| Previous changeset 1:6838c2fd1228 (2024-05-18) Next changeset 3:40fb54cc6628 (2024-09-08) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit ab5e1189217b6ed5f1c5d7c5ff6b79b6a4c18cff |
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modified:
blast2tsv.py rps2tsv.py test-data/blast2tsv_contigs.fa test-data/blast2tsv_contigs.txt test-data/blast2tsv_input.xml test-data/blast2tsv_output.tab test-data/blast2tsv_output_with_rn.tab test-data/blast2tsv_read_nb.tab test-data/blast2tsv_reads.txt test-data/blast2tsv_reads_with_rn.txt test-data/rps_test.tab test-data/rps_test.xml virAnnot_otu.xml |
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| diff -r 6838c2fd1228 -r 735a21808348 blast2tsv.py --- a/blast2tsv.py Sat May 18 18:14:42 2024 +0000 +++ b/blast2tsv.py Wed Aug 21 13:13:50 2024 +0000 |
| [ |
| @@ -28,11 +28,19 @@ def _guess_database(accession): """Guess the correct database for querying based off the format of the accession""" - database_mappings_refseq = {'AC_': 'nuccore', 'NC_': 'nuccore', 'NG_': 'nuccore', - 'NT_': 'nuccore', 'NW_': 'nuccore', 'NZ_': 'nuccore', - 'AP_': 'protein', 'NP_': 'protein', 'YP_': 'protein', - 'XP_': 'protein', 'WP_': 'protein'} - return database_mappings_refseq[accession[0:3]] + if accession.isdigit(): + db = 'taxonomy' + else: + database_mappings_refseq = {'AC': 'nuccore', 'NC': 'nuccore', 'NG': 'nuccore', + 'NT': 'nuccore', 'NW': 'nuccore', 'NZ': 'nuccore', + 'AP': 'protein', 'NP': 'protein', 'YP': 'protein', + 'XP': 'protein', 'WP': 'protein', 'OX': 'nuccore'} + try: + db = database_mappings_refseq[accession[0:2]] + except KeyError: + db = 'nuccore' + log.warning("DB not found for " + accession + ". Set to nuccore.") + return db def _read_xml(options): @@ -69,7 +77,7 @@ elif hit_count > 1: final_hit_count = hit_count - 1 hsp["evalue"] = cumul_hit_evalue / final_hit_count # The smaller the E-value, the better the match - hsp["query_id"] = blast_record.query_id + hsp["query_id"] = blast_record.query # or query_id hsp["query_length"] = blast_record.query_length # length of the query hsp["accession"] = aln.accession.replace("ref|", "") hsp["description"] = aln.hit_def @@ -101,7 +109,12 @@ hsp["tax_id"] = "" hsp["taxonomy"] = "" hsp["organism"] = "" - log.warning("RuntimeError - Taxid not found for " + hsp["accession"]) + log.warning(f"RuntimeError - Taxid not found for {hsp['accession']}") + except Exception as err: + hsp["tax_id"] = "" + hsp["taxonomy"] = "" + hsp["organism"] = "" + log.warning(f"Taxid not found for {hsp['accession']}. The error is {err}") if hsp["evalue"] <= options.max_evalue and hsp["queryOverlap"] >= options.min_qov and \ hsp["hitOverlap"] >= options.min_hov and hsp["score"] >= options.min_score: xml_results[hsp["query_id"]] = hsp |
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| diff -r 6838c2fd1228 -r 735a21808348 rps2tsv.py --- a/rps2tsv.py Sat May 18 18:14:42 2024 +0000 +++ b/rps2tsv.py Wed Aug 21 13:13:50 2024 +0000 |
| [ |
| @@ -56,7 +56,7 @@ hsp["accession"] = aln.accession hsp["pfam_id"] = hsp["description"].split(",")[0].replace("pfam", "PF") log.info("Requeting Interpro for " + hsp["pfam_id"]) - url = "https://www.ebi.ac.uk/interpro/api/entry/pfam/" + hsp["pfam_id"] + "/taxonomy/uniprot/" + url = "https://www.ebi.ac.uk/interpro/api/taxonomy/uniprot/entry/pfam/" + hsp["pfam_id"] req = request.Request(url) try: response = request.urlopen(req) @@ -69,13 +69,20 @@ decoded_response = encoded_response.decode() payload = json.loads(decoded_response) kingdoms = [] - for item in payload["taxonomy_subset"]: - lineage_string = item["lineage"] - lineage = [int(i) for i in lineage_string] - translation = ncbi.get_taxid_translator(lineage) - names = list(translation.values()) - taxonomy = names[1:] # remove 'root' at the begining - kingdoms.append(taxonomy[0]) + for item in payload["results"][:6]: + if item["metadata"]["parent"] is not None: + lineage_parent = item["metadata"]["parent"] + translation = ncbi.get_taxid_translator([int(lineage_parent)]) + names = list(translation.values()) + if len(names) > 0: + if names[0] == "root": + taxonomy = names[1:] # remove 'root' at the begining + else: + taxonomy = names + else: + taxonomy = names + if len(taxonomy) != 0: + kingdoms.append(taxonomy[0]) frequency = {kingdom: kingdoms.count(kingdom) for kingdom in kingdoms} # {'Pseudomonadota': 9, 'cellular organisms': 4} sorted_freq = dict(sorted(frequency.items(), key=lambda x: x[1], reverse=True)) concat_freq = ";".join("{}({})".format(k, v) for k, v in sorted_freq.items()) |
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| diff -r 6838c2fd1228 -r 735a21808348 test-data/blast2tsv_contigs.fa --- a/test-data/blast2tsv_contigs.fa Sat May 18 18:14:42 2024 +0000 +++ b/test-data/blast2tsv_contigs.fa Wed Aug 21 13:13:50 2024 +0000 |
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| b'@@ -1,16 +1,373 @@\n->ds2020-482-EDGG-1-Q4_42600\n-TCGGTGGGGGGACCTTGCGGACATGGGCGGCGGACCGTAAGATGTATAGAGGTGGGGGTA\n-GTAGTTTTGATGCCCTTTTGCTTTTGTGCCAAGCCA\n->ds2020-482-EDGG-1-Q4_107243\n-TATATCTGTGCTTTGGAACACAATGATTCTCAAAGTCTATGTCGAGACTGGAAACTCTCT\n->ds2020-482-EDGG-1-Q4_2681\n-CCTTCCTAGCGACCACGCACACGTCAAGACCGGCATCATCAATGTCGCGACAATCGTGAA\n-CCACTTTAGTATAGTCCACATCAAGATCATCATAAGGTAGATAAAAGGAATCAATTTCCC\n-TAGGAAAAAGTCCAGAATCATCTTCCTCATAAAAATCTGGTATCGAGGGATCAATGGTTC\n-GCACCACCATCTCGAATGTATCAAAGATCGTCGCGAAATCAAACTTTGCGGTATGCTTAA\n-CGACAAACTCGAAAAGGAAAAGTTTTACCCATTCGTCGTAGTTGTCATCTTTATGCACAC\n-CGAACGTCGAGAAAAACCCAAAGAACGTGTGCGTGGTCGCTAGGAAGG\n->ds2020-482-EDGG-1-Q4_107857\n-TCAAGATTGTCGAAAGTGCCACACAGATATTGGTTGCAGCTGTGATTACTGCAATTGGC\n->ds2020-482-EDGG-1-Q4_63163\n-AAGTTCATGGACTTCATCCGAGGAGTTGCCGTCATTGGGGAAGGGCAGTGGGGGATTGAG\n\\ No newline at end of file\n+>NODE_1_length_506_cov_10.687361\n+CTAACCTGTGTTGGGTGTGTTTGGTGTCTTGGGTCGGCATTAGCAACTAAATCAAAAGGC\n+ATAAACCTTGTGAGTTGATGATTGGCAGGAATGTTGACCGGCGTTTCCGGAGCAGATGTC\n+GCAGCGTAAATTACGTCGCGAGGAGCATGGGTAGCAGTAGCAGCAGCAGCGGGGCGTTGG\n+AGAAAGCAAATGTCTTGAGCACGGGCTTCGTCAGTAACGAAGTTGAGGTGGGTAAAGGCA\n+GCATAAAGGTTGGCTTTATTCGTTTCACGACCGGCAATCCATGTAGGAAGGGCGTAGGTT\n+GAATAACCATGCTTTATGATCGCAGAACCAGAGGGATTTTCAATCAGCTGGAACAGAGTC\n+ATGGTGGGGTTCGTAACGTCATTAGCAATAGCAGTGACGGCTTGAAGAACAACTTTAATT\n+TCACGTAGGTTGCCAGGAGTAGCAGCAAACAACATGTCATAGGCGTTCACATGATTTGTA\n+GCGAAGATAGGAGGCTGTAGTGACAG\n+>NODE_2_length_429_cov_3.631016\n+GTCTAACCTGTGTTGGGTGTGTTTGGTTAGTTGGCTGGAATTCATGCACCGTTGACACGG\n+GTTGCTTAACATCTTGCCTCATCCTAGTTTTGGCTGCTTGGTAGAACGTCAAAACAACAT\n+CCACCTTCTGCTTGGCTGCTATACTCTTGATGCTCTCTGGTTCGTACCTGTCCATATCCA\n+CTAATATTACATCGGTATTGTAGTCACACTTGCTGGTAATGTTAACCCCCAATTGTGATA\n+ACACCGCACATATTGAATGACCGTACCTGTAGGTCGTGGTCAACACCTCACGATTGTGCA\n+CCAAATCCAACACATTACTCAGCACCCTCTCACCGTGGGCTGGGCTTGTGTCTATGCTTC\n+CTACCTGATCCATGTCACCATAACATATTACATTTTTAAATGCCCAAACACACCCAACAC\n+AGGTTAGAC\n+>NODE_3_length_365_cov_1.074194\n+GTCTAACCTGTGTTGGGTGTGTTTGGTGGTCCGTTGAGCTAGATTGGAAGAAATTTGATA\n+GGGAGAGGCCAGCTGAGGACATTTCTTTCTGCATTGATGTATTTCTTTCATGTTTTGAGC\n+CGCGGTCTGAAAGGGAGACAAGACTTTTGAGGGCATATGGCATTTGTATGAGAAGAGCAC\n+TCGTGGAACGCCTGTTCGTGACGGATACGGGTTGCGTATTCGGTATCGACGGGATGGTTC\n+CAAGTGGCTCTCTATGGACTGGCTTCCTTGATACCGCGCTCAATATTCTATATATTTCTG\n+ATGTTCTTTTGGATATGGGTTTCTACCCCCCCCTGGCTTCCAAACACACCCAACACAGGT\n+TAGAC\n+>NODE_4_length_351_cov_1.547297\n+GTCTAACCTGTGTTGGGTGTGTTTGGTTTCTAGGTGAATGATGTCAACAAGCGCCCTGGA\n+CCGTCTGCTCATGCTGCCTCATGGAAAGAAGTTTCCTGGAAAACTAGCTTTGTATCCTTC\n+CTACAAAGTCTGCCTGTTCCTGAATTTCTTGTACCGATACTTAAACAGTTCAGTCACTTT\n+ACTACTGATCGAACTAAGAACGTATTCTTTATTCCATCTGCCGCTGGCTATGACCATAAC\n+ATCTTCTTTGGTCGCGTATTTCCTTTGAACATGTTTGCTGCCATTCATGATTGCACCGCT\n+ACACTGCCAAGCAATTCCTCAGAAGTTCCAAACACACCCAACACAGGTTAG\n+>NODE_5_length_344_cov_3.273356\n+CTAACCTGTGTTGGGTGTGTTTGGGCTGGGGGCGACCAACAAAACGGTTATTTCCTCTCA\n+CAATGTTGCTTGAGTTTGTTGTGATGTGTGATTGATTTTGCGCTCATTCATGGACATGTT\n+CTCCTATTTCTAATTAAGATTATCTCATGTAGTTTCCAGTCGTTATGAATCTCTTGTGGT\n+ATACTAACGGTCTTTGTATCATTTTTAATAGTTCACTTATGTTTTGATTTAACTCAAATT\n+CATTTATGTCATATTTTAGCTGAGTTGCATGTTTGCAACTCAGTACATCGTACCATGATC\n+TTAAATCTAGCTCCGTACCCAAACACACCCAACACAGGTTAGAC\n+>NODE_6_length_338_cov_1.314488\n+GTCTAACCTGTGTTGGGTGTGTTTGGGTATCCTTGAGGCTCTCGGATTCCGTGTCACGAA\n+CAAGTACTTCATCAAAGTTCTTGGCGATGACGTAATCTTCGGAATTTTAAAGCACATACC\n+CATTTCGAAATGGGCTGACTTTTTGCAAGACTTCTCTACTGAAGCTAAGCGCCGATTCAA\n+CGCTAAACTGAACCCCAATAAATGTGGCGCATCTGCAGGAATTCACGGTGCCCAAGTACT\n+AAGCTACTTCAACTGGAACGGATTTCCCAAGCGCGAAACCACCCAATTGTTAGCACAACT\n+ACTACACCGTACCCAAACACACCCAACACAGGTTAGAC\n+>NODE_7_length_335_cov_1.714286\n+GTCTAACCCGTGTTGGGTGTGTTTGGTGCCATCATGATTGCACCGCTACACTGCCAAGCA\n+ATTCCTCCAGAATTCCAGTACTTCAAGACCTGTTCGCCCGCGTCCTGTATTCGATTACTG\n+CTCCCGCTTTTACCTGCCTGATCCCCGATTTACTCGGTGCCTCCATTGATCAGACAACTA\n+CTACGCATGTTAACTATATCAACTCCAAGTTGTTCCAAATATTTAACGCTGTTTTCAACC\n+CAGTCCTGTTTCGTGACTATCAACGCCGCTCGTCTCTTGCTGCTCTGTCACTACAGCCTC\n+CCGCCAATCCCAAACACACCCAACACAGGTTAGAC\n+>NODE_8_length_331_cov_0.862319\n+GTCTAACCTGTGTTGGGTGTGTTTGGGATTGGAGTGAAGAAAAATTAGAGATGAGAAATG\n+ATAATAACGAAGAATGTGGCCCTTTCGTAGGAGCAGTAACCCCACCACGTGAGGAAGATT\n+TAACGAA'..b'AAATTTAAGTTTTTCCATGGTCTTTAGCTCATCACTTACATAACTTGACACAGCTATAT\n+AACTCCTGTTAGCATGTCCTCTCATCCATTGACTTAATTCATCTTTT\n+>NODE_50_length_226_cov_2.269006\n+GTCAACGGTGTGTTGGGTGTGTTTGGGAAAGGTCCTGGAATATGGGTGTCCGATCCTTAT\n+GGACTAACCGGAACAGTGCAACCTGTAAATCCGGCGTGGGGCGTGGAAGGTTTTGATCCT\n+TTTGTCCCGGGAGGAATAGCTTCTCATCATATTGCAGCAGGTACATTGGGCATATTAGCG\n+GGCCTATTCCATCTTAGCGTACGGTCACCCCAGCCAAACACACCCA\n+>NODE_51_length_225_cov_1.117647\n+GTCTAACCTGTGTTGGGTGTGTTTGGTCGATCTGGCCGTTGTTAAGTATTTGCTCACGAT\n+GTGCTTCAACCTTTGCTCGCCAAATTCTATAACATAAGTGGGTTGTCCATACTGTATCGT\n+CAATCTTTTGACTTTGTTCCTTTCCATTATTTCTTGCGCTAATTCATTTGAAAAACTAAA\n+CCCAACGGCCACCCATTTGCTTCGACCAAACACACCCAACACAGG\n+>NODE_52_length_225_cov_0.917647\n+GTCTAACCTGTGTTGGGTGTGTTTGGTTCCCTAGTGAGGCTGGTTTTCCCATGGTGTGAG\n+AATAGCCGCTATTAACTTGATTACGCATCTCTGGTTCAACCCATTCCCCGCTAACATTCA\n+CTTGGTCATGCGCGTAAGGACTATCGCTCGCGCTGAAACTTGGACCAGGTTGACCATCGT\n+CTTCAATCTCATCACACTACCAAACACACCCAACACAGGTTAGAC\n+>NODE_53_length_223_cov_3.303571\n+TCTAACCTGTGTTGGGTGTGTTTGGTTCTCATGTCAATTTGTAATGTGTGGGCTCATCCC\n+TTATTGGTATGTCATGGGTTTTCCACTTGGCACTGCTGGTCGGCAAATCTTTCCAAATCT\n+CGCCACATATTTGTATATCTTGATCTTGCATGAATCTGCGCCCAAAGTAGTTAGGGATAC\n+TTTGAGTTTTGAGCCGCATGCTATTAGCAATCATGGTTATTTC\n+>NODE_54_length_223_cov_1.803571\n+GTCTAACCTGTGTTGGGTGTGTTTGGTCGATTAATGGGAGTTCAACCAAATTCATAACTG\n+TCTCGATGTCATCCTTTCCTTCCTTTTTATTTTGATTGTCTAAATATTCAGCTAAGACCA\n+TTCCAACGCCCCCTTTCGCCATGCATAAACTGAACCCACAATTGGGATAAGCACGAAAAT\n+GAAAGCCTCACGTTCACCCAAACACACCCAACACAGGTTAGAC\n+>NODE_55_length_216_cov_1.596273\n+GTTTTACCATCACTCTGTTACCTTGTCTTGTTATGAATAAATTTGTTTTAGGTTTACTGT\n+TAACTAATACACTATACCCGAACGTGGAAATAAACAACTTGATGCAATTGTATAACAAAG\n+TTCCTCCTAACCTTTCGTCAGATCCCTCTTTGTATCTATTGGAACTCATTTTGAGGCTGT\n+CTGCTATTATTCTCACCTCCCAAACACACCCAACAC\n+>NODE_56_length_216_cov_1.180124\n+GTGTTGGGTGTGTTTGGGGTCTATGTGGTTTATTTGGTTCTACTGAACCAACATTAAATT\n+TTGAAATATTAACTAATCAGTCCTATCCTGTGGCCTTGGAAATAATATTTTATATTGGAT\n+TTTTTCTTGCTTTTGCTGTAAAATTACCAATCATACCCCTACATACATGGTTACCAGATA\n+CCCACGAGAGCCAAACACACCCAACACAGGTTAGAC\n+>NODE_57_length_216_cov_0.869565\n+GTCTAACCTGTGTTGGGTGTGTTTGGATAGTTAGCGAGGTAGGTACTGAGCTGTTTACAT\n+AGGGGGGGAGTTCGTGTGTTTAGCTTAGGTTTCTGCTAGTCTTGTTTTGATAAATATGAA\n+TATAGTATTAGATACTCTTGTGAAGTATAAATTTGTAAGATTGAGTAGTAGTTTGACTAA\n+GCCCATGATCGTGCCAAACACACCCAACACAGGTTA\n+>NODE_58_length_215_cov_1.668750\n+GTCTAACCTGTGTTGGGTGTGTTTGGGCACTGGGGTTCAATTTAAAGTTCATTGTGCACA\n+TAGACCGCAAGCTGCCTCCAAATTTTTGTTTGATCAAGTCCATCATAAATTTGAGTGCCA\n+CTGGATCTCGCGTTCCGTCTTCTTTCACTGCAGGTATCACTTCTGGCCTCATGGTCGTCC\n+AATACGCCCTTGCTGCCCAAACACACCCAACACAG\n+>NODE_59_length_215_cov_1.187500\n+GTCTAACCTGTGTTGGGTGTGTTTGGGGGTGGTAGGACGGTAGGGGTCGCTAGGTCAGGA\n+ACATCATCTTCAAAGTCATTGAAAAATTGGCGTTGAAAATAAAGGCTAGCGCGGGGGTCA\n+GGCTTATAATCATCTCTGAAGATGTTGTAAACACCTTGGCAAAATGAGTGAAAGTATAAA\n+TCTTGGCCGGCGGATGCATAGGCAATTCCGACAGC\n+>NODE_60_length_215_cov_0.843750\n+AAAGATCGAATTTTTAGTGGAGATGGCCACAACATGTACCAAGGGTCAACTGACACCCAC\n+TTGCATATAAACCAATTTTCTGGTAACTTTTTATTAATCAATGCCACATATTTCTTATTC\n+TGGCTGTTGATTTCATTCGGCCCAATCAGCACTTCATATATTCTTCCAATGGACAAGCGT\n+GACTACTTACCCAAACACACCCAACACAGGTTAGA\n+>NODE_61_length_214_cov_1.232704\n+GTCTAACCTGTGTTGGGTGTGTTTGGTTGTAAGGATGCTTGATGCGCATGAGCAAGTGTT\n+CTCGTCTGCTCTATATAATGTCCTGTCTGCCATTACTCATCGTGGGAGGCATAATCATGA\n+AACAGGTTTTCGTAACACAACGGTTCGTGCCTCTTCGGACTGGGCTATGATGTGGGAGGA\n+GGTCCACGCTGCGTATCCAAACACACCCAACACA\n+>NODE_62_length_213_cov_0.936709\n+GTCTAACCTGTGTTGGGTGTGTTTGGATCGAGTTGGGTTATGTTCATCAGGGACCATCCG\n+GCAACAAAGTATCTCAAGCCCCTGCGTGGACTCAGAAAGCATACGGCATTGCACTGCATC\n+AGTGATGAAGTAAGACCGAGGATCAGGTGCCTCCTGGGAGCATTAAACCCCCACCGCCGA\n+TGACCATCCAAACACACCCAACACAGGTTAGAC\n+>NODE_63_length_210_cov_1.225806\n+TGTGTTGGGTGTGTTTGGCTTTCTGGCTCCATAGGTTTTAACCACTACTCTGTCAGTTGG\n+ACCAACATTTTTGAGCAACCTTTCGGTTTTCCCGCTACCAGCAGGTCCTACAATGGCTTT\n+CATTTGGGCAATCAATCTTTTCATAGTGTCCCATGATGCTATTCCCCTGTTCACCGCTCT\n+TAGGCCAAACACACCCAACACAGGTTAGAC\n+>NODE_64_length_208_cov_1.019608\n+GTCTAACCTGTGTTGGGTGTGTTTGGTATGTTATTGCTCCTGATGTGCAAGGATACCCCC\n+TTGATCCTCGTCTCTACAACATGATCACTACGAGGTACCCAGATTACCTGCCCATCATTA\n+ACCTCTACTGCCGACCACTCGGAACCACCGAAGCTACCTTCGCTGATTTCAACAAAGAGC\n+AGATTCCCTCTGATCCCATCTCAGATGA\n' |
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| diff -r 6838c2fd1228 -r 735a21808348 test-data/blast2tsv_contigs.txt --- a/test-data/blast2tsv_contigs.txt Sat May 18 18:14:42 2024 +0000 +++ b/test-data/blast2tsv_contigs.txt Wed Aug 21 13:13:50 2024 +0000 |
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| @@ -1,1 +1,6 @@ -1 Viruses Riboviria Orthornavirae Kitrinoviricota Alsuviricetes Martellivirales Bromoviridae Ilarvirus Blackberry chlorotic ringspot virus +1 Viruses Monodnaviria Shotokuvirae Cossaviricota Papovaviricetes Zurhausenvirales Papillomaviridae Firstpapillomavirinae Upsilonpapillomavirus Upsilonpapillomavirus 2 +1 cellular organisms Bacteria Thermodesulfobacteriota Desulfovibrionia Desulfovibrionales Desulfovibrionaceae Desulfovibrio unclassified Desulfovibrio +2 cellular organisms Eukaryota Opisthokonta Metazoa Eumetazoa Bilateria Protostomia Ecdysozoa Panarthropoda Arthropoda Mandibulata Pancrustacea Hexapoda Insecta Dicondylia Pterygota Neoptera Polyneoptera Dictyoptera Blattodea Blattoidea Termitoidae Rhinotermitidae Heterotermitinae Heterotermes unclassified Heterotermes +1 cellular organisms Eukaryota Opisthokonta Metazoa Eumetazoa Bilateria Protostomia Spiralia Lophotrochozoa Nemertea Enopla Hoplonemertea Monostilifera Eumonostilifera Tetrastemmatidae Tetrastemma +1 cellular organisms Archaea environmental samples +1 cellular organisms Bacteria Terrabacteria group Actinomycetota Actinomycetes Mycobacteriales Nocardiaceae Nocardia unclassified Nocardia |
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| diff -r 6838c2fd1228 -r 735a21808348 test-data/blast2tsv_input.xml --- a/test-data/blast2tsv_input.xml Sat May 18 18:14:42 2024 +0000 +++ b/test-data/blast2tsv_input.xml Wed Aug 21 13:13:50 2024 +0000 |
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| b'@@ -1,593 +1,1665 @@\n <?xml version="1.0"?>\n <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">\n <BlastOutput>\n- <BlastOutput_program>tblastx</BlastOutput_program>\n- <BlastOutput_version>TBLASTX 2.10.1+</BlastOutput_version>\n+ <BlastOutput_program>rpstblastn</BlastOutput_program>\n+ <BlastOutput_version>RPSTBLASTN 2.14.1+</BlastOutput_version>\n <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>\n- <BlastOutput_db>/save/tcandresse/refseq/refseq.short.fa</BlastOutput_db>\n- <BlastOutput_query-ID>ds2020-482-EDGG-1-Q4_42600</BlastOutput_query-ID>\n- <BlastOutput_query-def>No definition line</BlastOutput_query-def>\n- <BlastOutput_query-len>96</BlastOutput_query-len>\n+ <BlastOutput_db>/data/db/databases/blast/2018-01-22/pfam/Pfam</BlastOutput_db>\n+ <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>\n+ <BlastOutput_query-def>NODE_1_length_506_cov_10.687361</BlastOutput_query-def>\n+ <BlastOutput_query-len>506</BlastOutput_query-len>\n <BlastOutput_param>\n <Parameters>\n <Parameters_matrix>BLOSUM62</Parameters_matrix>\n- <Parameters_expect>0.001</Parameters_expect>\n+ <Parameters_expect>0.0001</Parameters_expect>\n <Parameters_gap-open>11</Parameters_gap-open>\n <Parameters_gap-extend>1</Parameters_gap-extend>\n- <Parameters_filter>L;</Parameters_filter>\n+ <Parameters_filter>F</Parameters_filter>\n </Parameters>\n </BlastOutput_param>\n <BlastOutput_iterations>\n <Iteration>\n <Iteration_iter-num>1</Iteration_iter-num>\n- <Iteration_query-ID>ds2020-482-EDGG-1-Q4_42600</Iteration_query-ID>\n- <Iteration_query-def>No definition line</Iteration_query-def>\n- <Iteration_query-len>96</Iteration_query-len>\n-<Iteration_hits>\n-<Hit>\n- <Hit_num>1</Hit_num>\n- <Hit_id>ref|NC_035070.1|</Hit_id>\n- <Hit_def>Spinach amalgavirus 1 isolate SRP059420 fusion protein and putative coat protein genes, complete cds</Hit_def>\n- <Hit_accession>NC_035070</Hit_accession>\n- <Hit_len>3420</Hit_len>\n- <Hit_hsps>\n- <Hsp>\n- <Hsp_num>1</Hsp_num>\n- <Hsp_bit-score>51.4703</Hsp_bit-score>\n- <Hsp_score>106</Hsp_score>\n- <Hsp_evalue>6.20873e-08</Hsp_evalue>\n- <Hsp_query-from>3</Hsp_query-from>\n- <Hsp_query-to>95</Hsp_query-to>\n- <Hsp_hit-from>1338</Hsp_hit-from>\n- <Hsp_hit-to>1430</Hsp_hit-to>\n- <Hsp_query-frame>3</Hsp_query-frame>\n- <Hsp_hit-frame>3</Hsp_hit-frame>\n- <Hsp_identity>20</Hsp_identity>\n- <Hsp_positive>24</Hsp_positive>\n- <Hsp_gaps>0</Hsp_gaps>\n- <Hsp_align-len>31</Hsp_align-len>\n- <Hsp_qseq>GGGTLRTWAADRKMYRGGGSSFDALLLLCQA</Hsp_qseq>\n- <Hsp_hseq>GGGAMRSWEVDSQMYRGGGNSADALRLLGQA</Hsp_hseq>\n- <Hsp_midline>GGG +R+W D +MYRGGG+S DAL LL QA</Hsp_midline>\n- </Hsp>\n- </Hit_hsps>\n-</Hit>\n-</Iteration_hits>\n- <Iteration_stat>\n- <Statistics>\n- <Statistics_db-num>7073</Statistics_db-num>\n- <Statistics_db-len>36804204</Statistics_db-len>\n- <Statistics_hsp-len>24</Statistics_hsp-len>\n- <Statistics_eff-space>96786528</Statistics_eff-space>\n- <Statistics_kappa>0.133956144488482</Statistics_kappa>\n- <Statistics_lambda>0.317605957635731</Statistics_lambda>\n- <Statistics_entropy>0.401214524497119</Statistics_entropy>\n- </Statistics>\n- </Iteration_stat>\n-</Iteration>\n-<Iteration>\n- <Iteration_iter-num>2</Iteration_iter-num>\n- <Iteration_query-ID>ds2020-482-EDGG-1-Q4_60894</Iteration_query-ID>\n- <Iteration_query-def>No definition line</Iteration_query-def>\n- <Iteration_query-len>82</Iteration_query-len>\n+ <Iteration_query-ID>Query_1</Iteration_query-ID>\n+ <Iteration_query-def>NODE_1_length_506_cov_10.687361</Iteration_query-def>\n+ <Iteration_query-len>506</Iterati'..b'teration_iter-num>\n+ <Iteration_query-ID>Query_60</Iteration_query-ID>\n+ <Iteration_query-def>NODE_60_length_215_cov_0.843750</Iteration_query-def>\n+ <Iteration_query-len>215</Iteration_query-len>\n+<Iteration_hits>\n+</Iteration_hits>\n+ <Iteration_stat>\n+ <Statistics>\n+ <Statistics_db-num>16305</Statistics_db-num>\n+ <Statistics_db-len>2821655</Statistics_db-len>\n+ <Statistics_hsp-len>39</Statistics_hsp-len>\n+ <Statistics_eff-space>69944320</Statistics_eff-space>\n+ <Statistics_kappa>0.041</Statistics_kappa>\n+ <Statistics_lambda>0.267</Statistics_lambda>\n+ <Statistics_entropy>0.14</Statistics_entropy>\n+ </Statistics>\n+ </Iteration_stat>\n+ <Iteration_message>No hits found</Iteration_message>\n+</Iteration>\n+<Iteration>\n+ <Iteration_iter-num>61</Iteration_iter-num>\n+ <Iteration_query-ID>Query_61</Iteration_query-ID>\n+ <Iteration_query-def>NODE_61_length_214_cov_1.232704</Iteration_query-def>\n+ <Iteration_query-len>214</Iteration_query-len>\n+<Iteration_hits>\n+</Iteration_hits>\n+ <Iteration_stat>\n+ <Statistics>\n+ <Statistics_db-num>16305</Statistics_db-num>\n+ <Statistics_db-len>2821655</Statistics_db-len>\n+ <Statistics_hsp-len>39</Statistics_hsp-len>\n+ <Statistics_eff-space>69944320</Statistics_eff-space>\n+ <Statistics_kappa>0.041</Statistics_kappa>\n+ <Statistics_lambda>0.267</Statistics_lambda>\n+ <Statistics_entropy>0.14</Statistics_entropy>\n+ </Statistics>\n+ </Iteration_stat>\n+ <Iteration_message>No hits found</Iteration_message>\n+</Iteration>\n+<Iteration>\n+ <Iteration_iter-num>62</Iteration_iter-num>\n+ <Iteration_query-ID>Query_62</Iteration_query-ID>\n+ <Iteration_query-def>NODE_62_length_213_cov_0.936709</Iteration_query-def>\n+ <Iteration_query-len>213</Iteration_query-len>\n+<Iteration_hits>\n+</Iteration_hits>\n+ <Iteration_stat>\n+ <Statistics>\n+ <Statistics_db-num>16305</Statistics_db-num>\n+ <Statistics_db-len>2821655</Statistics_db-len>\n+ <Statistics_hsp-len>39</Statistics_hsp-len>\n+ <Statistics_eff-space>69944320</Statistics_eff-space>\n+ <Statistics_kappa>0.041</Statistics_kappa>\n+ <Statistics_lambda>0.267</Statistics_lambda>\n+ <Statistics_entropy>0.14</Statistics_entropy>\n+ </Statistics>\n+ </Iteration_stat>\n+ <Iteration_message>No hits found</Iteration_message>\n+</Iteration>\n+<Iteration>\n+ <Iteration_iter-num>63</Iteration_iter-num>\n+ <Iteration_query-ID>Query_63</Iteration_query-ID>\n+ <Iteration_query-def>NODE_63_length_210_cov_1.225806</Iteration_query-def>\n+ <Iteration_query-len>210</Iteration_query-len>\n+<Iteration_hits>\n+</Iteration_hits>\n+ <Iteration_stat>\n+ <Statistics>\n+ <Statistics_db-num>16305</Statistics_db-num>\n+ <Statistics_db-len>2821655</Statistics_db-len>\n+ <Statistics_hsp-len>38</Statistics_hsp-len>\n+ <Statistics_eff-space>70466080</Statistics_eff-space>\n+ <Statistics_kappa>0.041</Statistics_kappa>\n+ <Statistics_lambda>0.267</Statistics_lambda>\n+ <Statistics_entropy>0.14</Statistics_entropy>\n+ </Statistics>\n+ </Iteration_stat>\n+ <Iteration_message>No hits found</Iteration_message>\n+</Iteration>\n+<Iteration>\n+ <Iteration_iter-num>64</Iteration_iter-num>\n+ <Iteration_query-ID>Query_64</Iteration_query-ID>\n+ <Iteration_query-def>NODE_64_length_208_cov_1.019608</Iteration_query-def>\n+ <Iteration_query-len>208</Iteration_query-len>\n+<Iteration_hits>\n+</Iteration_hits>\n+ <Iteration_stat>\n+ <Statistics>\n+ <Statistics_db-num>16305</Statistics_db-num>\n+ <Statistics_db-len>2821655</Statistics_db-len>\n+ <Statistics_hsp-len>37</Statistics_hsp-len>\n+ <Statistics_eff-space>70987840</Statistics_eff-space>\n+ <Statistics_kappa>0.041</Statistics_kappa>\n+ <Statistics_lambda>0.267</Statistics_lambda>\n+ <Statistics_entropy>0.14</Statistics_entropy>\n </Statistics>\n </Iteration_stat>\n <Iteration_message>No hits found</Iteration_message>\n </Iteration>\n </BlastOutput_iterations>\n </BlastOutput>\n+\n' |
| b |
| diff -r 6838c2fd1228 -r 735a21808348 test-data/blast2tsv_output.tab --- a/test-data/blast2tsv_output.tab Sat May 18 18:14:42 2024 +0000 +++ b/test-data/blast2tsv_output.tab Wed Aug 21 13:13:50 2024 +0000 |
| b |
| b'@@ -1,6 +1,13 @@\n #algo\tquery_id\tnb_reads\tquery_length\taccession\tdescription\torganism\tpercentIdentity\tnb_hsps\tqueryOverlap\thitOverlap\tevalue\tscore\ttax_id\ttaxonomy\tsequence\n-TBLASTX\tds2020-482-EDGG-1-Q4_42600\t\t96\t\n-TBLASTX\tds2020-482-EDGG-1-Q4_107243\t\t60\t\n-TBLASTX\tds2020-482-EDGG-1-Q4_2681\t\t348\tNC_011554\tBlackberry chlorotic ringspot virus RNA2, complete genome\tBlackberry chlorotic ringspot virus\t56.3\t2\t100\t9.0\t1.04985e-23\t128.1421\t339420\tViruses;Riboviria;Orthornavirae;Kitrinoviricota;Alsuviricetes;Martellivirales;Bromoviridae;Ilarvirus;Blackberry chlorotic ringspot virus\tCCTTCCTAGCGACCACGCACACGTCAAGACCGGCATCATCAATGTCGCGACAATCGTGAACCACTTTAGTATAGTCCACATCAAGATCATCATAAGGTAGATAAAAGGAATCAATTTCCCTAGGAAAAAGTCCAGAATCATCTTCCTCATAAAAATCTGGTATCGAGGGATCAATGGTTCGCACCACCATCTCGAATGTATCAAAGATCGTCGCGAAATCAAACTTTGCGGTATGCTTAACGACAAACTCGAAAAGGAAAAGTTTTACCCATTCGTCGTAGTTGTCATCTTTATGCACACCGAACGTCGAGAAAAACCCAAAGAACGTGTGCGTGGTCGCTAGGAAGG\n-TBLASTX\tds2020-482-EDGG-1-Q4_107857\t\t59\t\n-TBLASTX\tds2020-482-EDGG-1-Q4_63163\t\t81\t\n+TBLASTX\tNODE_13_length_295_cov_0.945833\t\t295\t316155\tpfam13603, tRNA-synt_1_2, Leucyl-tRNA synthetase, Domain 2. This is a family of the conserved region of Leucine-tRNA ligase or Leucyl-tRNA synthetase, EC:6.1.1.4.\tTursiops truncatus papillomavirus 2\t41.5\t1\t100\t67.0\t2.277e-05\t38.6378\t316155\tViruses;Monodnaviria;Shotokuvirae;Cossaviricota;Papovaviricetes;Zurhausenvirales;Papillomaviridae;Firstpapillomavirinae;Upsilonpapillomavirus;Upsilonpapillomavirus 2;Tursiops truncatus papillomavirus 2\tTGTGTTGGGTGTGTTTGGTTTCCGGTTACCATAATCGCTATTCTTTCAAACAGAAAGCGCATGCTAAGTATTCTCACCCAGAGGAATATGCTGACAAGCCCTCCTCAAAAGGCTATTTTTACAATGCCACCTATGAGAATGCACGAACTCTTATTCACTTCATTAAGCAATATGGATTGCCCTTCAATCCTGTTATTGCACCAGAAGATGCTGAACTAACTGATGAACAGATTCAATCTTACATCAACACAGCAAACTCCTTCTTTAATGATTATCCGACGTTACTGTTCACCCG\n+TBLASTX\tNODE_16_length_278_cov_0.901345\t\t278\t306845\tpfam00421, PSII, Photosystem II protein. \t\t65.8\t1\t100\t47.0\t7.65615e-39\t132.634\t\t\tGTCTAACCTGTGTTGGGTGTGTTTGGGCTGTAATCGAGGTATAGTGTCGAACAAGTCGGTGTCACTGTTGAATTCTATGGCGGCGAACTCAATGGAGTCAGTTATAGTGATCCTGCTACTGTGAAAAAATATGCTAGACGTGCTCAATTGGGTGAAATTTTTGAATTAGATCGTGCTACTTTAAAATCGGATGGTGTTTTTCGTAGCAGTCCAAGGGGTTGGTTTACTTTTGGACATGCGTCGTTTGCTCTGCTCTTCTTCCAAACACACCCAACACA\n+TBLASTX\tNODE_19_length_271_cov_0.879630\t\t271\t306845\tpfam00421, PSII, Photosystem II protein. \t\t32.9\t1\t100\t42.0\t1.69015e-11\t56.3644\t\t\tGTCTAACCTGTGTTGGGTGTGTTTGGTATGGAGGGAGGTGTATATGATACCTGGGCACCCGGAGGGGGAGATGTAAGAAAAATTACCAACTTGACCCTTAACCCAAGCGTGATATTTGGTTATTTACTAAAATCTCCTTTTGGGGGAGAAGGATGGATTGTTAGTGTGGACGATTTAGAAGATATAATTGGAGGACATGTCTGGTTAGGCTCCATTTGTATACTTGGTGGAATTTGGCATATCTTAACCAAACACACCCAACACAGGTTAG\n+TBLASTX\tNODE_20_length_267_cov_1.429245\t\t267\t287774\tpfam10839, DUF2647, Protein of unknown function (DUF2647). This eukaryotic family of proteins are annotated as ycf68 but have no known function.