perf: use estimated counts instead of TPM

[balajtimate]

Description

• Use 'estimated counts' of transcript abundance from Kallisto (instead of TPM) for library source inference
• Update transcripts.fasta.gz to include additional organisms and transcripts from orthologues, which were previously removed (now it includes transcripts from 387 organisms)
• Repetitive sequences in transcripts have been masked using RepeatMasker

Type of change

• New feature (non-breaking change which adds functionality)

Checklist

Please carefully read these items and tick them off if the statements are true
or do not apply.

• I have performed a self-review of my own code
• My code follows the existing coding style, lints and generates no new
  warnings
• I have added type annotations to all function/method signatures, and I
  have added type annotations for any local variables that are non-trivial,
  potentially ambiguous or might otherwise benefit from explicit typing.
• I have commented my code in hard-to-understand areas
• I have added ["Google-style docstrings"] to all new modules, classes,
  methods/functions or updated previously existing ones
• I have added tests that prove my fix is effective or that my feature
  works
• New and existing unit tests pass locally with my changes and I have not
  reduced the code coverage relative to the previous state
• I have updated any sections of the app's documentation that are affected
  by the proposed changes

If for some reason you are unable to tick off all boxes, please leave a
comment explaining the issue you are facing so that we can work on it
together.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 100.00%. Comparing base (a081c35) to head (a536351).

Additional details and impacted files

@@            Coverage Diff            @@
##               dev      #170   +/-   ##
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  Coverage   100.00%   100.00%           
=========================================
  Files           13        13           
  Lines         1164      1164           
=========================================
  Hits          1164      1164           

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[uniqueg]

I'm not sure it is accurate to speak of "expression" when we use counts. Perhaps best to refer to "total estimated counts".