| Previous changeset 2:fd7104249a3c (2024-08-21) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f |
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modified:
otu.py rps2tsv.py test-data/rps_test.tab test-data/rps_test.xml virAnnot_rps2tsv.xml |
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added:
test-data/input_otu_blast_s1.tab test-data/input_otu_blast_s2.tab test-data/input_otu_rps_s1.tab test-data/input_otu_rps_s2.tab test-data/input_otu_s1.fasta test-data/input_otu_s2.fasta test-data/rps_s1_out.tab test-data/rps_s2_out.tab |
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removed:
test-data/otu_s1.fa test-data/otu_s1_rps.tab test-data/otu_s1_tblastx.tab test-data/otu_s2.fa test-data/otu_s2_rps.tab test-data/otu_s2_tblastx.tab |
| b |
| diff -r fd7104249a3c -r d1fd5579469d otu.py --- a/otu.py Wed Aug 21 13:13:28 2024 +0000 +++ b/otu.py Sun Sep 08 14:09:07 2024 +0000 |
| [ |
| @@ -186,6 +186,8 @@ os.mkdir(cdd_output) if os.path.exists(cdd_output + "/seq_to_align.fasta"): os.remove(cdd_output + "/seq_to_align.fasta") + if os.path.exists(cdd_output + "/seq_nucc.fasta"): + os.remove(cdd_output + "/seq_nucc.fasta") file_seq_to_align = cdd_output + "/seq_to_align.fasta" file_color_config = cdd_output + "/color_config.txt" f = open(file_seq_to_align, "a") @@ -298,6 +300,7 @@ cdd_output = options.output + "/" + hits_collection[cdd_id]["short_description"].replace(" ", "_") worksheet = workbook.add_worksheet(hits_collection[cdd_id]["short_description"]) # add a worksheet file_cluster = cdd_output + '/otu_cluster.csv' + file_fasta_nucc = cdd_output + '/representative_nucc.fasta' with open(file_cluster, 'r') as clust: otu_reader = csv.reader(clust, delimiter=',') samples_list = [] @@ -342,6 +345,8 @@ if sample not in ['contigs_list', 'global_taxonomy']: total_nb_read = 0 for contig in otu_collection[otu][sample]: + if otu_collection[otu][sample][contig]['nb'] == '': + otu_collection[otu][sample][contig]['nb'] = 0 total_nb_read += int(otu_collection[otu][sample][contig]['nb']) otu_collection[otu][sample]['total_nb_read'] = total_nb_read row = 0 @@ -355,26 +360,30 @@ worksheet.write(row, column + 2, 'contigs_list') row = 1 # column = 0 - for otu in otu_collection: - if isinstance(otu_collection[otu], dict): - column = 0 - worksheet.write(row, column, otu) - # prepare table with 0 in each cells - for sample in otu_collection[otu]: - column = 1 - for samp in samples_list: - worksheet.write(row, column, 0) - column += 1 - # fill in table with nb of read for each sample and each OTU - for sample in otu_collection[otu]: - column = 1 - for samp in samples_list: - if samp == sample: - worksheet.write(row, column, otu_collection[otu][sample]['total_nb_read']) - column += 1 - worksheet.write(row, len(samples_list) + 1, otu_collection[otu]['global_taxonomy'].replace(';', ' ')) - worksheet.write(row, len(samples_list) + 2, ",".join(otu_collection[otu]['contigs_list'])) - row += 1 + with open(file_fasta_nucc, "w+") as f_nucc: + for otu in otu_collection: + log.info(otu) + if isinstance(otu_collection[otu], dict): + column = 0 + worksheet.write(row, column, otu) + # prepare table with 0 in each cells + for sample in otu_collection[otu]: + column = 1 + for samp in samples_list: + worksheet.write(row, column, 0) + column += 1 + # fill in table with nb of read for each sample and each OTU + for sample in otu_collection[otu]: + column = 1 + for samp in samples_list: + if samp == sample: + worksheet.write(row, column, otu_collection[otu][sample]['total_nb_read']) + column += 1 + worksheet.write(row, len(samples_list) + 1, otu_collection[otu]['global_taxonomy'].replace(';', ' ')) + worksheet.write(row, len(samples_list) + 2, ",".join(otu_collection[otu]['contigs_list'])) + row += 1 + f_nucc.write(">" + cdd_id + "_" + otu + "_" + otu_collection[otu]['contigs_list'][0] + "\n") + f_nucc.write(str(hits_collection[cdd_id][otu_collection[otu]['contigs_list'][0]]['nuccleotide']) + "\n") workbook.close() read_file = pd.ExcelFile(file_xlsx) for sheet in read_file.sheet_names: @@ -392,21 +401,20 @@ if os.path.exists(map_file_path): os.remove(map_file_path) - map_file = open(map_file_path, "w+") - headers = ['#cdd_id', 'align_files', 'tree_files', 'cluster_files', 'cluster_nb_reads_files', 'pairwise_files', 'description', 'full_description\n'] - map_file.write("\t".join(headers)) - for cdd_id in hits_collection: - cdd_output = hits_collection[cdd_id]["short_description"].replace(" ", "_") - short_description = cdd_output - file_seq_aligned = cdd_output + '/seq_aligned.final_tree.fa' - tree_file = cdd_output + '/tree.dnd.png' - file_cluster = cdd_output + '/otu_cluster.csv' - file_matrix = cdd_output + "/identity_matrix.csv" - cluster_nb_reads_files = cdd_output + "/cluster_nb_reads_files.tab" - map_file.write(cdd_id + "\t" + file_seq_aligned + "\t" + tree_file + "\t") - map_file.write(file_cluster + "\t" + cluster_nb_reads_files + "\t" + file_matrix + "\t") - map_file.write(short_description + "\t" + hits_collection[cdd_id]["full_description"] + "\n") - map_file.close() + with open(map_file_path, "w+") as map_file: + headers = ['#cdd_id', 'align_files', 'tree_files', 'cluster_files', 'cluster_nb_reads_files', 'pairwise_files', 'description', 