\tDesulfovibrio sp. G100IX\t91.3\t1\t100\t99.0\t7.70073e-10\t48.4966\t287774\tcellular organisms;Bacteria;Thermodesulfobacteriota;Desulfovibrionia;Desulfovibrionales;Desulfovibrionaceae;Desulfovibrio;unclassified Desulfovibrio;Desulfovibrio sp. G100IX\tCTGTGTTGGGTGTGTTTGGACTTGGTATGTGAAGATACGTTGTTAGGTGCTCCGTTTTATTTTCCCATTGAGGCCGAACCTAAACCTGTGCTCGAGAGATAGCTGTCCATATACTGATAAGGGATGTATGGATTCTCGAGAAGAGAGGAGCCATGGTGGTCCCTCCCGGACCGCCCGGATCCCACGAGTGAATAGAAAGTTGGATCTACATTGGATCTCACCTGAATCGCCCCATAAACAACCAAACACACCCAACACAGGTTAGAC\n+TBLASTX\tNODE_22_length_262_cov_1.053140\t\t262\t306604\tpfam00124, Photo_RC, Photosynthetic reaction centre protein. \tHeterotermes sp. TMJ-2004j\t40.9\t1\t100\t77.0\t4.94039e-28\t99.6256\t306604\tcellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Protostomia;Ecdysozoa;Panarthropoda;Arthropoda;Mandibulata;Pancrustacea;Hexapoda;Insecta;Dicondylia;Pterygota;Neoptera;Polyneoptera;Dictyoptera;Blattodea;Blattoidea;Termitoidae;Rhinotermitidae;Heterotermitinae;Heterotermes;unclassified Heterotermes;Heterotermes sp. TMJ-2004j\tGTCTAACCTGTGTTGGGTGTGTTTGGCTAGTCAGTAGCTTGTTATATGGGTCGTGAGTGGGAAGTTAGCTTCCGTCTGGGTATGCGCCCGTGGATTGCTGTTGCATATTCAGCTCCTGTTGCAGCTGCTACTGC'..b'GGGAGGCTGAAAACTGCAAGCATAGATCTTTCGGCCCTTTCGAAGCTACCGCTTCCGAGAGCCTGGCTAAACTCTGCCCAGATTATCCGATCTGCTTGCCTGTACCTTACGACGTGATCAATAAAGTGTATAGGTATCTCAGAACGCTTAAGAAGCCTGATGTGCAGTCGCCCCACTACCAAACACACCCAACACAGGTTAGAC\n+TBLASTX\tNODE_29_length_250_cov_0.851282\t\t250\t278700\tpfam00283, Cytochrom_B559, Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits. \tuncultured archaeon CRE-PA11a\t58.6\t1\t100\t100\t7.31211e-08\t42.0012\t278700\tcellular organisms;Archaea;environmental samples;uncultured archaeon CRE-PA11a\tGTCTAACCTGTGTTGGGTGTGTTTGGGTTTCTTTGGAGCAACTCGATGAATTTAGTAAATCCTTTTAGGAGGTTCCCAATGACCATAGATCGAACCTATCCAATTTTTACAGTGCGATGGTTGGCTGTTCACGGACTGGCTGTACCTACTGTTTCTTTTTTAGGGTCAATATCAGCAATGCAGTTCATCCAACGATAAACCTAATTCAAATTATAGAGCTAGCACACCAAACACACCCAACACAGGTTAG\n+TBLASTX\tNODE_34_length_245_cov_1.000000\t\t245\t250270\tpfam00978, RdRP_2, RNA dependent RNA polymerase. This family may represent an RNA dependent RNA polymerase. The family also contains the following proteins: 2A protein from bromoviruses putative RNA dependent RNA polymerase from tobamoviruses Non structural polyprotein from togaviruses.\tNocardia sp. 431D04\t37.5\t1\t100\t38.0\t6.42106e-08\t45.7137\t250270\tcellular organisms;Bacteria;Terrabacteria group;Actinomycetota;Actinomycetes;Mycobacteriales;Nocardiaceae;Nocardia;unclassified Nocardia;Nocardia sp. 431D04\tGTCTAACCTGTGTTGGGTGTGTTTGGATGGTGATCGGCAATTTAAAGGAATGTGTGCGATATTTTCACCAATATTCAAGGAGCTTAAAAATCGACTAAAAAGCGTGTTAGATATTAAATACATGTATGCAGACGGATTGAGACCTGATCAGTTGTCGGAGCGCATGTCACAGATAGGTGCAGGTAAATATTTTATAGAGAATGATATGGAACAGCATCTCGCCAAACACACCCAACACAGGTTAG\n+TBLASTX\tNODE_46_length_229_cov_1.091954\t\t229\t306604\tpfam00124, Photo_RC, Photosynthetic reaction centre protein. \tHeterotermes sp. TMJ-2004j\t43.9\t1\t100\t66.0\t4.26406e-23\t86.1436\t306604\tcellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Protostomia;Ecdysozoa;Panarthropoda;Arthropoda;Mandibulata;Pancrustacea;Hexapoda;Insecta;Dicondylia;Pterygota;Neoptera;Polyneoptera;Dictyoptera;Blattodea;Blattoidea;Termitoidae;Rhinotermitidae;Heterotermitinae;Heterotermes;unclassified Heterotermes;Heterotermes sp. TMJ-2004j\tTGTGTTGGGTGTGTTTGGTTGGATGCCTGGAATACAATCATGAAATTGAAAGTACCAGATATTCCTAAAGGCATGCCATCTGAAAAACTTCCTTGACCAATAGGGTAGATCAAGAAAACAGCTGTAGCAGCCGCGACAGGAGCTGAATATGCAACAGCAATCCAAGGACGCATACCCAGACGGAAACTAAGCTCCCTCTCGCTCCAAACACACCCAACACAGGTTAGAC\n+TBLASTX\tNODE_47_length_229_cov_0.816092\t\t229\t306687\tpfam00223, PsaA_PsaB, Photosystem I psaA/psaB protein. \t\t66.7\t1\t100\t14.0\t1.79906e-13\t61.3066\t\t\tTTGGTAAATTGGCGGAAAGAGGAGGACTCAATGATTATTCGTTCGCCGGAACCAGAAGTAAAAATTTTGGTAGATAGGGATCACATAAAAACTTCTTTCGAGGAATGGGCCAGGCCGGGTCATTTCTCAAGAACACTAGCTAAAGGCCCTGACACTACCACTTGGATCTGGAACCTACATGCTGATGCTCACGATCTTAATAGCCAAACACACCCAACACAGGTTAGAC\n+TBLASTX\tNODE_50_length_226_cov_2.269006\t\t226\t306845\tpfam00421, PSII, Photosystem II protein. \t\t60.3\t1\t100\t41.0\t2.77182e-23\t89.1064\t\t\tGTCAACGGTGTGTTGGGTGTGTTTGGGAAAGGTCCTGGAATATGGGTGTCCGATCCTTATGGACTAACCGGAACAGTGCAACCTGTAAATCCGGCGTGGGGCGTGGAAGGTTTTGATCCTTTTGTCCCGGGAGGAATAGCTTCTCATCATATTGCAGCAGGTACATTGGGCATATTAGCGGGCCTATTCCATCTTAGCGTACGGTCACCCCAGCCAAACACACCCA\n+TBLASTX\tNODE_56_length_216_cov_1.180124\t\t216\t306795\tpfam00361, Proton_antipo_M, Proton-conducting membrane transporter. This is a family of membrane transporters that inlcudes some 7 of potentially 14-16 TM regions. In many instances the family forms part of complex I that catalyzes the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane, and in this context is a combination predominantly of subunits 2, 4, 5, 14, L, M and N. In many bacterial species these proteins are probable stand-alone transporters not coupled with oxidoreduction. The family in total represents homologs across the phyla.\t\t26.7\t1\t100\t62.0\t5.23486e-07\t42.6815\t\t\tGTGTTGGGTGTGTTTGGGGTCTATGTGGTTTATTTGGTTCTACTGAACCAACATTAAATTTTGAAATATTAACTAATCAGTCCTATCCTGTGGCCTTGGAAATAATATTTTATATTGGATTTTTTCTTGCTTTTGCTGTAAAATTACCAATCATACCCCTACATACATGGTTACCAGATACCCACGAGAGCCAAACACACCCAACACAGGTTAGAC\n' |
| b |
| diff -r 6838c2fd1228 -r 735a21808348 test-data/blast2tsv_output_with_rn.tab --- a/test-data/blast2tsv_output_with_rn.tab Sat May 18 18:14:42 2024 +0000 +++ b/test-data/blast2tsv_output_with_rn.tab Wed Aug 21 13:13:50 2024 +0000 |
| b |
| b'@@ -1,6 +1,13 @@\n #algo\tquery_id\tnb_reads\tquery_length\taccession\tdescription\torganism\tpercentIdentity\tnb_hsps\tqueryOverlap\thitOverlap\tevalue\tscore\ttax_id\ttaxonomy\tsequence\n-TBLASTX\tds2020-482-EDGG-1-Q4_42600\t12\t96\t\n-TBLASTX\tds2020-482-EDGG-1-Q4_107243\t63\t60\t\n-TBLASTX\tds2020-482-EDGG-1-Q4_2681\t8\t348\tNC_011554\tBlackberry chlorotic ringspot virus RNA2, complete genome\tBlackberry chlorotic ringspot virus\t56.3\t2\t100\t9.0\t1.04985e-23\t128.1421\t339420\tViruses;Riboviria;Orthornavirae;Kitrinoviricota;Alsuviricetes;Martellivirales;Bromoviridae;Ilarvirus;Blackberry chlorotic ringspot virus\tCCTTCCTAGCGACCACGCACACGTCAAGACCGGCATCATCAATGTCGCGACAATCGTGAACCACTTTAGTATAGTCCACATCAAGATCATCATAAGGTAGATAAAAGGAATCAATTTCCCTAGGAAAAAGTCCAGAATCATCTTCCTCATAAAAATCTGGTATCGAGGGATCAATGGTTCGCACCACCATCTCGAATGTATCAAAGATCGTCGCGAAATCAAACTTTGCGGTATGCTTAACGACAAACTCGAAAAGGAAAAGTTTTACCCATTCGTCGTAGTTGTCATCTTTATGCACACCGAACGTCGAGAAAAACCCAAAGAACGTGTGCGTGGTCGCTAGGAAGG\n-TBLASTX\tds2020-482-EDGG-1-Q4_107857\t402\t59\t\n-TBLASTX\tds2020-482-EDGG-1-Q4_63163\t88\t81\t\n+TBLASTX\tNODE_13_length_295_cov_0.945833\t264\t295\t316155\tpfam13603, tRNA-synt_1_2, Leucyl-tRNA synthetase, Domain 2. This is a family of the conserved region of Leucine-tRNA ligase or Leucyl-tRNA synthetase, EC:6.1.1.4.\tTursiops truncatus papillomavirus 2\t41.5\t1\t100\t67.0\t2.277e-05\t38.6378\t316155\tViruses;Monodnaviria;Shotokuvirae;Cossaviricota;Papovaviricetes;Zurhausenvirales;Papillomaviridae;Firstpapillomavirinae;Upsilonpapillomavirus;Upsilonpapillomavirus 2;Tursiops truncatus papillomavirus 2\tTGTGTTGGGTGTGTTTGGTTTCCGGTTACCATAATCGCTATTCTTTCAAACAGAAAGCGCATGCTAAGTATTCTCACCCAGAGGAATATGCTGACAAGCCCTCCTCAAAAGGCTATTTTTACAATGCCACCTATGAGAATGCACGAACTCTTATTCACTTCATTAAGCAATATGGATTGCCCTTCAATCCTGTTATTGCACCAGAAGATGCTGAACTAACTGATGAACAGATTCAATCTTACATCAACACAGCAAACTCCTTCTTTAATGATTATCCGACGTTACTGTTCACCCG\n+TBLASTX\tNODE_16_length_278_cov_0.901345\t377\t278\t306845\tpfam00421, PSII, Photosystem II protein. \t\t65.8\t1\t100\t47.0\t7.65615e-39\t132.634\t\t\tGTCTAACCTGTGTTGGGTGTGTTTGGGCTGTAATCGAGGTATAGTGTCGAACAAGTCGGTGTCACTGTTGAATTCTATGGCGGCGAACTCAATGGAGTCAGTTATAGTGATCCTGCTACTGTGAAAAAATATGCTAGACGTGCTCAATTGGGTGAAATTTTTGAATTAGATCGTGCTACTTTAAAATCGGATGGTGTTTTTCGTAGCAGTCCAAGGGGTTGGTTTACTTTTGGACATGCGTCGTTTGCTCTGCTCTTCTTCCAAACACACCCAACACA\n+TBLASTX\tNODE_19_length_271_cov_0.879630\t67\t271\t306845\tpfam00421, PSII, Photosystem II protein. \t\t32.9\t1\t100\t42.0\t1.69015e-11\t56.3644\t\t\tGTCTAACCTGTGTTGGGTGTGTTTGGTATGGAGGGAGGTGTATATGATACCTGGGCACCCGGAGGGGGAGATGTAAGAAAAATTACCAACTTGACCCTTAACCCAAGCGTGATATTTGGTTATTTACTAAAATCTCCTTTTGGGGGAGAAGGATGGATTGTTAGTGTGGACGATTTAGAAGATATAATTGGAGGACATGTCTGGTTAGGCTCCATTTGTATACTTGGTGGAATTTGGCATATCTTAACCAAACACACCCAACACAGGTTAG\n+TBLASTX\tNODE_20_length_267_cov_1.429245\t2\t267\t287774\tpfam10839, DUF2647, Protein of unknown function (DUF2647). This eukaryotic family of proteins are annotated as ycf68 but have no known function.