diff test-data/consensus_anno_stats.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/consensus_anno_stats.txt	Mon Dec 15 16:43:36 2025 +0000
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+Starting processing for FASTA: test-data/consensus_anno_test.fasta
+=== PARAMETERS USED ===
+input_anno: test-data/consensus_test_header.tabular
+input_unanno: test-data/consensus_anno_test.fasta
+eval_plot: test-data/consensus_eval.png
+taxa_output: test-data/consensus_taxa.txt
+circle_data: test-data/consensus_circle.txt
+header_anno: test-data/consensus_annotations.xlsx
+anno_stats: test-data/consensus_anno_stats.txt
+filtered_fasta: test-data/consensus_filtered_fasta.fasta
+uncertain_threshold: 90.0
+eval_threshold: 1e-10
+use_counts: False
+ignore_rank: unkown
+ignore_taxonomy: environmental
+bitscore_perc_cutoff: 10.0
+min_bitscore: 40
+ignore_obiclean_type: singleton
+ignore_illuminapairend_type: pairend
+min_identity: 70
+min_coverage: 70
+ignore_seqids: 
+min_support: 2
+=== END PARAMETERS ===
+Filtered FASTA written to: test-data/consensus_filtered_fasta.fasta (269 sequences)
+FASTA: total headers: 1937
+FASTA: headers kept after filters and min_support=2: 269
+FASTA: removed due to header filters (illumina/obiclean/etc.): 365
+FASTA: removed due to low dereplicated count (<2): 1303
+FASTA: total invalid (header filter + low support): 1668
+Reading BLAST annotations: test-data/consensus_test_header.tabular
+BLAST: total hits read: 889
+BLAST: hits kept after quality filters: 767
+BLAST: hits filtered (evalue/coverage/identity/bitscore): 122
+BLAST: hits removed due to invalid taxon: 0
+BLAST: hits removed due to ignored seqids: 0
+Note: 37 BLAST q_ids not in FASTA (showing up to 10): ['M01687:460:000000000-LGY9G:1:1101:12578:8821_CONS(1)', 'M01687:460:000000000-LGY9G:1:1102:19139:9563_CONS(1)', 'M01687:460:000000000-LGY9G:1:2114:3286:13205_CONS(1)', 'M01687:460:000000000-LGY9G:1:2115:26033:6510_CONS(1)', 'M01687:460:000000000-LGY9G:1:2115:28971:12582_CONS(1)', 'M01687:460:000000000-LGY9G:1:2115:9332:15134_CONS(1)', 'M01687:460:000000000-LGY9G:1:2112:16849:24934_CONS(1)', 'M01687:460:000000000-LGY9G:1:2113:2910:9568_CONS(2)', 'M01687:460:000000000-LGY9G:1:2113:24519:22653_CONS(1)', 'M01687:460:000000000-LGY9G:1:2108:19954:3938_CONS(1)']
+ANNOTATION: total FASTA headers considered: 269
+ANNOTATION: reads with BLAST hits: 4
+ANNOTATION: reads without BLAST hits: 265
+ANNOTATION: unique annotated count (from header counts): 384
+ANNOTATION: total unique count (from FASTA): 24251
+E-value plot written to: test-data/consensus_eval.png
+Taxa summary written to: test-data/consensus_taxa.txt
+Header annotations written to: test-data/consensus_annotations.xlsx
+Circle diagram JSON written to: test-data/consensus_circle.txt
+=== ANNOTATION STATISTICS ===
+percentage_annotated: 0.20650490449148168
+annotated_sequences: 4
+total_sequences: 1937
+percentage_unique_annotated: 1.5834398581501794
+unique_annotated: 384
+total_unique: 24251
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