'full_description\n'] + map_file.write("\t".join(headers)) + for cdd_id in hits_collection: + cdd_output = hits_collection[cdd_id]["short_description"].replace(" ", "_") + short_description = cdd_output + file_seq_aligned = cdd_output + '/seq_aligned.final_tree.fa' + tree_file = cdd_output + '/tree.dnd.png' + file_cluster = cdd_output + '/otu_cluster.csv' + file_matrix = cdd_output + "/identity_matrix.csv" + cluster_nb_reads_files = cdd_output + "/cluster_nb_reads_files.tab" + map_file.write(cdd_id + "\t" + file_seq_aligned + "\t" + tree_file + "\t") + map_file.write(file_cluster + "\t" + cluster_nb_reads_files + "\t" + file_matrix + "\t") + map_file.write(short_description + "\t" + hits_collection[cdd_id]["full_description"] + "\n") log.info("Writing HTML report") html_cmd = os.path.join(options.tool_path, 'rps2tree_html.py') + ' -m ' + map_file_path + ' -o ' + options.output log.debug(html_cmd) |
| b |
| diff -r fd7104249a3c -r d1fd5579469d rps2tsv.py --- a/rps2tsv.py Wed Aug 21 13:13:28 2024 +0000 +++ b/rps2tsv.py Sun Sep 08 14:09:07 2024 +0000 |
| [ |
| @@ -48,7 +48,7 @@ hsp["evalue"] = hit_evalue hsp["startQ"] = hit_startQ hsp["endQ"] = hit_endQ - hsp["query_id"] = blast_record.query_id + hsp["query_id"] = blast_record.query hsp["cdd_id"] = aln.hit_def.split(",")[0] hsp["hit_id"] = aln.hit_id hsp["query_length"] = blast_record.query_length # length of the query |
| b |
| diff -r fd7104249a3c -r d1fd5579469d test-data/input_otu_blast_s1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_otu_blast_s1.tab Sun Sep 08 14:09:07 2024 +0000 |
| b |
| b'@@ -0,0 +1,139 @@\n+#algo\tquery_id\tnb_reads\tquery_length\taccession\tdescription\torganism\tpercentIdentity\tnb_hsps\tqueryOverlap\thitOverlap\tevalue\tscore\ttax_id\ttaxonomy\tsequence\n+TBLASTX\tds2020-267_5\t\t2029\tXM_017248196\tPREDICTED: Drosophila bipectinata mucin-2-like (LOC108129900), mRNA\tDrosophila bipectinata\t22.6\t2\t100\t33.0\t0.000934457\t77.73910000000001\t42026\tcellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Protostomia;Ecdysozoa;Panarthropoda;Arthropoda;Mandibulata;Pancrustacea;Hexapoda;Insecta;Dicondylia;Pterygota;Neoptera;Endopterygota;Diptera;Brachycera;Muscomorpha;Eremoneura;Cyclorrhapha;Schizophora;Acalyptratae;Ephydroidea;Drosophilidae;Drosophilinae;Drosophilini;Drosophila;Sophophora;melanogaster group;ananassae subgroup;bipectinata species complex;Drosophila