[ENH] Add sequence_statistics utility for RNA/DNA sequence analysis#579
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Vaishnav88sk wants to merge 1 commit into
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[ENH] Add sequence_statistics utility for RNA/DNA sequence analysis#579Vaishnav88sk wants to merge 1 commit into
Vaishnav88sk wants to merge 1 commit into
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Add gc_content(), nucleotide_composition(), and sequence_summary() utility functions for aptamer sequence profiling and screening. These functions provide essential metrics (GC content, nucleotide breakdown, batch statistics) that researchers need during aptamer design workflows.
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Add gc_content(), nucleotide_composition(), and sequence_summary() utility functions for aptamer sequence profiling and screening.
These functions provide essential metrics (GC content, nucleotide breakdown, batch statistics) that researchers need during aptamer design workflows.
Reference Issues/PRs
Fixes #576
What does this implement/fix? Explain your changes.
Adds a new
pyaptamer/utils/_sequence_stats.pymodule with three utility functions for aptamer sequence profiling:gc_content(sequence)— Computes GC content as a float (0.0–1.0). Case-insensitive, supports both DNA (ACGT) and RNA (ACGU).nucleotide_composition(sequence)— Returns a dict with per-nucleotide counts and frequencies. Unknown characters grouped under"other".sequence_summary(sequences)— Batch analysis returning apd.DataFramewith columns: sequence, length, gc_content, A, C, G, T, U.All three are exported from
pyaptamer.utils:What should a reviewer concentrate their feedback on?
Did you add any tests for the change?
Yes - pyaptamer/utils/tests/test_sequence_stats.py with 15 tests covering:
Any other comments?
PR checklist
pre-commit install.To run hooks independent of commit, execute
pre-commit run --all-files