\tDesulfovibrio sp. G100IX\t91.3\t1\t100\t99.0\t7.70073e-10\t48.4966\t287774\tcellular organisms;Bacteria;Thermodesulfobacteriota;Desulfovibrionia;Desulfovibrionales;Desulfovibrionaceae;Desulfovibrio;unclassified Desulfovibrio;Desulfovibrio sp. G100IX\tCTGTGTTGGGTGTGTTTGGACTTGGTATGTGAAGATACGTTGTTAGGTGCTCCGTTTTATTTTCCCATTGAGGCCGAACCTAAACCTGTGCTCGAGAGATAGCTGTCCATATACTGATAAGGGATGTATGGATTCTCGAGAAGAGAGGAGCCATGGTGGTCCCTCCCGGACCGCCCGGATCCCACGAGTGAATAGAAAGTTGGATCTACATTGGATCTCACCTGAATCGCCCCATAAACAACCAAACACACCCAACACAGGTTAGAC\n+TBLASTX\tNODE_22_length_262_cov_1.053140\t262\t262\t306604\tpfam00124, Photo_RC, Photosynthetic reaction centre protein. \tHeterotermes sp. TMJ-2004j\t40.9\t1\t100\t77.0\t4.94039e-28\t99.6256\t306604\tcellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Protostomia;Ecdysozoa;Panarthropoda;Arthropoda;Mandibulata;Pancrustacea;Hexapoda;Insecta;Dicondylia;Pterygota;Neoptera;Polyneoptera;Dictyoptera;Blattodea;Blattoidea;Termitoidae;Rhinotermitidae;Heterotermitinae;Heterotermes;unclassified Heterotermes;Heterotermes sp. TMJ-2004j\tGTCTAACCTGTGTTGGGTGTGTTTGGCTAGTCAGTAGCTTGTTATATGGGTCGTGAGTGGGAAGTTAGCTTCCGTCTGGGTATGCGCCCGTGGATTGCTGTTGCATATTCAG'..b'AGCATAGATCTTTCGGCCCTTTCGAAGCTACCGCTTCCGAGAGCCTGGCTAAACTCTGCCCAGATTATCCGATCTGCTTGCCTGTACCTTACGACGTGATCAATAAAGTGTATAGGTATCTCAGAACGCTTAAGAAGCCTGATGTGCAGTCGCCCCACTACCAAACACACCCAACACAGGTTAGAC\n+TBLASTX\tNODE_29_length_250_cov_0.851282\t428\t250\t278700\tpfam00283, Cytochrom_B559, Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits. \tuncultured archaeon CRE-PA11a\t58.6\t1\t100\t100\t7.31211e-08\t42.0012\t278700\tcellular organisms;Archaea;environmental samples;uncultured archaeon CRE-PA11a\tGTCTAACCTGTGTTGGGTGTGTTTGGGTTTCTTTGGAGCAACTCGATGAATTTAGTAAATCCTTTTAGGAGGTTCCCAATGACCATAGATCGAACCTATCCAATTTTTACAGTGCGATGGTTGGCTGTTCACGGACTGGCTGTACCTACTGTTTCTTTTTTAGGGTCAATATCAGCAATGCAGTTCATCCAACGATAAACCTAATTCAAATTATAGAGCTAGCACACCAAACACACCCAACACAGGTTAG\n+TBLASTX\tNODE_34_length_245_cov_1.000000\t183\t245\t250270\tpfam00978, RdRP_2, RNA dependent RNA polymerase. This family may represent an RNA dependent RNA polymerase. The family also contains the following proteins: 2A protein from bromoviruses putative RNA dependent RNA polymerase from tobamoviruses Non structural polyprotein from togaviruses.\tNocardia sp. 431D04\t37.5\t1\t100\t38.0\t6.42106e-08\t45.7137\t250270\tcellular organisms;Bacteria;Terrabacteria group;Actinomycetota;Actinomycetes;Mycobacteriales;Nocardiaceae;Nocardia;unclassified Nocardia;Nocardia sp. 431D04\tGTCTAACCTGTGTTGGGTGTGTTTGGATGGTGATCGGCAATTTAAAGGAATGTGTGCGATATTTTCACCAATATTCAAGGAGCTTAAAAATCGACTAAAAAGCGTGTTAGATATTAAATACATGTATGCAGACGGATTGAGACCTGATCAGTTGTCGGAGCGCATGTCACAGATAGGTGCAGGTAAATATTTTATAGAGAATGATATGGAACAGCATCTCGCCAAACACACCCAACACAGGTTAG\n+TBLASTX\tNODE_46_length_229_cov_1.091954\t471\t229\t306604\tpfam00124, Photo_RC, Photosynthetic reaction centre protein. \tHeterotermes sp. TMJ-2004j\t43.9\t1\t100\t66.0\t4.26406e-23\t86.1436\t306604\tcellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Protostomia;Ecdysozoa;Panarthropoda;Arthropoda;Mandibulata;Pancrustacea;Hexapoda;Insecta;Dicondylia;Pterygota;Neoptera;Polyneoptera;Dictyoptera;Blattodea;Blattoidea;Termitoidae;Rhinotermitidae;Heterotermitinae;Heterotermes;unclassified Heterotermes;Heterotermes sp. TMJ-2004j\tTGTGTTGGGTGTGTTTGGTTGGATGCCTGGAATACAATCATGAAATTGAAAGTACCAGATATTCCTAAAGGCATGCCATCTGAAAAACTTCCTTGACCAATAGGGTAGATCAAGAAAACAGCTGTAGCAGCCGCGACAGGAGCTGAATATGCAACAGCAATCCAAGGACGCATACCCAGACGGAAACTAAGCTCCCTCTCGCTCCAAACACACCCAACACAGGTTAGAC\n+TBLASTX\tNODE_47_length_229_cov_0.816092\t470\t229\t306687\tpfam00223, PsaA_PsaB, Photosystem I psaA/psaB protein. \t\t66.7\t1\t100\t14.0\t1.79906e-13\t61.3066\t\t\tTTGGTAAATTGGCGGAAAGAGGAGGACTCAATGATTATTCGTTCGCCGGAACCAGAAGTAAAAATTTTGGTAGATAGGGATCACATAAAAACTTCTTTCGAGGAATGGGCCAGGCCGGGTCATTTCTCAAGAACACTAGCTAAAGGCCCTGACACTACCACTTGGATCTGGAACCTACATGCTGATGCTCACGATCTTAATAGCCAAACACACCCAACACAGGTTAGAC\n+TBLASTX\tNODE_50_length_226_cov_2.269006\t315\t226\t306845\tpfam00421, PSII, Photosystem II protein. \t\t60.3\t1\t100\t41.0\t2.77182e-23\t89.1064\t\t\tGTCAACGGTGTGTTGGGTGTGTTTGGGAAAGGTCCTGGAATATGGGTGTCCGATCCTTATGGACTAACCGGAACAGTGCAACCTGTAAATCCGGCGTGGGGCGTGGAAGGTTTTGATCCTTTTGTCCCGGGAGGAATAGCTTCTCATCATATTGCAGCAGGTACATTGGGCATATTAGCGGGCCTATTCCATCTTAGCGTACGGTCACCCCAGCCAAACACACCCA\n+TBLASTX\tNODE_56_length_216_cov_1.180124\t166\t216\t306795\tpfam00361, Proton_antipo_M, Proton-conducting membrane transporter. This is a family of membrane transporters that inlcudes some 7 of potentially 14-16 TM regions. In many instances the family forms part of complex I that catalyzes the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane, and in this context is a combination predominantly of subunits 2, 4, 5, 14, L, M and N. In many bacterial species these proteins are probable stand-alone transporters not coupled with oxidoreduction. The family in total represents homologs across the phyla.\t\t26.7\t1\t100\t62.0\t5.23486e-07\t42.6815\t\t\tGTGTTGGGTGTGTTTGGGGTCTATGTGGTTTATTTGGTTCTACTGAACCAACATTAAATTTTGAAATATTAACTAATCAGTCCTATCCTGTGGCCTTGGAAATAATATTTTATATTGGATTTTTTCTTGCTTTTGCTGTAAAATTACCAATCATACCCCTACATACATGGTTACCAGATACCCACGAGAGCCAAACACACCCAACACAGGTTAGAC\n' |
| b |
| diff -r 6838c2fd1228 -r 735a21808348 test-data/blast2tsv_read_nb.tab --- a/test-data/blast2tsv_read_nb.tab Sat May 18 18:14:42 2024 +0000 +++ b/test-data/blast2tsv_read_nb.tab Wed Aug 21 13:13:50 2024 +0000 |
| b |
| @@ -1,6 +1,64 @@ -ds2020-482-EDGG-1-Q4_42600 12 -ds2020-482-EDGG-1-Q4_107243 63 -ds2020-482-EDGG-1-Q4_2681 8 -ds2020-482-EDGG-1-Q4_107857 402 -ds2020-482-EDGG-1-Q4_63163 88 -ds2020-482-EDGG-1-Q4_47667 1 +NODE_1_length_506_cov_10.687361 56 +NODE_2_length_429_cov_3.631016 301 +NODE_3_length_365_cov_1.074194 23 +NODE_4_length_351_cov_1.547297 183 +NODE_5_length_344_cov_3.273356 220 +NODE_6_length_338_cov_1.314488 121 +NODE_7_length_335_cov_1.714286 6 +NODE_8_length_331_cov_0.862319 322 +NODE_9_length_324_cov_2.141264 153 +NODE_10_length_324_cov_1.371747 235 +NODE_11_length_317_cov_1.125954 136 +NODE_12_length_311_cov_1.535156 196 +NODE_13_length_295_cov_0.945833 264 +NODE_14_length_294_cov_1.891213 155 +NODE_15_length_280_cov_1.413333 348 +NODE_16_length_278_cov_0.901345 377 +NODE_17_length_277_cov_1.540541 160 +NODE_18_length_274_cov_3.872146 25 +NODE_19_length_271_cov_0.879630 67 +NODE_20_length_267_cov_1.429245 2 +NODE_21_length_263_cov_1.177885 361 +NODE_22_length_262_cov_1.053140 262 +NODE_23_length_260_cov_1.590244 316 +NODE_24_length_258_cov_0.935961 101 +NODE_25_length_256_cov_0.945274 46 +NODE_26_length_256_cov_0.895522 153 +NODE_27_length_254_cov_0.793970 127 +NODE_28_length_253_cov_1.313131 20 +NODE_29_length_250_cov_0.851282 428 +NODE_30_length_249_cov_1.298969 249 +NODE_31_length_249_cov_0.979381 445 +NODE_32_length_248_cov_0.979275 496 +NODE_33_length_245_cov_1.000000 281 +NODE_34_length_245_cov_1.000000 183 +NODE_35_length_242_cov_0.818182 222 +NODE_36_length_240_cov_1.259459 179 +NODE_37_length_239_cov_1.032609 98 +NODE_38_length_239_cov_1.032609 405 +NODE_39_length_238_cov_1.038251 426 +NODE_40_length_238_cov_0.879781 105 +NODE_41_length_236_cov_1.049724 225 +NODE_42_length_235_cov_1.855556 440 +NODE_43_length_234_cov_1.061453 106 +NODE_44_length_232_cov_1.073446 136 +NODE_45_length_232_cov_1.073446 430 +NODE_46_length_229_cov_1.091954 471 +NODE_47_length_229_cov_0.816092 470 +NODE_48_length_227_cov_1.273256 450 +NODE_49_length_227_cov_1.017442 190 +NODE_50_length_226_cov_2.269006 315 +NODE_51_length_225_cov_1.117647 384 +NODE_52_length_225_cov_0.917647 405 +NODE_53_length_223_cov_3.303571 414 +NODE_54_length_223_cov_1.803571 355 +NODE_55_length_216_cov_1.596273 317 +NODE_56_length_216_cov_1.180124 166 +NODE_57_length_216_cov_0.869565 247 +NODE_58_length_215_cov_1.668750 267 +NODE_59_length_215_cov_1.187500 163 +NODE_60_length_215_cov_0.843750 124 +NODE_61_length_214_cov_1.232704 103 +NODE_62_length_213_cov_0.936709 421 +NODE_63_length_210_cov_1.225806 290 +NODE_64_length_208_cov_1.019608 498 \ No newline at end of file |
| b |
| diff -r 6838c2fd1228 -r 735a21808348 test-data/blast2tsv_reads.txt --- a/test-data/blast2tsv_reads.txt Sat May 18 18:14:42 2024 +0000 +++ b/test-data/blast2tsv_reads.txt Wed Aug 21 13:13:50 2024 +0000 |
| b |
| @@ -1,1 +1,6 @@ -0 Viruses Riboviria Orthornavirae Kitrinoviricota Alsuviricetes Martellivirales Bromoviridae Ilarvirus Blackberry chlorotic ringspot virus +0 Viruses Monodnaviria Shotokuvirae Cossaviricota Papovaviricetes Zurhausenvirales Papillomaviridae Firstpapillomavirinae Upsilonpapillomavirus Upsilonpapillomavirus 2 +0 cellular organisms Bacteria Thermodesulfobacteriota Desulfovibrionia Desulfovibrionales Desulfovibrionaceae Desulfovibrio unclassified Desulfovibrio +0 cellular organisms Eukaryota Opisthokonta Metazoa Eumetazoa Bilateria Protostomia Ecdysozoa Panarthropoda Arthropoda Mandibulata Pancrustacea Hexapoda Insecta Dicondylia Pterygota Neoptera Polyneoptera Dictyoptera Blattodea Blattoidea Termitoidae Rhinotermitidae Heterotermitinae Heterotermes unclassified Heterotermes +0 cellular organisms Eukaryota Opisthokonta Metazoa Eumetazoa Bilateria Protostomia Spiralia Lophotrochozoa Nemertea Enopla Hoplonemertea Monostilifera Eumonostilifera Tetrastemmatidae Tetrastemma +0 cellular organisms Archaea environmental samples +0 cellular organisms Bacteria Terrabacteria group Actinomycetota Actinomycetes Mycobacteriales Nocardiaceae Nocardia unclassified Nocardia |
