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TEagle v3.3.0

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@tunabirgun tunabirgun released this 31 Jul 13:56
· 13 commits to main since this release
v3.3.0
fd92e06

Two scientific additions and a rework of the optional Linux (WSL) backend installer.

Added

  • LTR cis-elements. The polyadenylation-signal motif, counted only when a GU/U-rich downstream element follows it, plus the seven verified non-canonical terminal motifs. Both are advisory and reported with their limits — a motif, never a located cleavage site.
  • Whole-genome transposable-element annotation. RepeatMasker over a genome you have already downloaded, processed in contig chunks so progress is visible, resumable, with the cost stated before the run starts. Transposable elements are counted separately from tandem and non-TE repeats, because merging them overstates TE content.
  • Flanking sequence from any feature — copy it, export FASTA, or design primers on it. Amplifying across an insertion from its flanks is how an insertion is genotyped.
  • A BACKEND button in the window header opens the backend installer from anywhere.
  • A Library choice on panel 03. RepeatMasker searches curated Dfam families unless it is asked for both, so the optional uncurated partitions were unreachable from single-sequence naming — you could download 3.9 GB and get the identical blank result. The setting is sealed into the run's provenance. Measured on yeast Ty1 (M18706): curated-only finds nothing; including uncurated finds an LTR/Copia family.

Fixed

  • The poly(A) downstream-element window was measured from the wrong point (+10–30 instead of +20–60), so it judged the wrong stretch of sequence. Results may differ from 3.2.1 for LTR elements.
  • A false claim about curated Dfam coverage. The app said the curated library holds 9 families for Drosophila melanogaster and lacks copia, gypsy, hobo and mdg1. Measured against famdb: 399 models, and it does contain Copia_I, Copia_LTR, Gypsy_I, Gypsy_LTR, hobo and MDG1_I/LTR. The 9 was the yeast figure attached to the wrong organism.
  • A Dfam download showed no progress — curl draws its meter with carriage returns and no newline, so a 40–60 minute transfer was one unreadable line. Progress is now reported as whole lines every 15 seconds.
  • An interrupted multi-gigabyte download was deleted by the checksum gate, despite the panel promising it resumes.
  • The free space a partition needs was understated by roughly half — the uncurated eukaryote partition unpacks to 22.6 GiB, not the ~14 GB claimed.
  • micromamba could refuse to create its environment permanently if a Dfam partition was installed before the environment existed.
  • The methods panel claimed a 21-model Pfam panel after it had grown to 30.

Performance

Startup import graph 537 ms → 151 ms.

Verification

580 tests. README, manual and report audited claim by claim against the build; all 44 figures re-captured; both PDFs rebuilt and inspected page by page. Eight specimens across six organisms checked against published architecture — 6 of 8 match, both mismatches documented.

TEagle-Setup-3.3.0.exe — SHA256 112e0b9226089fe648a84d610b7ba08d1a7b4b607d9e9fcdff4491f52796c747
Per-user install, no administrator rights. The optional Linux backend installs from inside the app.

Assets 4
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