Mercurial > repos > onnodg > blast_annotations_processor

comparison tests/test_blast_annotations_processor.py @ 3:ca2f07b71581 draft default tip

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planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit 600e5a50a13a3a16a1970d6d4d31cb4f7bd549bf-dirty
author onnodg
date Thu, 12 Feb 2026 13:52:07 +0000
parents 9ca209477dfd
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2:9ca209477dfd 3:ca2f07b71581
48 read4(25) subject4 id4.1 subject4 80.0 85 1e-40 140 database1 Archaea / Euryarchaeota / Methanobacteria / Methanobacteriales / Methanobacteriaceae / Methanobrevibacter / Methanobrevibacter_eclhi 48 read4(25) subject4 id4.1 subject4 80.0 85 1e-40 140 database1 Archaea / Euryarchaeota / Methanobacteria / Methanobacteriales / Methanobacteriaceae / Methanobrevibacter / Methanobrevibacter_eclhi
49 read4(25) subject4 id4 subject4 80.0 85 1e-35 140 database1 Archaea / Euryarchaeota / Methanobacteria / Methanobacteriales / Methanobacteriaceae / Methanobrevibacter / Methanobrevibacter_elchi 49 read4(25) subject4 id4 subject4 80.0 85 1e-35 140 database1 Archaea / Euryarchaeota / Methanobacteria / Methanobacteriales / Methanobacteriaceae / Methanobrevibacter / Methanobrevibacter_elchi
50 read4(25) subject4 id4.2 subject4 90.0 87 1e-50 160 database1 Archaea / Euryarchaeota / Methanobacteria / Methanobacteriales / Methanobacteriaceae / Methanobrevibacter / Methanobrevibacter_smithii 50 read4(25) subject4 id4.2 subject4 90.0 87 1e-50 160 database1 Archaea / Euryarchaeota / Methanobacteria / Methanobacteriales / Methanobacteriaceae / Methanobrevibacter / Methanobrevibacter_smithii
51 """ 51 """
52 52
53 fasta_content = """>read1(100) count=100; 53 fasta_content = """>read1(100) count=100; obiclean_count={'XXX': 100};
54 ATCGATCGATCGATCG 54 ATCGATCGATCGATCG
55 >read2(50) count=50; 55 >read2(50) count=50; obiclean_count={'XXX': 50}
56 GCTAGCTAGCTAGCTA 56 GCTAGCTAGCTAGCTA
57 >read3(25) count=25; 57 >read3(25) count=25; obiclean_count={'XXX': 25}
58 TGACTGACTGACTGAC 58 TGACTGACTGACTGAC
59 >read4(25) count=25; 59 >read4(25) count=25; obiclean_count={'XXX': 25}
60 TGAAAAAAACACCAC 60 TGAAAAAAACACCAC
61 """ 61 """
62 62
63 blast_file = input_dir / "test_blast.tabular" 63 blast_file = input_dir / "test_blast.tabular"
64 fasta_file = input_dir / "test_sequences.fasta" 64 fasta_file = input_dir / "test_sequences.fasta"
257 read1(100) source=NCBI sequenceID=KR738670 superkingdom=Eukaryota kingdom=Viridiplantae phylum=Streptophyta subphylum=Streptophytina class=Magnoliopsida subclass=NA infraclass=NA order=Malvales suborder=NA infraorder=NA superfamily=NA family=Malvaceae genus=Hibiscus species=Hibiscus trionum markercode=trnL lat=0.304 lon=36.87 source=NCBI N/A 100.000 100 7.35e-14 54.7 Viridiplantae / Streptophyta / Magnoliopsida / Malvales / Malvaceae / Hibiscus / Hibiscus trionum 257 read1(100) source=NCBI sequenceID=KR738670 superkingdom=Eukaryota kingdom=Viridiplantae phylum=Streptophyta subphylum=Streptophytina class=Magnoliopsida subclass=NA infraclass=NA order=Malvales suborder=NA infraorder=NA superfamily=NA family=Malvaceae genus=Hibiscus species=Hibiscus trionum markercode=trnL lat=0.304 lon=36.87 source=NCBI N/A 100.000 100 7.35e-14 54.7 Viridiplantae / Streptophyta / Magnoliopsida / Malvales / Malvaceae / Hibiscus / Hibiscus trionum
258 read2.1(50) 1 2 3 4 5 6 7 8 9 258 read2.1(50) 1 2 3 4 5 6 7 8 9
259 read3(25) source=NCBI sequenceID=KR737595 superkingdom=Eukaryota kingdom=Viridiplantae phylum=Streptophyta subphylum=Streptophytina class=Magnoliopsida subclass=NA infraclass=NA order=Malvales suborder=NA infraorder=NA superfamily=NA family=Malvaceae genus=Hibiscus species=Hibiscus trionum markercode=trnL lat=0.304 lon=36.87 source=NCBI N/A 97.561 87 1.68e-14 71.3 Viridiplantae / Streptophyta / Magnoliopsida / Malvales / Malvaceae / Hibiscus / Hibiscus trionum 259 read3(25) source=NCBI sequenceID=KR737595 superkingdom=Eukaryota kingdom=Viridiplantae phylum=Streptophyta subphylum=Streptophytina class=Magnoliopsida subclass=NA infraclass=NA order=Malvales suborder=NA infraorder=NA superfamily=NA family=Malvaceae genus=Hibiscus species=Hibiscus trionum markercode=trnL lat=0.304 lon=36.87 source=NCBI N/A 97.561 87 1.68e-14 71.3 Viridiplantae / Streptophyta / Magnoliopsida / Malvales / Malvaceae / Hibiscus / Hibiscus trionum
260 """ 260 """
261 261
262 fasta_content = """>read1(100) count=100; 262 fasta_content = """>read1(100) count=100; obiclean_count={'XXX': 100};
