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nx_bio_sequence.nx

buildroot/runtime/_hdl_build/nx_bio_sequence.nx

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docs dependencies structs consts functions

about

nx_bio_sequence.nx -- SOVEREIGN EXACT molecular-biology sequence engine (science-exceed arc, rung BIO-SEQUENCE; lifts the weakest domain). Exact, DETERMINISTIC DNA/RNA/protein transforms -- no float, no cloud, no license: transcribe DNA -> RNA (T -> U) translate RNA -> protein (codon table = knowledge/registry/sci_codon_table.tsv, stop-aware) revcomp DNA -> reverse complement (A<->T, C<->G, reversed) gc_count exact integer G+C count EXCEED vs Mathematica GenomeData/SequenceAlignment (cloud-tethered, proprietary): Nishi does the core transforms sovereign + offline + exact (the universal genetic code is a DATA table, not a service call). Honest scope: not GenomeData's breadth -- the exact deterministic primitives every downstream bio rung builds on (hardware-rung-up). BAKED GATE proves each transform on known sequences + a negative control (unknown codon rejected) before verdict=GREEN. module: nishi-core.science.bio_sequence depends: nishi-core.sys.syscalls capability: EXACT_DETERMINISTIC_BIOSEQUENCE license_tier: ORIGINAL

dependencies 2 imports · 0 importers

imports: nx_syscalls.nxnx_itoa_lib.nx

imported by: nobody (leaf or entry point)

call flow from main pre-order; caps 40 nodes / depth 6 declared; ↻ = already shown

structs

none

consts

23	const BS_MAGIC_16384: i64 = 16384
25	const BS_TABLE: *u8 = "knowledge/registry/sci_codon_table.tsv"
26	const BS_LOG: *u8 = "knowledge/status/bio_sequence.log"

functions

28	func bs_w(fd: i64, s: *u8) -> i64 { var n: i64=0; while s[n]!=(0 as u8){n=n+1} sys_write(fd,s,n); return 0 } called by 1: main calls 1: sys_write
33	func bs_wn(fd: i64, v: i64) -> i64 { nxi_fd(fd, v); return 0 } called by 1: main calls 1: nxi_fd
35	func bs_read(path: u8, buf: u8, cap: i64) -> i64 called by 1: main calls 3: sys_openat_rd sys_read sys_close
45	func bs_field(buf: u8, ls: i64, le: i64, f: i64, dst: u8, cap: i64) -> i64 called by 1: bs_codon_lookup
58	func bs_streq(a: u8, b: u8) -> i64 called by 2: bs_codon_lookup main
66	func bs_transcribe(dna: u8, dlen: i64, out: u8) -> i64 called by 1: main
78	func bs_revcomp(dna: u8, dlen: i64, out: u8) -> i64 called by 1: main
94	func bs_gc_count(seq: *u8, slen: i64) -> i64 called by 1: main
106	func bs_codon_lookup(tbuf: u8, tn: i64, codon: u8, aa: *u8) -> i64 called by 2: bs_translate main calls 3: sys_mmap bs_field bs_streq
126	func bs_translate(rna: u8, rlen: i64, tbuf: u8, tn: i64, out: *u8) -> i64 called by 1: main calls 2: sys_mmap bs_codon_lookup
143	func main() -> i64 calls 13: sys_mmap bs_read bs_w sys_exit bs_transcribe bs_streq+7