| b |
| diff -r 6838c2fd1228 -r 735a21808348 test-data/blast2tsv_reads_with_rn.txt --- a/test-data/blast2tsv_reads_with_rn.txt Sat May 18 18:14:42 2024 +0000 +++ b/test-data/blast2tsv_reads_with_rn.txt Wed Aug 21 13:13:50 2024 +0000 |
| b |
| b'@@ -1,6 +1,13 @@\n #algo\tquery_id\tnb_reads\tquery_length\taccession\tdescription\torganism\tpercentIdentity\tnb_hsps\tqueryOverlap\thitOverlap\tevalue\tscore\ttax_id\ttaxonomy\tsequence\n-TBLASTX\tds2020-482-EDGG-1-Q4_42600\t12\t96\t\n-TBLASTX\tds2020-482-EDGG-1-Q4_107243\t63\t60\t\n-TBLASTX\tds2020-482-EDGG-1-Q4_2681\t8\t348\tNC_011554\tBlackberry chlorotic ringspot virus RNA2, complete genome\tBlackberry chlorotic ringspot virus\t56.3\t2\t100\t9.0\t1.04985e-23\t128.1421\t339420\tViruses;Riboviria;Orthornavirae;Kitrinoviricota;Alsuviricetes;Martellivirales;Bromoviridae;Ilarvirus;Blackberry chlorotic ringspot virus\tCCTTCCTAGCGACCACGCACACGTCAAGACCGGCATCATCAATGTCGCGACAATCGTGAACCACTTTAGTATAGTCCACATCAAGATCATCATAAGGTAGATAAAAGGAATCAATTTCCCTAGGAAAAAGTCCAGAATCATCTTCCTCATAAAAATCTGGTATCGAGGGATCAATGGTTCGCACCACCATCTCGAATGTATCAAAGATCGTCGCGAAATCAAACTTTGCGGTATGCTTAACGACAAACTCGAAAAGGAAAAGTTTTACCCATTCGTCGTAGTTGTCATCTTTATGCACACCGAACGTCGAGAAAAACCCAAAGAACGTGTGCGTGGTCGCTAGGAAGG\n-TBLASTX\tds2020-482-EDGG-1-Q4_107857\t402\t59\t\n-TBLASTX\tds2020-482-EDGG-1-Q4_63163\t88\t81\t\n+TBLASTX\tNODE_13_length_295_cov_0.945833\t264\t295\t316155\tpfam13603, tRNA-synt_1_2, Leucyl-tRNA synthetase, Domain 2. This is a family of the conserved region of Leucine-tRNA ligase or Leucyl-tRNA synthetase, EC:6.1.1.4.\tTursiops truncatus papillomavirus 2\t41.5\t1\t100\t67.0\t2.277e-05\t38.6378\t316155\tViruses;Monodnaviria;Shotokuvirae;Cossaviricota;Papovaviricetes;Zurhausenvirales;Papillomaviridae;Firstpapillomavirinae;Upsilonpapillomavirus;Upsilonpapillomavirus 2;Tursiops truncatus papillomavirus 2\tTGTGTTGGGTGTGTTTGGTTTCCGGTTACCATAATCGCTATTCTTTCAAACAGAAAGCGCATGCTAAGTATTCTCACCCAGAGGAATATGCTGACAAGCCCTCCTCAAAAGGCTATTTTTACAATGCCACCTATGAGAATGCACGAACTCTTATTCACTTCATTAAGCAATATGGATTGCCCTTCAATCCTGTTATTGCACCAGAAGATGCTGAACTAACTGATGAACAGATTCAATCTTACATCAACACAGCAAACTCCTTCTTTAATGATTATCCGACGTTACTGTTCACCCG\n+TBLASTX\tNODE_16_length_278_cov_0.901345\t377\t278\t306845\tpfam00421, PSII, Photosystem II protein. \t\t65.8\t1\t100\t47.0\t7.65615e-39\t132.634\t\t\tGTCTAACCTGTGTTGGGTGTGTTTGGGCTGTAATCGAGGTATAGTGTCGAACAAGTCGGTGTCACTGTTGAATTCTATGGCGGCGAACTCAATGGAGTCAGTTATAGTGATCCTGCTACTGTGAAAAAATATGCTAGACGTGCTCAATTGGGTGAAATTTTTGAATTAGATCGTGCTACTTTAAAATCGGATGGTGTTTTTCGTAGCAGTCCAAGGGGTTGGTTTACTTTTGGACATGCGTCGTTTGCTCTGCTCTTCTTCCAAACACACCCAACACA\n+TBLASTX\tNODE_19_length_271_cov_0.879630\t67\t271\t306845\tpfam00421, PSII, Photosystem II protein. \t\t32.9\t1\t100\t42.0\t1.69015e-11\t56.3644\t\t\tGTCTAACCTGTGTTGGGTGTGTTTGGTATGGAGGGAGGTGTATATGATACCTGGGCACCCGGAGGGGGAGATGTAAGAAAAATTACCAACTTGACCCTTAACCCAAGCGTGATATTTGGTTATTTACTAAAATCTCCTTTTGGGGGAGAAGGATGGATTGTTAGTGTGGACGATTTAGAAGATATAATTGGAGGACATGTCTGGTTAGGCTCCATTTGTATACTTGGTGGAATTTGGCATATCTTAACCAAACACACCCAACACAGGTTAG\n+TBLASTX\tNODE_20_length_267_cov_1.429245\t2\t267\t287774\tpfam10839, DUF2647, Protein of unknown function (DUF2647). This eukaryotic family of proteins are annotated as ycf68 but have no known function.\tDesulfovibrio sp. G100IX\t91.3\t1\t100\t99.0\t7.70073e-10\t48.4966\t287774\tcellular organisms;Bacteria;Thermodesulfobacteriota;Desulfovibrionia;Desulfovibrionales;Desulfovibrionaceae;Desulfovibrio;unclassified Desulfovibrio;Desulfovibrio sp. G100IX\tCTGTGTTGGGTGTGTTTGGACTTGGTATGTGAAGATACGTTGTTAGGTGCTCCGTTTTATTTTCCCATTGAGGCCGAACCTAAACCTGTGCTCGAGAGATAGCTGTCCATATACTGATAAGGGATGTATGGATTCTCGAGAAGAGAGGAGCCATGGTGGTCCCTCCCGGACCGCCCGGATCCCACGAGTGAATAGAAAGTTGGATCTACATTGGATCTCACCTGAATCGCCCCATAAACAACCAAACACACCCAACACAGGTTAGAC\n+TBLASTX\tNODE_22_length_262_cov_1.053140\t262\t262\t306604\tpfam00124, Photo_RC, Photosynthetic reaction centre protein. \tHeterotermes sp. TMJ-2004j\t40.9\t1\t100\t77.0\t4.94039e-28\t99.6256\t306604\tcellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Protostomia;Ecdysozoa;Panarthropoda;Arthropoda;Mandibulata;Pancrustacea;Hexapoda;Insecta;Dicondylia;Pterygota;Neoptera;Polyneoptera;Dictyoptera;Blattodea;Blattoidea;Termitoidae;Rhinotermitidae;Heterotermitinae;Heterotermes;unclassified Heterotermes;Heterotermes sp. TMJ-2004j\tGTCTAACCTGTGTTGGGTGTGTTTGGCTAGTCAGTAGCTTGTTATATGGGTCGTGAGTGGGAAGTTAGCTTCCGTCTGGGTATGCGCCCGTGGATTGCTGTTGCATATTCAG'..b'AGCATAGATCTTTCGGCCCTTTCGAAGCTACCGCTTCCGAGAGCCTGGCTAAACTCTGCCCAGATTATCCGATCTGCTTGCCTGTACCTTACGACGTGATCAATAAAGTGTATAGGTATCTCAGAACGCTTAAGAAGCCTGATGTGCAGTCGCCCCACTACCAAACACACCCAACACAGGTTAGAC\n+TBLASTX\tNODE_29_length_250_cov_0.851282\t428\t250\t278700\tpfam00283, Cytochrom_B559, Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits. \tuncultured archaeon CRE-PA11a\t58.6\t1\t100\t100\t7.31211e-08\t42.0012\t278700\tcellular organisms;Archaea;environmental samples;uncultured archaeon CRE-PA11a\tGTCTAACCTGTGTTGGGTGTGTTTGGGTTTCTTTGGAGCAACTCGATGAATTTAGTAAATCCTTTTAGGAGGTTCCCAATGACCATAGATCGAACCTATCCAATTTTTACAGTGCGATGGTTGGCTGTTCACGGACTGGCTGTACCTACTGTTTCTTTTTTAGGGTCAATATCAGCAATGCAGTTCATCCAACGATAAACCTAATTCAAATTATAGAGCTAGCACACCAAACACACCCAACACAGGTTAG\n+TBLASTX\tNODE_34_length_245_cov_1.000000\t183\t245\t250270\tpfam00978, RdRP_2, RNA dependent RNA polymerase. This family may represent an RNA dependent RNA polymerase. The family also contains the following proteins: 2A protein from bromoviruses putative RNA dependent RNA polymerase from tobamoviruses Non structural polyprotein from togaviruses.\tNocardia sp. 431D04\t37.5\t1\t100\t38.0\t6.42106e-08\t45.7137\t250270\tcellular organisms;Bacteria;Terrabacteria group;Actinomycetota;Actinomycetes;Mycobacteriales;Nocardiaceae;Nocardia;unclassified Nocardia;Nocardia sp. 431D04\tGTCTAACCTGTGTTGGGTGTGTTTGGATGGTGATCGGCAATTTAAAGGAATGTGTGCGATATTTTCACCAATATTCAAGGAGCTTAAAAATCGACTAAAAAGCGTGTTAGATATTAAATACATGTATGCAGACGGATTGAGACCTGATCAGTTGTCGGAGCGCATGTCACAGATAGGTGCAGGTAAATATTTTATAGAGAATGATATGGAACAGCATCTCGCCAAACACACCCAACACAGGTTAG\n+TBLASTX\tNODE_46_length_229_cov_1.091954\t471\t229\t306604\tpfam00124, Photo_RC, Photosynthetic reaction centre protein. \tHeterotermes sp. TMJ-2004j\t43.9\t1\t100\t66.0\t4.26406e-23\t86.1436\t306604\tcellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Protostomia;Ecdysozoa;Panarthropoda;Arthropoda;Mandibulata;Pancrustacea;Hexapoda;Insecta;Dicondylia;Pterygota;Neoptera;Polyneoptera;Dictyoptera;Blattodea;Blattoidea;Termitoidae;Rhinotermitidae;Heterotermitinae;Heterotermes;unclassified Heterotermes;Heterotermes sp. TMJ-2004j\tTGTGTTGGGTGTGTTTGGTTGGATGCCTGGAATACAATCATGAAATTGAAAGTACCAGATATTCCTAAAGGCATGCCATCTGAAAAACTTCCTTGACCAATAGGGTAGATCAAGAAAACAGCTGTAGCAGCCGCGACAGGAGCTGAATATGCAACAGCAATCCAAGGACGCATACCCAGACGGAAACTAAGCTCCCTCTCGCTCCAAACACACCCAACACAGGTTAGAC\n+TBLASTX\tNODE_47_length_229_cov_0.816092\t470\t229\t306687\tpfam00223, PsaA_PsaB, Photosystem I psaA/psaB protein. \t\t66.7\t1\t100\t14.0\t1.79906e-13\t61.3066\t\t\tTTGGTAAATTGGCGGAAAGAGGAGGACTCAATGATTATTCGTTCGCCGGAACCAGAAGTAAAAATTTTGGTAGATAGGGATCACATAAAAACTTCTTTCGAGGAATGGGCCAGGCCGGGTCATTTCTCAAGAACACTAGCTAAAGGCCCTGACACTACCACTTGGATCTGGAACCTACATGCTGATGCTCACGATCTTAATAGCCAAACACACCCAACACAGGTTAGAC\n+TBLASTX\tNODE_50_length_226_cov_2.269006\t315\t226\t306845\tpfam00421, PSII, Photosystem II protein. \t\t60.3\t1\t100\t41.0\t2.77182e-23\t89.1064\t\t\tGTCAACGGTGTGTTGGGTGTGTTTGGGAAAGGTCCTGGAATATGGGTGTCCGATCCTTATGGACTAACCGGAACAGTGCAACCTGTAAATCCGGCGTGGGGCGTGGAAGGTTTTGATCCTTTTGTCCCGGGAGGAATAGCTTCTCATCATATTGCAGCAGGTACATTGGGCATATTAGCGGGCCTATTCCATCTTAGCGTACGGTCACCCCAGCCAAACACACCCA\n+TBLASTX\tNODE_56_length_216_cov_1.180124\t166\t216\t306795\tpfam00361, Proton_antipo_M, Proton-conducting membrane transporter. This is a family of membrane transporters that inlcudes some 7 of potentially 14-16 TM regions. In many instances the family forms part of complex I that catalyzes the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane, and in this context is a combination predominantly of subunits 2, 4, 5, 14, L, M and N. In many bacterial species these proteins are probable stand-alone transporters not coupled with oxidoreduction. The family in total represents homologs across the phyla.\t\t26.7\t1\t100\t62.0\t5.23486e-07\t42.6815\t\t\tGTGTTGGGTGTGTTTGGGGTCTATGTGGTTTATTTGGTTCTACTGAACCAACATTAAATTTTGAAATATTAACTAATCAGTCCTATCCTGTGGCCTTGGAAATAATATTTTATATTGGATTTTTTCTTGCTTTTGCTGTAAAATTACCAATCATACCCCTACATACATGGTTACCAGATACCCACGAGAGCCAAACACACCCAACACAGGTTAGAC\n' |
| b |
| diff -r 6838c2fd1228 -r 735a21808348 test-data/rps_test.tab --- a/test-data/rps_test.tab Sat May 18 18:14:42 2024 +0000 +++ b/test-data/rps_test.tab Wed Aug 21 13:13:50 2024 +0000 |
