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… c-i, no call) Runs hmmsearch --cut_ga with the M1/M2 models of the lectin spec against Pfam, writes per-proteome per-model counts, a hit table and the report text. The (a2) group section appears only when signal peptide data are given. No call, no status file. Includes an optional sbatch wrapper (not submitted), a comparison script against review2/whole_proteome_hits.tsv and a stub-based pytest test. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
…ASTP check; name list and duplicate-ID warning Extracts the six F27 proteins from the source proteomes (exactly 6 verified), runs SignalP 6 (fast, eukarya) on them, and checks identity to FleA (Q4WW81) by BLASTP. The report script gets --name-list, a SignalP 6 tab-format fix, a warning for IDs in two proteomes, and the F27 and Kerr 2016 notes in the (a2) section. No call, no status. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
…nput, endemic note, duplicate and empty FASTA handling, README) Strict read_signalp (two formats, CRLF stripped, error otherwise). ENDEMIC_NOTE follows the L3b result. Repeated IDs inside one proteome are counted once and warned. An empty FASTA gives 0 proteins and a warning. --name-list accepts a bare accession. Adds README.md. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
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Script for option (c-i) of the lectin class spec (PR #78). It makes a report only. It makes no call and writes no status file. No change to src/, family_table.tsv or categories.yaml.
analysis/lectin_class_report/lectin_report.py: runshmmsearch --cut_ga(Pfam 38.2) with the 15 M1/M2 models of spec 3.1; writes counts, a hit table and a markdown report. PF07938 hits carry the D7 family label only. Report text states a hit does not show surface location, secretion or host-glycan binding. M3 house-keeping models are listed, not scanned.--signalp FILEand--name-list FILEproduce the (a2) section naming the six pool S Onygenales PF07938 proteins (f27_six/). SignalP 6.0h (fast, eukarya, one run): all six have a signal peptide. BLASTP of the six vs FleA Q4WW81: 38.4 to 44.7% identity. This is a check, not an orthology claim.domain_ge_gaandn_hit_domain_ge_gagive the domain-GA rule used by the tool's Pfam module (owner decision).Validation (login node, HMMER 3.4): 25-proteome sample matches
review2/whole_proteome_hits.tsv(PF07938: 36 proteins, 14 proteomes, max score difference 0.0); six Phase C proteomes match F23 in 78 of 78 cells (using the domain column).Not checked: all 653 proteomes; the SLURM wrapper (not submitted); H and U values in the "not called" table are copied by hand from the spec; the six proteins' orthology and function.
Do not merge: needs owner review.
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