bipectinata\tATCGCACATGATAAAGCCCGATATCTAAGGAGCAGCACGTCCGCAACCCTCTGCCTCCAACAATAAAGCAGATTTCTTTGCTCTTCTAACAGCTATTACTTACCACAATGGACCACCTCACTTCCCTTTTCGAGCTTTTTGCTATCACACCGAAAACACAAAACAATCTACAGTTTGTTGGGATCTACCACAGACCTCCACACTCCGTTCGAGCAAACCTCCGCAACGTTGAAAAACACAAAATCACAGTCGCTCACGCCATGCACAAGTACCTTTACCCGCATGAAATCGACTTTGTTATCAACCAAATGCGACGCTCAGACGTCACTGAAGATGCCATACTTGCTGACTTTTTCGACAACAACGTCGAACCACTTGAACCTGTTCTTGACGAACACTTCGAACGTGGACTCTCCGCAATGCTGGACGCTTTTCGCCCTCCGCAGAAATGCCTACCTGCCCACATCTATGATGTGCAGCACCACTACCCATATAAATGGCAAGTGAACGCTGAAGCCCCCTTCTCCACCGATTCCTATTTCTTAGCGAATCGACCAACCTTCCGCGCAGTGTTTGAACGACTCGAATCGCTCTACACACACCTCGCAACCGATTGGCACCGCCGATACGGAAACAAAACCGACAATGATGATTTTATGAATGATCATGTCCCTGCGAAATTTGGCCCTATGAAAGAAACAGTCTTCTCATGGACTCACCGATGGCACCACGTCATCAAATCCAACTTCACCGACACAGCTGGATTGTCTAAAGACTATTACTTCAAAAACCGATACATCTTCCCAATGCTACTTCACACGAAGACAGCGATTGTCAAGAAAGACGACCCGAATAAGATGCGAACCATCTGGGGCTGTTCAAAGCCTTGGATCATCGCAGACACCATGCTATGGTGGGAATACGTCGCGTACGCTAAGTTACAACCTGGAGCCACACCAATGCTCTGGAGTTACGAAACCTTCACAGGTGGCTGGCTTAGACTCAACCACGCACTTTTCTCTTCATACATACGGCACTCGTACATCACACTCGACTGGAAACGCTTCGACAAGAAAGCGTATTTCTGCATCATCGACAAAATTTTCGATGGCGTTGAAACATTCCTCGACTTTGACAACGGCTATTTGCCTACGAAAGATTATCCCGATACCAAATCGACTTGGACACAAGAACGTTCCACCCGCCTCAAACGCCTGTTTGACTGGACAAAAGAGAACTTCTACCATGCACCAATTGTCCTACCCAATGGGCACATGTACGTCCGAAAATTCGCTGGAATACCCTCTGGCCTATTTATCACTCAACTGATCGATTCCTGGTACAACTACACCATGCTCGCAACCATCCTATCCGCGATGGGCTTCGACCCTCGGTCCTGTATTATTAAAGTCCAAGGTGATGACTCAATCATCCGCCTCAGTGCACTCATCCCTCCGGATGCTCACGATTCTTTTTTAACTAAGGTCCAAGAACTCGCCGACTACTACTTTCAATCAGTAGTCTCCGTGAACAAGTCTGAAGTACGCAACGAGCTCAACGGATGCGAAGTTTTATCGTACCGACACAGACACGGTTTACCATACCGCGATGAACTAGCTATGCTAGCTCAACTGTATCACACGAAAGCACGCAACCCAAGTCCCGAAATCACAATGGCACAATCCATCGGCTTCGCCTACGCTTCCTTCGGAAATCATGAAAGAGTACGTCTCGTACTACATGATATCTACGAATATTACAAGCATCAAGGCTACACACCCAACCGAGCCGGACTCAGCCTCGTCTTCGGAAACTCTCCTGACCTCATGATCCCGCACTACACACTTGATCACTTTCCCTCAATCAGGGAAATAAAAATGTTCCTGACTAATGCAAAATATGCCAATGAAGAAACCAACTCACGAACGTGGCCTTTAACCCACTTTCTCCATCTTCCTTGTCATCGCACTTAGTATTTGAGCAATTGCAATTACAACATAATTACAAAAAAAGGATTGCGGACGTGCTG\n+TBLASTX\tds2020-267_7\t\t1772\tXR_002501664\tPREDICTED: Aedes aegypti uncharacterized LOC110678502 (LOC110678502), ncRNA\tAedes aegypti\t28.0\t1\t100\t14.0\t0.00030013\t55.5941\t7159\tcellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Protostomia;Ecdysozoa;Panarthropoda;Arthropoda;Mandibulata;Pancrustacea;Hexapoda;Insecta;Dicondylia;Pterygota;Neoptera;Endopterygota;Diptera;Nematocera;Culicomorpha;Culicoidea;Culicidae;Culicinae;Aedini;Aedes;Stegomyia;Aedes