| b |
| b'@@ -1,105 +1,26 @@\n #query_id\tquery_length\tcdd_id\thit_id\tevalue\tstartQ\tendQ\tframe\tdescription\tsuperkingdom\n-ds2020-267_120\t339\tpfam01333\tgnl|CDD|366578\t0.000848733\t197\t325\t-3\tpfam01333, Apocytochr_F_C, Apocytochrome F, C-terminal. This is a sub-family of cytochrome C. See pfam00034.\tEukaryota(19);Bacteria(1)\n-ds2020-267_374\t242\tpfam00124\tgnl|CDD|365890\t5.09126e-07\t21\t125\t3\tpfam00124, Photo_RC, Photosynthetic reaction centre protein. \tBacteria(10);Eukaryota(5);Viruses(4);unclassified sequences(1)\n-ds2020-267_471\t230\tpfam00201\tgnl|CDD|278624\t3.12575e-07\t46\t210\t1\tpfam00201, UDPGT, UDP-glucoronosyl and UDP-glucosyl transferase. \tEukaryota(20)\n-ds2020-267_710\t213\tpfam01127\tgnl|CDD|366480\t0.000723904\t46\t210\t1\tpfam01127, Sdh_cyt, Succinate dehydrogenase/Fumarate reductase transmembrane subunit. This family includes a transmembrane protein from both the Succinate dehydrogenase and Fumarate reductase complexes.\tBacteria(20)\n-ds2020-267_692\t214\tpfam00680\tgnl|CDD|366242\t4.79875e-05\t70\t180\t1\tpfam00680, RdRP_1, RNA dependent RNA polymerase. \tViruses(20)\n-ds2020-267_817\t208\tpfam05656\tgnl|CDD|377540\t3.45664e-06\t86\t190\t-1\tpfam05656, DUF805, Protein of unknown function (DUF805). This family consists of several bacterial proteins of unknown function.\tBacteria(17);unclassified sequences(2);Archaea(1)\n-ds2020-267_98\t379\tpfam16203\tgnl|CDD|374428\t1.33948e-30\t131\t280\t-1\tpfam16203, ERCC3_RAD25_C, ERCC3/RAD25/XPB C-terminal helicase. This is the C-terminal helicase domain of ERCC3, RAD25 and XPB helicases.\tBacteria(11);Eukaryota(6);Archaea(2);unclassified sequences(1)\n-ds2020-267_21\t858\tpfam00680\tgnl|CDD|366242\t8.36679e-11\t295\t729\t-1\tpfam00680, RdRP_1, RNA dependent RNA polymerase. \tViruses(20)\n-ds2020-267_261\t260\tpfam01051\tgnl|CDD|376444\t1.77523e-19\t26\t217\t-2\tpfam01051, Rep_3, Initiator Replication protein. This protein is an initiator of plasmid replication. RepB possesses nicking-closing (topoisomerase I) like activity. It is also able to perform a strand transfer reaction on ssDNA that contains its target. This family also includes RepA which is an E.coli protein involved in plasmid replication. The RepA protein binds to DNA repeats that flank the repA gene.\tBacteria(19);unclassified sequences(1)\n-ds2020-267_773\t210\tpfam01641\tgnl|CDD|376583\t5.23903e-34\t16\t174\t1\tpfam01641, SelR, SelR domain. Methionine sulfoxide reduction is an important process, by which cells regulate biological processes and cope with oxidative stress. MsrA, a protein involved in the reduction of methionine sulfoxides in proteins, has been known for four decades and has been extensively characterized with respect to structure and function. However, recent studies revealed that MsrA is only specific for methionine-S-sulfoxides. Because oxidized methionines occur in a mixture of R and S isomers in vivo, it was unclear how stereo-specific MsrA could be responsible for the reduction of all protein methionine sulfoxides. It appears that a second methionine sulfoxide reductase, SelR, evolved that is specific for methionine-R-sulfoxides, the activity that is different but complementary to that of MsrA. Thus, these proteins, working together, could reduce both stereoisomers of methionine sulfoxide. This domain is found both in SelR proteins and fused with the peptide methionine sulfoxide reductase enzymatic domain pfam01625. The domain has two conserved cysteine and histidines. The domain binds both selenium and zinc. The final cysteine is found to be replaced by the rare amino acid selenocysteine in some members of the family. This family has methionine-R-sulfoxide reductase activity.\tBacteria(18);Archaea(1);unclassified sequences(1)\n-ds2020-267_287\t256\tpfam00115\tgnl|CDD|376293\t2.8946e-26\t13\t237\t1\tpfam00115, COX1, Cytochrome C and Quinol oxidase polypeptide I. \tEukaryota(18);Bacteria(2)\n-ds2020-267_139\t320\tpfam05860\tgnl|CDD|368641\t1.34887e-13\t167\t298\t2\tpfam05860, Haemagg_act, haemagglutination activity domain. This domain is suggested to be a carbohydrate- dependent haemag'..b' nuclear location to the expanded polyglutamine repeat protein aggregates that are characteristic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.\tEukaryota(1);cellular organisms(1);Opisthokonta(1);Metazoa(1)\n+ds2020-267_4\t2297\tpfam00680\tgnl|CDD|366242\t4.43825e-05\t995\t1510\t-2\tpfam00680, RdRP_1, RNA dependent RNA polymerase. \tViruses(1);Riboviria(1);Orthornavirae(1);Pisuviricota(1)\n+ds2020-267_16\t1165\tpfam00680\tgnl|CDD|366242\t8.1737e-06\t707\t1042\t-1\tpfam00680, RdRP_1, RNA dependent RNA polymerase. \tViruses(1);Riboviria(1);Orthornavirae(1);Pisuviricota(1)\n+ds2020-267_438\t234\tpfam00078\tgnl|CDD|365856\t0.000870142\t707\t1042\t-1\tpfam00078, RVT_1, Reverse transcriptase (RNA-dependent DNA polymerase). A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.\tViruses(1);Riboviria(1);Pararnavirae(1);Artverviricota(1)\n+ds2020-267_370\t242\tpfam00146\tgnl|CDD|376297\t2.41391e-10\t22\t111\t1\tpfam00146, NADHdh, NADH dehydrogenase. \tcellular organisms(1);Eukaryota(1);Opisthokonta(1);Metazoa(1)\n+ds2020-267_278\t258\tpfam00012\tgnl|CDD|365808\t4.1355e-19\t50\t232\t2\tpfam00012, HSP70, Hsp70 protein. Hsp70 chaperones help to fold many proteins. Hsp70 assisted folding involves repeated cycles of substrate binding and release. Hsp70 activity is ATP dependent. Hsp70 proteins are made up of two regions: the amino terminus is the ATPase domain and the carboxyl terminus is the substrate binding region.\tcellular organisms(2);Eukaryota(1);Bacteria(1)\n+ds2020-267_364\t243\tpfam00216\tgnl|CDD|365952\t1.5507e-10\t134\t241\t-3\tpfam00216, Bac_DNA_binding, Bacterial DNA-binding protein. \tBacteria(2);cellular organisms(1);Pseudomonadota(1)\n+ds2020-267_558\t222\tpfam03737\tgnl|CDD|377116\t4.93695e-13\t57\t179\t-2\tpfam03737, RraA-like, Aldolase/RraA. Members of this family include regulator of ribonuclease E activity A (RraA) and 4-hydroxy-4-methyl-2-oxoglutarate (HMG)/4-carboxy- 4-hydroxy-2-oxoadipate (CHA) aldolase, also known as RraA-like protein. RraA acts as a trans-acting modulator of RNA turnover, binding essential endonuclease RNase E and inhibiting RNA processing. RraA-like proteins seem to contain aldolase and/or decarboxylase activity either in place of or in addition to the RNase E inhibitor functions.\tBacteria(2);cellular organisms(1);Pseudomonadota(1)\n+ds2020-267_218\t274\tpfam01348\tgnl|CDD|279664\t1.66328e-05\t51\t257\t3\tpfam01348, Intron_maturas2, Type II intron maturase. Group II introns use intron-encoded reverse transcriptase, maturase and DNA endonuclease activities for site-specific insertion into DNA. Although this type of intron is self splicing in vitro they require a maturase protein for splicing in vivo. It has been shown that a specific region of the aI2 intron is needed for the maturase function. This region was found to be conserved in group II introns and called domain X.\tcellular organisms(1);Eukaryota(1);Viridiplantae(1);Streptophyta(1)\n+ds2020-267_363\t243\tpfam00416\tgnl|CDD|366086\t2.02528e-05\t15\t134\t-2\tpfam00416, Ribosomal_S13, Ribosomal protein S13/S18. This family includes ribosomal protein S13 from prokaryotes and S18 from eukaryotes.\tcellular organisms(2);Bacteria(2)\n+ds2020-267_746\t211\tpfam01490\tgnl|CDD|279788\t0.000177299\t15\t134\t-2\tpfam01490, Aa_trans, Transmembrane amino acid transporter protein. This transmembrane region is found in many amino acid transporters including UNC-47 and MTR. UNC-47 encodes a vesicular amino butyric acid (GABA) transporter, (VGAT). UNC-47 is predicted to have 10 transmembrane domains. MTR is a N system amino acid transporter system protein involved in methyltryptophan resistance. Other members of this family include proline transporters and amino acid permeases.\tcellular organisms(1);Eukaryota(1);Opisthokonta(1);Metazoa(1)\n' |
| b |
| diff -r 6838c2fd1228 -r 735a21808348 test-data/rps_test.xml --- a/test-data/rps_test.xml Sat May 18 18:14:42 2024 +0000 +++ b/test-data/rps_test.xml Wed Aug 21 13:13:50 2024 +0000 |
| b |
