How oohs/tigrfinder works
TIGRFinder is a command-line analyzer for detecting and annotating dual-repeat and stem-loop TIGR arrays in FASTA sequences. Its main workflow loads records, runs either or both architecture-specific detectors (optionally in worker processes), then writes CSV and GFF3 results and a run log. The README recommends preparing Tas-neighborhood sequences upstream; HMMER is not invoked by this tool. Detector internals are only partially sampled, so the graph shows documented stages and directly evidenced orchestration and output relationships, omitting uncertain internal wiring.
Main entry points: main.py CLI orchestration · stem_loop.py Contig filters · dual_repeat.py Dual-repeat detector · tasprofile.hmm Tas HMM profile
Components 17
Input workflow
- Tas candidates
- Tas HMM profile
tasprofile.hmm - Tas loci FASTA
Array detection
- CLI orchestration
tigrfinder/main.py - FASTA loading
tigrfinder/main.py - Record dispatch
tigrfinder/main.py - Dual-repeat detector
tigrfinder/dual_repeat.py - Stem-loop detector
tigrfinder/stem_loop.py - Contig filters
tigrfinder/stem_loop.py
Results and reporting
- Dual-repeat rows
tigrfinder/dual_repeat.py - Stem-loop rows
tigrfinder/stem_loop.py - CSV annotations
tigrfinder/main.py - GFF3 annotations
tigrfinder/main.py - Run log
tigrfinder/main.py - Known annotations
TIGR_ANNOTATIONS_FULL
Other components
- User
- TIGRSafari
Connections 23
- User → Tas candidates: identifies
- Tas HMM profile → Tas candidates: screens
- Tas candidates → Tas loci FASTA: guides extraction
- User → Tas loci FASTA: prepares
- Tas loci FASTA → CLI orchestration: supplies FASTA
- User → CLI orchestration: runs
- CLI orchestration → FASTA loading: parses
- FASTA loading → Record dispatch: provides records
- Record dispatch → Dual-repeat detector: dispatches mode
- Record dispatch → Stem-loop detector: dispatches mode
- Dual-repeat detector → Dual-repeat rows: returns rows
- Stem-loop detector → Stem-loop rows: returns rows
- CLI orchestration → Contig filters: filters rows
- Stem-loop rows → Contig filters: supplies rows
- Dual-repeat rows → CLI orchestration: returns results
- Contig filters → CLI orchestration: returns filtered rows
- CLI orchestration → CSV annotations: writes CSV
- CLI orchestration → GFF3 annotations: writes GFF3
- CLI orchestration → Run log: writes log
- User → CSV annotations: inspects
- User → GFF3 annotations: inspects
- User → Run log: inspects
- Known annotations → TIGRSafari: browses collection