============================== Mappy: Minimap2 Python Binding ============================== Mappy provides a convenient interface to `minimap2 `_, a fast and accurate C program to align genomic and transcribe nucleotide sequences. Installation ------------ Mappy depends on `zlib `_. It can be installed with `pip `_: .. code:: shell pip install --user mappy or from the minimap2 github repo (`Cython `_ 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") s = a.seq("MT_human", 100, 200) # retrieve a subsequence from the index print(mp.revcomp(s)) # reverse complement 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 two global function. Class mappy.Aligner ~~~~~~~~~~~~~~~~~~~ .. code:: python mappy.Aligner(fn_idx_in=None, 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. This option has no effect if **seq** is set. * **seq**: a single sequence to index. The sequence name will be set to :code:`N/A`. * **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 (initial chaining and extension) * **bw_long**: chaining and alignment band width (RMQ-based rechaining and closing gaps) * **best_n**: max number of alignments to return * **n_threads**: number of indexing threads; 3 by default * **extra_flags**: additional flags defined in minimap.h * **fn_idx_out**: name of file to which the index is written. This parameter has no effect if **seq** is set. * **scoring**: scoring system. It is a tuple/list consisting of 4, 6 or 7 positive integers. The first 4 elements specify match scoring, mismatch penalty, gap open and gap extension penalty. The 5th and 6th elements, if present, set long-gap open and long-gap extension penalty. The 7th sets a mismatch penalty involving ambiguous bases. .. code:: python mappy.Aligner.map(seq, seq2=None, cs=False, MD=False) This method aligns :code:`seq` against the index. It is a generator, *yielding* a series of :code:`mappy.Alignment` objects. If :code:`seq2` is present, mappy performs paired-end alignment, assuming the two ends are in the FR orientation. Alignments of the two ends can be distinguished by the :code:`read_num` field (see Class mappy.Alignment below). Argument :code:`cs` asks mappy to generate the :code:`cs` tag; :code:`MD` is similar. These two arguments might slightly degrade performance and are not enabled by default. .. code:: python mappy.Aligner.seq(name, start=0, end=0x7fffffff) This method retrieves a (sub)sequence from the index and returns it as a Python string. :code:`None` is returned if :code:`name` is not present in the index or the start/end coordinates are invalid. .. code:: python mappy.Aligner.seq_names This property gives the array of sequence names in the index. 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 positions 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) * **read_num**: read number that the alignment corresponds to; 1 for the first read and 2 for the second read * **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. * **MD**: the :code:`MD` tag as in the SAM format. It is an empty string unless the :code:`MD` argument is applied when calling :code:`mappy.Aligner.map()`. * **cs**: the :code:`cs` tag. 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). Miscellaneous Functions ~~~~~~~~~~~~~~~~~~~~~~~ .. code:: python mappy.fastx_read(fn, read_comment=False) 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. If :code:`read_comment` is True, this generator yields a :code:`(name,seq,qual,comment)` tuple instead. .. code:: python mappy.revcomp(seq) Return the reverse complement of DNA string :code:`seq`. This function recognizes IUB code and preserves the letter cases. Uracil :code:`U` is complemented to :code:`A`.