| b'@@ -1196,613 +1196,6 @@\n </Iteration_stat>\n </Iteration>\n <Iteration>\n- <Iteration_iter-num>49</Iteration_iter-num>\n- <Iteration_query-ID>ds2020-267_321</Iteration_query-ID>\n- <Iteration_query-def>No definition line</Iteration_query-def>\n- <Iteration_query-len>250</Iteration_query-len>\n-<Iteration_hits>\n-</Iteration_hits>\n- <Iteration_stat>\n- <Statistics>\n- <Statistics_db-num>17919</Statistics_db-num>\n- <Statistics_db-len>3004588</Statistics_db-len>\n- <Statistics_hsp-len>48</Statistics_hsp-len>\n- <Statistics_eff-space>75056660</Statistics_eff-space>\n- <Statistics_kappa>0.041</Statistics_kappa>\n- <Statistics_lambda>0.267</Statistics_lambda>\n- <Statistics_entropy>0.14</Statistics_entropy>\n- </Statistics>\n- </Iteration_stat>\n- <Iteration_message>No hits found</Iteration_message>\n-</Iteration>\n-<Iteration>\n- <Iteration_iter-num>50</Iteration_iter-num>\n- <Iteration_query-ID>ds2020-267_940</Iteration_query-ID>\n- <Iteration_query-def>No definition line</Iteration_query-def>\n- <Iteration_query-len>128</Iteration_query-len>\n-<Iteration_hits>\n-</Iteration_hits>\n- <Iteration_stat>\n- <Statistics>\n- <Statistics_db-num>17919</Statistics_db-num>\n- <Statistics_db-len>3004588</Statistics_db-len>\n- <Statistics_hsp-len>15</Statistics_hsp-len>\n- <Statistics_eff-space>73866681</Statistics_eff-space>\n- <Statistics_kappa>0.041</Statistics_kappa>\n- <Statistics_lambda>0.267</Statistics_lambda>\n- <Statistics_entropy>0.14</Statistics_entropy>\n- </Statistics>\n- </Iteration_stat>\n- <Iteration_message>No hits found</Iteration_message>\n-</Iteration>\n-<Iteration>\n- <Iteration_iter-num>51</Iteration_iter-num>\n- <Iteration_query-ID>ds2020-267_61</Iteration_query-ID>\n- <Iteration_query-def>No definition line</Iteration_query-def>\n- <Iteration_query-len>465</Iteration_query-len>\n-<Iteration_hits>\n-</Iteration_hits>\n- <Iteration_stat>\n- <Statistics>\n- <Statistics_db-num>17919</Statistics_db-num>\n- <Statistics_db-len>3004588</Statistics_db-len>\n- <Statistics_hsp-len>79</Statistics_hsp-len>\n- <Statistics_eff-space>120763012</Statistics_eff-space>\n- <Statistics_kappa>0.041</Statistics_kappa>\n- <Statistics_lambda>0.267</Statistics_lambda>\n- <Statistics_entropy>0.14</Statistics_entropy>\n- </Statistics>\n- </Iteration_stat>\n- <Iteration_message>No hits found</Iteration_message>\n-</Iteration>\n-<Iteration>\n- <Iteration_iter-num>52</Iteration_iter-num>\n- <Iteration_query-ID>ds2020-267_21</Iteration_query-ID>\n- <Iteration_query-def>No definition line</Iteration_query-def>\n- <Iteration_query-len>858</Iteration_query-len>\n-<Iteration_hits>\n-<Hit>\n- <Hit_num>1</Hit_num>\n- <Hit_id>gnl|CDD|366242</Hit_id>\n- <Hit_def>pfam00680, RdRP_1, RNA dependent RNA polymerase. </Hit_def>\n- <Hit_accession>366242</Hit_accession>\n- <Hit_len>470</Hit_len>\n- <Hit_hsps>\n- <Hsp>\n- <Hsp_num>1</Hsp_num>\n- <Hsp_bit-score>60.0628</Hsp_bit-score>\n- <Hsp_score>146</Hsp_score>\n- <Hsp_evalue>8.36679e-11</Hsp_evalue>\n- <Hsp_query-from>295</Hsp_query-from>\n- <Hsp_query-to>729</Hsp_query-to>\n- <Hsp_hit-from>205</Hsp_hit-from>\n- <Hsp_hit-to>342</Hsp_hit-to>\n- <Hsp_query-frame>-1</Hsp_query-frame>\n- <Hsp_hit-frame>0</Hsp_hit-frame>\n- <Hsp_identity>33</Hsp_identity>\n- <Hsp_positive>59</Hsp_positive>\n- <Hsp_gaps>13</Hsp_gaps>\n- <Hsp_align-len>148</Hsp_align-len>\n- <Hsp_qseq>PIAVGQSWYHGGSQEFIDRMAPFDKFFCFDAKKFDSSINEWMVTIAINICRKQYYDGDNP---DYDTYWAFVAESLLRAPIYRDDGVRMQKYVGTTSGHSHNTLLQSIITLLIGYAALFELDGGLTIDNIDEHAWMESLGDDNIMAVS</Hsp_qseq>\n- <Hsp_hseq>GIAVGINPFSRDWERLGALIRKGSDVLDVDYSAFDSTLSPFVFDLVEDI-RSEFCGGLEPTRLALLEL--------LSNPIHILGGTIIKVEGGLPSGQPATSVINSILNNIYVLYALIKHTGESELD-DHETIRFISYGDDNLVAVN</Hsp_hseq>\n- <Hsp_midline> IAVG + + + + D FDS+++ ++ + +I R ++ G P L PI+ G ++ G SG +++ SI+ + AL + G +D E S GDDN++AV+</Hsp_midlin'..b'n_query-len>\n-<Iteration_hits>\n-</Iteration_hits>\n- <Iteration_stat>\n- <Statistics>\n- <Statistics_db-num>17919</Statistics_db-num>\n- <Statistics_db-len>3004588</Statistics_db-len>\n- <Statistics_hsp-len>46</Statistics_hsp-len>\n- <Statistics_eff-space>74130676</Statistics_eff-space>\n- <Statistics_kappa>0.041</Statistics_kappa>\n- <Statistics_lambda>0.267</Statistics_lambda>\n- <Statistics_entropy>0.14</Statistics_entropy>\n- </Statistics>\n- </Iteration_stat>\n- <Iteration_message>No hits found</Iteration_message>\n-</Iteration>\n-<Iteration>\n- <Iteration_iter-num>487</Iteration_iter-num>\n- <Iteration_query-ID>ds2020-267_805</Iteration_query-ID>\n- <Iteration_query-def>No definition line</Iteration_query-def>\n- <Iteration_query-len>209</Iteration_query-len>\n-<Iteration_hits>\n-</Iteration_hits>\n- <Iteration_stat>\n- <Statistics>\n- <Statistics_db-num>17919</Statistics_db-num>\n- <Statistics_db-len>3004588</Statistics_db-len>\n- <Statistics_hsp-len>37</Statistics_hsp-len>\n- <Statistics_eff-space>74930720</Statistics_eff-space>\n- <Statistics_kappa>0.041</Statistics_kappa>\n- <Statistics_lambda>0.267</Statistics_lambda>\n- <Statistics_entropy>0.14</Statistics_entropy>\n- </Statistics>\n- </Iteration_stat>\n- <Iteration_message>No hits found</Iteration_message>\n-</Iteration>\n-<Iteration>\n- <Iteration_iter-num>488</Iteration_iter-num>\n- <Iteration_query-ID>ds2020-267_685</Iteration_query-ID>\n- <Iteration_query-def>No definition line</Iteration_query-def>\n- <Iteration_query-len>214</Iteration_query-len>\n-<Iteration_hits>\n-<Hit>\n- <Hit_num>1</Hit_num>\n- <Hit_id>gnl|CDD|370442</Hit_id>\n- <Hit_def>pfam09334, tRNA-synt_1g, tRNA synthetases class I (M). This family includes methionyl tRNA synthetases.</Hit_def>\n- <Hit_accession>370442</Hit_accession>\n- <Hit_len>391</Hit_len>\n- <Hit_hsps>\n- <Hsp>\n- <Hsp_num>1</Hsp_num>\n- <Hsp_bit-score>63.8538</Hsp_bit-score>\n- <Hsp_score>156</Hsp_score>\n- <Hsp_evalue>1.80219e-14</Hsp_evalue>\n- <Hsp_query-from>16</Hsp_query-from>\n- <Hsp_query-to>117</Hsp_query-to>\n- <Hsp_hit-from>124</Hsp_hit-from>\n- <Hsp_hit-to>157</Hsp_hit-to>\n- <Hsp_query-frame>-2</Hsp_query-frame>\n- <Hsp_hit-frame>0</Hsp_hit-frame>\n- <Hsp_identity>18</Hsp_identity>\n- <Hsp_positive>22</Hsp_positive>\n- <Hsp_gaps>0</Hsp_gaps>\n- <Hsp_align-len>34</Hsp_align-len>\n- <Hsp_qseq>PKKGMFLSDRFIKGTCPKCKSEDQYGDSCEDIGT</Hsp_qseq>\n- <Hsp_hseq>PSDERFLPDRYVEGTCPHCGSEDARGDQCENCGR</Hsp_hseq>\n- <Hsp_midline>P FL DR+++GTCP C SED GD CE+ G </Hsp_midline>\n- </Hsp>\n- </Hit_hsps>\n-</Hit>\n-</Iteration_hits>\n- <Iteration_stat>\n- <Statistics>\n- <Statistics_db-num>17919</Statistics_db-num>\n- <Statistics_db-len>3004588</Statistics_db-len>\n- <Statistics_hsp-len>39</Statistics_hsp-len>\n- <Statistics_eff-space>73783904</Statistics_eff-space>\n- <Statistics_kappa>0.041</Statistics_kappa>\n- <Statistics_lambda>0.267</Statistics_lambda>\n- <Statistics_entropy>0.14</Statistics_entropy>\n- </Statistics>\n- </Iteration_stat>\n-</Iteration>\n-<Iteration>\n- <Iteration_iter-num>489</Iteration_iter-num>\n- <Iteration_query-ID>ds2020-267_60</Iteration_query-ID>\n- <Iteration_query-def>No definition line</Iteration_query-def>\n- <Iteration_query-len>471</Iteration_query-len>\n-<Iteration_hits>\n-</Iteration_hits>\n- <Iteration_stat>\n- <Statistics>\n- <Statistics_db-num>17919</Statistics_db-num>\n- <Statistics_db-len>3004588</Statistics_db-len>\n- <Statistics_hsp-len>79</Statistics_hsp-len>\n- <Statistics_eff-space>123940986</Statistics_eff-space>\n- <Statistics_kappa>0.041</Statistics_kappa>\n- <Statistics_lambda>0.267</Statistics_lambda>\n- <Statistics_entropy>0.14</Statistics_entropy>\n- </Statistics>\n- </Iteration_stat>\n- <Iteration_message>No hits found</Iteration_message>\n-</Iteration>\n </BlastOutput_iterations>\n </BlastOutput>\n' |
| b |
| diff -r 6838c2fd1228 -r 735a21808348 virAnnot_otu.xml --- a/virAnnot_otu.xml Sat May 18 18:14:42 2024 +0000 +++ b/virAnnot_otu.xml Wed Aug 21 13:13:50 2024 +0000 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="virannot_otu" name="virAnnot OTU" version="1.0.0+galaxy0" profile="21.05"> +<tool id="virannot_otu" name="virAnnot OTU" version="1.0.1+galaxy0" profile="21.05"> <description>create viral OTUs based on RPS and Blast annotations</description> <macros> <import>macros.xml</import> @@ -47,9 +47,9 @@ ]]></command> <inputs> - <param type="data" name="blast_files" format="tsv" label="Blast results file with taxonomy" multiple="true" optional="true" + <param type="data" name="blast_files" format="tabular" label="Blast results file with taxonomy" multiple="true" optional="true" help="Give one file per sample. If a file is missing, give none." /> - <param type="data" name="rps_files" format="tsv" label="RPS results file" multiple="true" /> + <param type="data" name="rps_files" format="tabular" label="RPS results file" multiple="true" /> <param type="data" name="fasta_files" format="fasta" label="Contigs file" multiple="true" /> <param type="integer" name="percentage" label="Similarity threshold percentage for OTUs cutoff" value="90" min="10" max="100" /> <param type="select" name="viral_portion" label="Minimun portion of viral sequences in RPS domain to be included"> @@ -100,4 +100,4 @@ ]]></help> <expand macro="citations" /> -</tool> \ No newline at end of file +</tool> |