Add per sequence analysis to analyze coverage; generalize analyze coverage and pick test targets to work with PCR

[priyappillai]

Add the following features to analyze_coverage.py:

• Primer terminal mismatches
• Maximum target length
• Autofinding most recent Cas13a model
• Per sequence analysis

Also, allow pick_test_targets.py to work with variable primer/guide lengths

Details

In coverage_analysis.py

• Primer terminal mismatches & bases from terminal as inputs to CoverageAnalyzer
• Evaluating by both mismatches and terminal mismatches
• Saving mismatches by position for evaluating by mismatches
• Generalize activities_where_guide_binds to scores_where_oligo_binds/scores_where_guide_binds
• Allow seqs_where_targets_bind to allow using terminal mismatches to evaluate primers
• Add seqs_where_primers_bind to allow primers to be assessed alone
• Add per_seq_guide and per_seq_primer_mismatches
• Move mean_activity_of_guides to be only in CoverageAnalyzerWithPredictedActivity

In test_coverage_analysis.py

• Tests for primer terminal mismatches
• Tests for per_seq functions
• Tests for score_where_guide_binds
• Tests for highly active

In analyze_coverage.py

• Allow files with only primers to still be analyzed
• Add write_per_seq function and --write-per-seq option
• Separate out the main function into parsing arguments (argv_to_args) and running (run)
• Add --predict-cas13a-activity-model option

Add test_analyze_coverage.py

In guide.py

• Allow variable sequence lengths

In seq_io.py

• Add warning if sequence names are repeated

In test_design.py

• Fix line parsing by removing final new line character

[codecov[bot]]

Codecov Report

Merging #59 (c371c12) into main (a96ce8d) will increase coverage by 1.16%. The diff coverage is 95.08%.

@@            Coverage Diff             @@
##             main      #59      +/-   ##
==========================================
+ Coverage   85.15%   86.31%   +1.16%     
==========================================
  Files          48       50       +2     
  Lines        7599     8171     +572     
==========================================
+ Hits         6471     7053     +582     
+ Misses       1128     1118      -10     

Impacted Files	Coverage Δ
adapt/utils/seq_io.py	32.84% <50.00%> (+0.66%)	:arrow_up:
bin/analyze_coverage.py	93.13% <91.39%> (ø)
bin/tests/test_analyze_coverage.py	93.42% <93.42%> (ø)
adapt/coverage_analysis.py	97.16% <96.72%> (+13.91%)	:arrow_up:
adapt/tests/test_coverage_analysis.py	99.31% <100.00%> (+12.64%)	:arrow_up:
adapt/utils/guide.py	100.00% <100.00%> (ø)
bin/tests/test_design.py	99.51% <100.00%> (ø)
... and 1 more

---

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update a96ce8d...c371c12. Read the comment docs.