to which the index is written
        
        .. code:: python
        
        	mappy.Aligner.map(seq)
        
        This method aligns :code:`seq` against the index. It is a generator, *yielding*
        a series of :code:`mappy.Alignment` objects.
        
        Class mappy.Alignment
        ~~~~~~~~~~~~~~~~~~~~~
        
        This class describes an alignment. An object of this class has the following
        properties:
        
        * **ctg**: name of the reference sequence the query is mapped to
        
        * **ctg_len**: total length of the reference sequence
        
        * **r_st** and **r_en**: start and end positions on the reference
        
        * **q_st** and **q_en**: start and end positions on the query
        
        * **strand**: +1 if on the forward strand; -1 if on the reverse strand
        
        * **mapq**: mapping quality
        
        * **blen**: length of the alignment, including both alignment matches and gaps
          but excluding ambiguous bases.
        
        * **mlen**: length of the matching bases in the alignment, excluding ambiguous
          base matches.
        
        * **NM**: number of mismatches, gaps and ambiguous poistions in the alignment
        
        * **trans_strand**: transcript strand. +1 if on the forward strand; -1 if on the
          reverse strand; 0 if unknown
        
        * **is_primary**: if the alignment is primary (typically the best and the first
          to generate)
        
        * **cigar_str**: CIGAR string
        
        * **cigar**: CIGAR returned as an array of shape :code:`(n_cigar,2)`. The two
          numbers give the length and the operator of each CIGAR operation.
        
        An :code:`Alignment` object can be converted to a string with :code:`str()` in
        the following format:
        
        ::
        
        	q_st  q_en  strand  ctg  ctg_len  r_st  r_en  mlen  blen  mapq  cg:Z:cigar_str
        
        It is effectively the PAF format without the QueryName and QueryLength columns
        (the first two columns in PAF).
        
        Function mappy.fastx_read
        ~~~~~~~~~~~~~~~~~~~~~~~~~
        
        .. code:: python
        
        	mappy.fastx_read(fn)
        
        This generator function opens a FASTA/FASTQ file and *yields* a
        :code:`(name,seq,qual)` tuple for each sequence entry. The input file may be
        optionally gzip'd.
        
Keywords: sequence-alignment
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: POSIX
Classifier: Programming Language :: C
Classifier: Programming Language :: Cython
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
