diff test-data/test_curated_nov_anno_out.txt @ 2:9ca209477dfd draft default tip

planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 4017d38cf327c48a6252e488ba792527dae97a70-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_curated_nov_anno_out.txt	Mon Dec 15 16:43:36 2025 +0000
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+Starting processing for FASTA: test-data/test_curated_nov.fasta
+=== PARAMETERS USED ===
+input_anno: test-data/test_curated_nov_blast_headers.tabular
+input_unanno: test-data/test_curated_nov.fasta
+eval_plot: test-data/test_curated_nov_eval.png
+taxa_output: test-data/test_curated_nov_taxa_output.txt
+circle_data: test-data/test_curated_nov_circle_data.txt
+header_anno: test-data/test_curated_nov_header_anno_excel.xlsx
+anno_stats: test-data/test_curated_nov_anno_out.txt
+filtered_fasta: test-data/test_curated_nov_filtered.fasta
+uncertain_threshold: 0.9
+eval_threshold: 1e-10
+use_counts: True
+ignore_rank: unknown
+ignore_taxonomy: environmental
+bitscore_perc_cutoff: 8.0
+min_bitscore: 100
+ignore_obiclean_type: singleton
+ignore_illuminapairend_type: pairend
+min_identity: 80
+min_coverage: 70
+ignore_seqids: 
+min_support: 1
+=== END PARAMETERS ===
+Filtered FASTA written to: test-data/test_curated_nov_filtered.fasta (1790 sequences)
+FASTA: total headers: 2156
+FASTA: headers kept after filters and min_support=1: 1790
+FASTA: removed due to header filters (illumina/obiclean/etc.): 366
+FASTA: removed due to low dereplicated count (<1): 0
+FASTA: total invalid (header filter + low support): 366
+Reading BLAST annotations: test-data/test_curated_nov_blast_headers.tabular
+BLAST: total hits read: 4977
+BLAST: hits kept after quality filters: 3145
+BLAST: hits filtered (evalue/coverage/identity/bitscore): 1832
+BLAST: hits removed due to invalid taxon: 0
+BLAST: hits removed due to ignored seqids: 0
+Note: 30 BLAST q_ids not in FASTA (showing up to 10): ['M01687:460:000000000-LGY9G:1:1101:11918:3518_CONS(1)', 'M01687:460:000000000-LGY9G:1:1101:12996:3690_CONS(1)', 'M01687:460:000000000-LGY9G:1:1101:11564:11468_CONS(1)', 'M01687:460:000000000-LGY9G:1:1102:19358:5472_CONS(1)', 'M01687:460:000000000-LGY9G:1:2114:4805:4734_CONS(1)', 'M01687:460:000000000-LGY9G:1:2114:7472:19038_CONS(1)', 'M01687:460:000000000-LGY9G:1:2112:26865:11154_CONS(1)', 'M01687:460:000000000-LGY9G:1:2113:29518:11119_CONS(1)', 'M01687:460:000000000-LGY9G:1:2113:14681:23251_CONS(1)', 'M01687:460:000000000-LGY9G:1:2110:17890:1754_CONS(2)']
+ANNOTATION: total FASTA headers considered: 1790
+ANNOTATION: reads with BLAST hits: 622
+ANNOTATION: reads without BLAST hits: 1168
+ANNOTATION: unique annotated count (from header counts): 49571
+ANNOTATION: total unique count (from FASTA): 66132
+E-value plot written to: test-data/test_curated_nov_eval.png
+Taxa summary written to: test-data/test_curated_nov_taxa_output.txt
+Header annotations written to: test-data/test_curated_nov_header_anno_excel.xlsx
+Circle diagram JSON written to: test-data/test_curated_nov_circle_data.txt
+=== ANNOTATION STATISTICS ===
+percentage_annotated: 28.84972170686456
+annotated_sequences: 622
+total_sequences: 2156
+percentage_unique_annotated: 74.95766043670235
+unique_annotated: 49571
+total_unique: 66132
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