Question: Migrating from Khmer

[dcdanko]

Hi,

My team is currently using Khmer and we want to upgrade to Oxli. We currently use khmer's Nodetable to store binary present/not-present kmer sets. We have a few large precomputed nodetables.

My questions:

• Do we need to recreate the large files or can we use them as is?
• What is the corresponding class in Oxli to khmer's nodetable?

Thank you for your help!

[Adamtaranto]

Hi David,

Atm there are three ways to manually set the counts in a KmerCountTable object.

1. Populate KmerCountTable from json file.

Oxli supports serialisation of KmerCountTable objects into json format, you can modify this file and load it back into a new object. See wiki description.

2) Set individual kmer values using dictionary syntax.

from oxli import KmerCountTable

# Create new count table
kct = KmerCountTable(ksize=4) # Note: Use "store_kmers=True" only if you need to retrieve a list of all kmers in table. This option slows counting.

# Manually add new kmer and set count
kct['GGGG'] = 1000

# Only canonical kmer is stored
kct.get('GGGG')
>>> 1000

kct.get('CCCC')
>> 1000

3) Add counts with user specified hash.

This might be useful if you only have hashes for canonical kmers stored.

# Add and increment count for hash
kct.count_hash(6779379503393060785)

kct.get("AACC")
>>> 1

kct.get("GGTT")
>>> 1

# Increment count
kct.count_hash(6779379503393060785)

kct.get("AACC")
>>> 2

I could add support for bulk kmer + count upload from a tab delimited file if that would be useful. See #77.

Do you need to store kmers and their reverse complement separately? Oxli currently stores counts under the canonical kmer.

[Adamtaranto]

@ctb might be worth adding a khmer migration tutorial to the wiki.

lmk what you think is the most efficient way to do this.