126 lines
3.6 KiB
ReStructuredText
126 lines
3.6 KiB
ReStructuredText
=======================
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Minimap2 Python Binding
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=======================
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`Minimap2 <https://github.com/lh3/minimap2>`_ is a fast and accurate pairwise
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aligner for genomic and transcribed nucleotide sequences. This module wraps
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minimap2 and provides a convenient interface to calling minimap2 in Python.
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Installation
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------------
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The minimap2 model can be installed directly with:
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.. code:: shell
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git clone https://github.com/lh3/minimap2
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cd minimap2
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python setup.py install
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or with `pip <https://en.wikipedia.org/wiki/Pip_(package_manager)>`_:
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.. code:: shell
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pip install --user minimap2
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Usage
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-----
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The following Python program shows the key functionality of this module:
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.. code:: python
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import minimap2 as mm
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a = mm.Aligner("test/MT-human.fa")
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if not a: raise Exception("ERROR: failed to load/build index")
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for hit in a.map("GGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGT"):
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print("{}\t{}\t{}\t{}".format(hit.ctg, hit.r_st, hit.r_en, hit.cigar_str))
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It builds an index from the specified sequence file (or loads an index if a
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pre-built index is supplied), aligns a sequence against it, traverses each hit
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and prints them out.
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APIs
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----
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Class minimap2.Aligner
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~~~~~~~~~~~~~~~~~~~~~~
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.. code:: python
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Aligner(fn_idx_in, preset=None, ...)
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Arguments:
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* **fn_idx_in**: index or sequence file name. Minimap2 automatically tests the
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file type. If a sequence file is provided, minimap2 builds an index. The
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sequence file can be optionally gzip'd.
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* **preset**: minimap2 preset. Currently, minimap2 supports the following
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presets: **sr** for single-end short reads; **map-pb** for PacBio
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read-to-reference mapping; **map-ont** for Oxford Nanopore read mapping;
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**splice** for long-read spliced alignment; **asm5** for assembly-to-assembly
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alignment; **asm10** for full genome alignment of closely related species. Note
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that the Python module does not support all-vs-all read overlapping.
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* **k**: k-mer length, no larger than 28
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* **w**: minimizer window size, no larger than 255
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* **min_cnt**: mininum number of minimizers on a chain
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* **min_chain_score**: minimum chaing score
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* **bw**: chaining and alignment band width
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* **best_n**: max number of alignments to return
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* **n_threads**: number of indexing threads; 3 by default
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* **fn_idx_out**: name of file to which the index is written
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.. code:: python
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map(query_seq)
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This methods maps :code:`query_seq` against the index. It *yields* a generator,
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generating a series of :code:`Alignment` objects.
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Class minimap2.Alignment
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~~~~~~~~~~~~~~~~~~~~~~~~
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This class has the following properties:
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* **ctg**: name of the reference sequence the query is mapped to
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* **ctg_len**: total length of the reference sequence
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* **r_st** and **r_en**: start and end positions on the reference
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* **q_st** and **q_en**: start and end positions on the query
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* **strand**: +1 if on the forward strand; -1 if on the reverse strand
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* **mapq**: mapping quality
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* **NM**: number of mismatches and gaps in the alignment
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* **blen**: length of the alignment, including both alignment matches and gaps
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* **trans_strand**: transcript strand. +1 if on the forward strand; -1 if on the
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reverse strand; 0 if unknown
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* **is_primary**: if the alignment is primary (typically the best and the first
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to generate)
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* **cigar_str**: CIGAR string
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* **cigar**: CIGAR returned as an array of shape :code:`(n_cigar,2)`. The two
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numbers give the length and the operator of each CIGAR operation.
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An Alignment object can be converted to a string in the following format:
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::
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q_st q_en strand ctg ctg_len r_st r_en blen-NM blen mapq cg:Z:cigar_str
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