115 lines
3.3 KiB
Markdown
115 lines
3.3 KiB
Markdown
## Minimap2 Python Binding
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[Minimap2][minimap2] is a fast and accurate pairwise aligner for genomic and
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transcribed nucleotide sequences. This module wraps minimap2 and provides a
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convenient interface to calling minimap2 in Python.
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### Installation
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The minimap2 model can be installed directly with:
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```sh
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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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```
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or with [pip][pip]:
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```sh
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pip install --user minimap2
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```
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### Usage
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The following Python program shows the key functionality of this module:
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```python
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import minimap2 as mm
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a = mm.Aligner("test/MT-human.fa")
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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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```
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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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#### Class minimap2.Aligner
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```python
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Aligner(fn_idx_in, preset=None, ...)
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```
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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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```python
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map(query_seq)
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```
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This methods maps `query_seq` against the index. It *yields* a generator,
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generating a series of `Alignment` objects.
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#### Class minimap2.Alignment
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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 `(n_cigar,2)`. The two numbers
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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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```
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[minimap2]: https://github.com/lh3/minimap2
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[pip]: https://pypi.python.org/pypi/pip
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