ANIb

[baileythegreen]

@widdowquinn I'm trying to make sense of the work that has already been done on this. The file, anib.py seems to contain code applicable both for running blastn and blastall; is that accurate? My guess is that it might be largely copied over from version 2's implementation. I'm going to attempt to separate the two, but if you had something else in mind, let me know.

[baileythegreen]

It also seems like there is some (possibly redundant) code in subcmd_anib.py as it currently is, but I may be misunderstanding.

Parts of lines 150–173:

    # Create output directories. We create the main parent directory (args.outdir), but
    # also subdirectories for the BLAST databases,
    logger.debug("Creating output directory %s", args.outdir)
    try:
        os.makedirs(args.outdir, exist_ok=True)
    except IOError:
        logger.error(
            f"Could not create output directory {args.outdir} (exiting)", exc_info=True
        )
        raise SystemError(1)
    fragdir = Path(str(args.outdir)) / "fragments"
    blastdbdir = Path(str(args.outdir)) / "blastdbs"
    logger.debug("\t...creating subdirectories")
    os.makedirs(fragdir, exist_ok=True)
    os.makedirs(blastdbdir, exist_ok=True)

    # Create a new sequence fragment file and a new BLAST+ database for each input genome,
    # and add this data to the database as a row in BlastDB
    logger.info("Creating input sequence fragment files")
    for genome in genomes:
        fragpath, fraglengths = fragment_fasta_file(
            Path(str(genome.path)), Path(str(fragdir)), args.fragsize
        )
        print(fragpath, len(fraglengths))

seem very similar to parts of lines 233–243:

    # Split the input genome files into contiguous fragments of the specified size,
    # as described in Goris et al. We create a new directory to hold sequence
    # fragments, away from the main genomes
    logger.info("Splitting input genome files into %snt fragments...", args.fragsize)
    fragdir = Path(args.outdir) / "fragments"
    os.makedirs(fragdir, exist_ok=True)
    fragfiles, fraglens = anib.fragment_fasta_files(
        [Path(str(_.path)) for _ in genomes],
        Path(args.outdir) / "fragments",
        args.fragsize,
    )

Are both necessary, or is the code after the (first) raise NotImplementedError more of a scratchpad?

[widdowquinn]

Yes - that looks like accidental duplication. It wouldn't have caused a bug/error, but there's no reason to try creating that directory twice.

[widdowquinn]

And you're correct - I approached the subcmd_anib.py code by copying over relevant sections from v0.2 and refactoring/modifying/updating it.