openvax / vaxrank / 25176385878

LAST BUILD BRANCH: v3.1.8
DEFAULT BRANCH: master
Ran
Jobs 0
Files 0
Run time –
Badge
Embed ▾
README BADGES
x

If you need to use a raster PNG badge, change the '.svg' to '.png' in the link

Markdown

Textile

RDoc

HTML

Rst
25176385878

push

github

web-flow 
mRNA: polyA tail + structured manifest + three FASTAs + CSV (closes #252) (#253)

* mRNA: polyA tail + structured manifest + three-FASTA / CSV outputs (closes #252)

Outputs reorganized: --output-mrna is now a *directory*. Three FASTAs
land in it — cds.fasta (start codon → stop codon), no_polyA.fasta
(5' UTR + CDS + 3' UTR), full.fasta (no_polyA + polyA tail).

PolyA tail
----------
RNAConstructConfig gains four fields:
  poly_a_length: int = 120        # BNT122 / Sahin 2017 default
  poly_a_segmented: bool = False  # BNT162b2 architecture (Xia 2021)
  poly_a_first_segment: int = 30
  poly_a_segment_linker: str = "GCATATGACT"

Segmented mode emits A_first + linker + A_rest, where the linker's
bases don't count toward poly_a_length (mirrors Xia's description of
A30 + GCAUAUGACU + A70 = 100 A's split by a 10-nt linker).

Structured manifest
-------------------
RNAConstruct now carries cds_aa, cds_nt, no_polya_nt, full_nt,
poly_a_nt, antigens (per-antigen aa+nt), and elements (per-layer
aa+nt for signal peptide / linkers / MITD; nt only for UTRs / polyA).
``sequence`` is preserved as full_nt for back-compat with callers.
The 2.12 components dict stays in the manifest under 'components'
for back-compat with downstream readers.

CSV export
----------
New --output-mrna-csv flag writes a long-format CSV: one row per
(construct, element) with columns construct / element_kind / index /
name / aa / nt / length_aa / length_nt / note. Lets the user open
a vaccine in a spreadsheet and inspect every layer side by side.

CLI flags
---------
  --output-mrna OUT_DIR              # was a single FASTA path
  --output-mrna-csv FILE.csv         # new
  --mrna-poly-a-length N             # default 120
  --mrna-poly-a-segmented            # toggle BNT162b2 architecture
  --mrna-poly-a-first-segment N      # default 30
  --mrna-poly-a-segment-linker SEQ   # default GCATATGACT

Tests (+9)
----------
- build_poly_a default 120 / zero / segmented BNT162b2 / negative-raises
- fu... (continued)
Source Files on build 25176385878
Detailed source file information is not available for this build.