263 ATCG 263 ATCG
264 >read2(50) merged_sample={}; count=1011; direction=right; seq_b_insertion=0; sminR=40.0; ali_length=53; seq_b_deletion=248; seq_a_deletion=248; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=0; seq_b_single=0; 264 >read2(50) merged_sample={}; count=1011; obiclean_count={'XXX': 1011}; direction=right; seq_b_insertion=0; sminR=40.0; ali_length=53; seq_b_deletion=248; seq_a_deletion=248; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=0; seq_b_single=0;
265 gggcaatcctgagccaagtgactggagttcagataggtgcagagactcaatgg 265 gggcaatcctgagccaagtgactggagttcagataggtgcagagactcaatgg
266 >read3(25) merged_sample={}; count=179; direction=right; sminR=40.0; ali_length=49; seq_b_deletion=252; seq_a_deletion=252; seq_b_insertion=0; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=0; seq_b_single=0; 266 >read3(25) merged_sample={}; count=179; obiclean_count={'XXX': 179}; direction=right; sminR=40.0; ali_length=49; seq_b_deletion=252; seq_a_deletion=252; seq_b_insertion=0; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=0; seq_b_single=0;
267 gggcaatcctgagccaactggagttcagataggtgcagagactcaatgg 267 gggcaatcctgagccaactggagttcagataggtgcagagactcaatgg
268 """ 268 """
269 269
270 blast_file = input_dir / "test_sync.tabular" 270 blast_file = input_dir / "test_sync.tabular"
271 fasta_file = input_dir / "test_sync.fasta" 271 fasta_file = input_dir / "test_sync.fasta"
409 409
410 fasta = input_dir / "combined_filters.fasta" 410 fasta = input_dir / "combined_filters.fasta"
411 blast = input_dir / "combined_filters.tabular" 411 blast = input_dir / "combined_filters.tabular"
412 412
413 fasta.write_text( 413 fasta.write_text(
414 ">lowSupport(1) count=1;\nACGT\n" 414 ">lowSupport(1) obiclean_count={'XXX': 1}; count=1;\nACGT\n"
415 ">obicleanFail(10) count=10; obiclean_status={'XXX': 's'};\nACGT\n" 415 ">obicleanFail(10) count=10; obiclean_count={'XXX': 10}; obiclean_status={'XXX': 's'};\nACGT\n"
416 ">pairendFail_PairEnd(10) count=10;\nACGT\n" 416 ">pairendFail_PairEnd(10) count=10; obiclean_count={'XXX': 10}; \nACGT\n"
417 ">identityFail(10) count=10;\nACGT\n" 417 ">identityFail(10) count=10; obiclean_count={'XXX': 10}; \nACGT\n"
418 ">coverageFail(10) count=10;\nACGT\n" 418 ">coverageFail(10) count=10; obiclean_count={'XXX': 10}; \nACGT\n"
419 ">bitscoreFail(10) count=10;\nACGT\n" 419 ">bitscoreFail(10) count=10; obiclean_count={'XXX': 10}; ACGT\n"
420 ">bscutoffHigh(10) count=10;\nACGT\n" 420 ">bscutoffHigh(10) count=10; obiclean_count={'XXX': 10}; \nACGT\n"
421 ">envTaxFail(10) count=10;\nACGT\n" 421 ">envTaxFail(10) count=10; obiclean_count={'XXX': 10}; \nACGT\n"
422 ">rankFail(10) count=10;\nACGT\n" 422 ">rankFail(10) count=10; obiclean_count={'XXX': 10}; \nACGT\n"
423 ">seqidFail(10) count=10;\nACGT\n" 423 ">seqidFail(10) count=10; obiclean_count={'XXX': 10}; \nACGT\n"
424 ">readOK(10) count=10;\nACGT\n" 424 ">readOK(10) count=10; obiclean_count={'XXX': 10}; \nACGT\n"
425 ">readOK_multiple_id(10) count=10;\nACGT\n" 425 ">readOK_multiple_id(10) count=10; obiclean_count={'XXX': 10}; \nACGT\n"
426 ) 426 )
427 427
428 blast.write_text( 428 blast.write_text(
429 # min_support (count=1 < 5) 429 # min_support (count=1 < 5)
430 "lowSupport(1)\ts\tid1\t123\t99\t99\t1e-50\t200\tsrc\tA / B / C / D / E / F / G\n" 430 "lowSupport(1)\ts\tid1\t123\t99\t99\t1e-50\t200\tsrc\tA / B / C / D / E / F / G\n"
493 args = Args() 493 args = Args()
494 process_single_file(args.input_anno, args.input_unanno, args, log_messages=[]) 494 process_single_file(args.input_anno, args.input_unanno, args, log_messages=[])
495 495
496 with open(args.filtered_fasta) as f: 496 with open(args.filtered_fasta) as f:
497 headers = [l.strip() for l in f if l.startswith(">")] 497 headers = [l.strip() for l in f if l.startswith(">")]
498 assert '>obicleanFail(10) count=10;' not in headers 498 assert ">obicleanFail(10) count=10; obiclean_count={'XXX': 10};" not in headers
499 assert '>pairendFail_PairEnd(10) count=10;' not in headers 499 assert ">pairendFail_PairEnd(10) count=10; obiclean_count={'XXX': 10};" not in headers
500 assert len(headers) == 9, "FASTA filtering only applies to header-based rules" 500 assert len(headers) == 9, "FASTA filtering only applies to header-based rules"
501 501
502 df = pd.read_excel(args.header_anno, sheet_name="Individual_Reads") 502 df = pd.read_excel(args.header_anno, sheet_name="Individual_Reads")
503 seq_ids = { 503 seq_ids = {
504 sid 504 sid