MAF Conversion & Summary

Convert and summarize multiple alignment format (MAF) files, such as whole-genome alignments. See the CLI guidelines for MAF conversion and MAF summary for details on the output files.

MAF Conversion

Install PySEGUL using pip if you haven’t done it yet

pip install pysegul

Create a new Python script, import the library, and write python code.

import pysegul

def convert_maf():
    input_dir = 'tests/maf-data'
    output_dir = 'tests/output'
    convert = pysegul.MafConversion(
        output_dir,
        # Optional. Default: 'fasta'
        output_fmt='nexus',
        # Optional. Without a BED file, write one file per 'block'
        # or per reference chromosome ('chrom').
        group_by='block',
        )
    convert.from_dir(input_dir)

To extract loci, provide a BED file. Each block goes to every locus it overlaps.

import pysegul

def convert_maf_loci():
    convert = pysegul.MafConversion(
        'tests/output',
        output_fmt='fasta',
        # BED file of loci (.bed or .bed.gz)
        bed='loci.bed',
        # Optional. Set to False to keep whole blocks instead of clipping to loci.
        clip=True,
        # Optional. Reverse complement loci on the minus strand.
        strand_aware=False,
        # Optional. Write blocks that match no locus to the unmatched directory.
        write_unmatched=False,
        # Optional. Name of the locus report CSV.
        output_prefix='loci',
        )
    convert.from_files(['alignment.maf'])

All conversion options:

Option	Default	Description
`output_fmt`	`'fasta'`	`'fasta'`, `'nexus'`, `'phylip'`, or the interleaved `-int` versions
`group_by`	`'block'`	Without a BED file, write one file per `'block'` or per `'chrom'`
`bed`	`None`	BED file of loci
`clip`	`True`	Clip blocks to the loci. Requires `bed`
`strand_aware`	`False`	Reverse complement loci on the minus strand. Requires `bed`
`write_unmatched`	`False`	Write blocks that match no locus. Requires `bed`
`full_source_name`	`False`	Use full source names (e.g. `hg18.chr7`) as sample names instead of the assembly prefix (`hg18`)
`ref_species`	`None`	Reference species. Defaults to the first species in the first block
`species`	`None`	List of species to keep. The reference is still used for coordinates
`min_block_len`	`None`	Skip blocks with fewer reference bases
`min_species`	`None`	Skip blocks with fewer species, counting the reference
`min_score`	`None`	Skip blocks with a lower score
`output_prefix`	`None`	Name of the locus report CSV written with `bed`

Errors, such as an unreadable BED file, raise a ValueError.

MAF Summary

Summarize MAF files per species and per file.

import pysegul

def summarize_maf():
    summary = pysegul.MafSummary(
        'tests/output',
        # Optional
        output_prefix='maf',
        # Optional. Use full source names as sample names.
        full_source_name=False,
        # Optional. Reference species.
        ref_species=None,
        # Optional. List of species to keep.
        species=None,
        )
    summary.from_dir('tests/maf-data')