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[EXP] add an Index class that loads directly from a screed-loadable file #1783

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[EXP] add an Index class that loads directly from a screed-loadable file #1783

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@ctb ctb commented Jan 6, 2022 •
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This class makes the following command work:

sourmash search podar-ref/1.fa.sig podar-ref/?.fa

by wrapping FASTA/FASTQ files in an Index subclass that generates the "right" MinHash sketches dynamically.

Proof of concept/thought experiment for now. Relevant to #1647, although it does the dirty work via Index rather than via a SourmashSignature.

Options I considered and may try --

  • can implement as a container (e.g. a zip container or whatever) that tracks selects and builds compatible MinHash when needed - WHAT I DID
  • can provide an individual Signature-style wrapper that overloads .minhash
  • can provide load_signature???
  • can subclass MinHash to be a sequence-containing-class that dynamically produces a MinHash from a sequence

other thoughts for this PR

should probably add options for (a) multiple fasta files/one signature per, (b) overriding name.

this could connect to sketch lists, too.

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codecov bot commented Jan 6, 2022 •
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Codecov Report

Merging #1783 (8a36bc5) into latest (73aeb15) will increase coverage by 6.19%.
The diff coverage is 33.84%.

Impacted file tree graph

@@            Coverage Diff             @@
##           latest    #1783      +/-   ##
==========================================
+ Coverage   83.44%   89.64%   +6.19%     
==========================================
  Files         113       88      -25     
  Lines       12145     8504    -3641     
  Branches     1614     1627      +13     
==========================================
- Hits        10134     7623    -2511     
+ Misses       1752      620    -1132     
- Partials      259      261       +2
Flag Coverage Δ
python 89.64% <33.84%> (-0.47%) ⬇️
rust ?

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
src/sourmash/screed_index.py 25.86% <25.86%> (ø)
src/sourmash/sourmash_args.py 92.21% <100.00%> (-0.49%) ⬇️
src/core/src/index/storage.rs
src/core/src/sketch/nodegraph.rs
src/core/src/sketch/hyperloglog/mod.rs
src/core/src/encodings.rs
src/core/src/sketch/hyperloglog/estimators.rs
src/core/src/lib.rs
src/core/src/errors.rs
... and 19 more

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