Script for extracting and intersecting hashes and their abundances from a sketch or a group of sketches

[ccbaumler]

@ctb @bettafische

Place holder to find a time to meet to make this script.

[ctb]

code from here should work: https://github.com/ctb/sourmash_plugin_abundhist/blob/4f1b7bfb50adf9f6388a14828618e9f1d2a605c4/src/sourmash_plugin_abundhist.py#L112

extracted and adjusted:

#! /usr/bin/env python 
import sys
import sourmash

def extract_hashes_and_abunds(minhash):
    assert minhash.track_abundance, "track abundance must be set"

    # will return list of (hash, abund) 
    return list(minhash.hashes.items())


KSIZE=31
MOLTYPE='DNA'

db = sourmash.load_file_as_index(sys.argv[1])
db = db.select(ksize=KSIZE, moltype=MOLTYPE)
assert len(db) == 1

sig = list(db.signatures())[0]

print(extract_hashes_and_abunds(sig.minhash))

rough procedure would be:

• build the intersection you're interested in, using sig intersect ... -A <abundances-from> to make sure you're borrowing the abundances from the sketch (usually the reads or the WGS data set), and/or use sig merg to merge your sketches;
• run this script :)