aegypti\tCAGCACGTCCGCAAAGTTCGCTCTCTTCATTGAGCTAATTGGTTAAAAGTCTACTTGTTAAGTAGCATTCACATCAAGGAAAGAATTTCGTCAAAATGGCATACCAAAAGCCCGACAAATCGACCGTCTCCGGCACGACTCTTACGCCAGATGACTCAGCCTCACAAGCTGGTCCACAAAATGATACCCCCAATCCTGCGAAGTCCGGACGCCCAAAGCGTTCATCAAAGATTTCAAAGGGCAAAGATCTACCTCCGGGTGCGATCAAGGTACCAAAAGGTGGCGCCAACATGACGGGGAAAGCATCTCCCGTACAGTCTGCAACCATTCCATTTCGGGATGGGGAGAAATAGACCTCAACTCTCATAGAAATGAGATTGAGCCGGTCTTCACAGTCGACGCTCAGCCGTATGACGACCTTGTCAACGTGGTGTACTCATCACTTCAGTCGCGATACTCAAATGCGGCGAAGCACATCCCGTTTGGCCTCTTCCGCTACTACTGCATGCAATTGTGGTGGTATCGGGTTCTTTTTCTGCATCGCACGAACGGCAATGCTCTCACATCTGACGAACGTCAGTTCATGAGCATCATGGAGACTGGACAAGAGTTCCAAATCCCCTCCCAAATAGCACAGTATCTTGCCAACCTTGGCAATTTCATGCAAGGAGGAGAGAACTTCTTTTTCCGC'..b'GTGAACGTGTCGAGCGCTTGCTAGATGCCGGTACGCCATTTTTGGAAGTCTCACCGATGGCAGCGTATGGCATGTATGATGCCGATATCACGGGTAACGGCTTGCGGACGTGCTG\n+TBLASTX\tds2020-267_843\t\t207\tXM_012292849\tPREDICTED: Megachile rotundata gamma-gliadin-like (LOC105663506), mRNA\tMegachile rotundata\t48.1\t2\t100\t11.0\t2.41079e-05\t70.4077\t143995\tcellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Protostomia;Ecdysozoa;Panarthropoda;Arthropoda;Mandibulata;Pancrustacea;Hexapoda;Insecta;Dicondylia;Pterygota;Neoptera;Endopterygota;Hymenoptera;Apocrita;Aculeata;Apoidea;Anthophila;Megachilidae;Megachilinae;Megachilini;Megachile;Megachile rotundata\tCTATCTAAGGAGCAGCACGTCCGCAACAAGACTACACTCGCACGTCCTCAAAAGTGTTAGGGTGTCCCAGCACGTCCGCAATAAGACTACACTCGCACGTCCGCAAAAGTGTGAGGGTGGCCCAGCACGTCCGCAATAGGACTACACTCGCACGTCCGCAAAAGTGTGAGGGTGGCCGACTTGCGGACGTGCTGCTCCTTAGATAGA\n+TBLASTX\tds2020-267_852\t\t207\t\n+TBLASTX\tds2020-267_855\t\t206\tNR_149697\tEremothecium gossypii ATCC 10895 25S ribosomal RNA copy 30 (AGOS_RDNA25_30), rRNA\tEremothecium gossypii ATCC 10895\t75.5\t3\t100\t10.0\t8.295481666666668e-08\t189.6928\t284811\tcellular organisms;Eukaryota;Opisthokonta;Fungi;Dikarya;Ascomycota;saccharomyceta;Saccharomycotina;Saccharomycetes;Saccharomycetales;Saccharomycetaceae;Eremothecium;Eremothecium gossypii;Eremothecium gossypii ATCC 10895\tTATCTAAGGAGCAGACGACTTAAGCGCCATCCATTTTAAGGGCTAGTTGTTTCGGCAGGTGAGTTGTTACACACTCCTTAGCGGTTTACAACTTCCATGTCCACCGTCCTGCTGTCTTAAACAACCAACACCTAGGGCAGCACGTCCGCAAAACAGTTAGGCTGTATTGCGGACGTGCTGAGTGAGCCTCCCTTGCGGACGTGCTG\n+TBLASTX\tds2020-267_858\t\t206\tXM_021957467\tPREDICTED: Prunus avium protein GRAVITROPIC IN THE LIGHT 1 (LOC110756088), mRNA\tPrunus avium\t93.3\t2\t100\t11.0\t7.859985e-15\t172.13\t42229\tcellular organisms;Eukaryota;Viridiplantae;Streptophyta;Streptophytina;Embryophyta;Tracheophyta;Euphyllophyta;Spermatophyta;Magnoliopsida;Mesangiospermae;eudicotyledons;Gunneridae;Pentapetalae;rosids;fabids;Rosales;Rosaceae;Amygdaloideae;Amygdaleae;Prunus;Prunus avium\tCAGCACGTCCGCAATAGACCCACCATTATAAATCCCCCCACCCAAACCAAAAAAATAAAAGCTTTTATATATATGAGTTTTTATATTTTCTGATCTGATTGAGAGTACTTGTTCTGTTTTCTCAGTAACTGCACTCTCTTTCCTCTTTTTCCCGCGCTTTAAAAATCCCAACTTTTTCTCACCCCCCGCAATTTGCGGACGTGCTG\n+TBLASTX\tds2020-267_860\t\t206\tXM_023097363\tPREDICTED: Cucurbita moschata monooxygenase 2-like (LOC111455625), transcript variant X1, mRNA\tCucurbita moschata\t95.7\t1\t100\t5.0\t6.41544e-05\t52.3867\t3662\tcellular organisms;Eukaryota;Viridiplantae;Streptophyta;Streptophytina;Embryophyta;Tracheophyta;Euphyllophyta;Spermatophyta;Magnoliopsida;Mesangiospermae;eudicotyledons;Gunneridae;Pentapetalae;rosids;fabids;Cucurbitales;Cucurbitaceae;Cucurbiteae;Cucurbita;Cucurbita moschata\tGACGCACTGACCGTTCCGGAGTACCTAACAACGTATCTTCACAGACCAAGAACTACGAGATCGCCCCTTTCATTCTGGGGTGACGGAGGGATCGTACCATTCGAGCCTTTTTTTTTCATGCTTTTCCCGGAGGTCTGGAGAAAGCTGCAATCAATAGGATTTTCCTAATCCTCCCTTCCCGGGGGGTGTTGTACGGTCAGTGCGTC\n+TBLASTX\tds2020-267_874\t\t206\tXM_022032753\tPREDICTED: Carica papaya uncharacterized LOC110807581 (LOC110807581), partial mRNA\tCarica papaya\t86.0\t3\t100\t75.0\t1.8354816108372398e-14\t291.7496\t3649\tcellular organisms;Eukaryota;Viridiplantae;Streptophyta;Streptophytina;Embryophyta;Tracheophyta;Euphyllophyta;Spermatophyta;Magnoliopsida;Mesangiospermae;eudicotyledons;Gunneridae;Pentapetalae;rosids;malvids;Brassicales;Caricaceae;Carica;Carica papaya\tCAGCACGTCCGCAATCTGGGAGGGTTGAGACCAAGCCAAGGGCAGGGGCCTAAAGTATCGAAAAGGCAAGGACTCCAAGAAGAAGCCAAGCCTGAGGCCAAGAAAAGCGAGTTCAAGATCAGGAGCCAAAGCGGGCCGAGAAGAAAGAAGGAAGGCTTCATCTGCTCCAAGCCCCTAAAGAGGCTCAGCGGGTAGCGGACGTGCTG\n+TBLASTX\tds2020-267_896\t\t152\tXM_019781697\tPREDICTED: Branchiostoma belcheri fibropellin-1-like (LOC109479706), partial mRNA\tBranchiostoma belcheri\t66.7\t4\t100\t5.0\t0.000909993\t93.1618\t7741\tcellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Deuterostomia;Chordata;Cephalochordata;Leptocardii;Amphioxiformes;Branchiostomatidae;Branchiostoma;Branchiostoma belcheri\tTACCTTTGCCGTGTTCACAGGGTTTCTGTGTCCTTTGCCGTGTTCACAGGGTTTCTGTGTCCTTGCCGTGTTCACAGGGTTTCTGTGTCCTTTACCTTACCTTTGCCGTGTTCACAGGGTTTCTGTGTCCTTTGCCGTGTTCACAGGGTTTC\n' |
| b |
| diff -r fd7104249a3c -r d1fd5579469d test-data/input_otu_blast_s2.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_otu_blast_s2.tab Sun Sep 08 14:09:07 2024 +0000 |
| b |
| b'@@ -0,0 +1,129 @@\n+#algo\tquery_id\tnb_reads\tquery_length\taccession\tdescription\torganism\tpercentIdentity\tnb_hsps\tqueryOverlap\thitOverlap\tevalue\tscore\ttax_id\ttaxonomy\tsequence\n+TBLASTX\tds2020-328_1\t\t2975\tXM_003097640\tCaenorhabditis remanei hypothetical protein (CRE_14174) mRNA, complete cds\tCaenorhabditis remanei\t55.4\t7\t100\t100\t1.8358885722218487e-09\t1048.9798\t31234\tcellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Protostomia;Ecdysozoa;Nematoda;Chromadorea;Rhabditida;Rhabditina;Rhabditomorpha;Rhabditoidea;Rhabditidae;Peloderinae;Caenorhabditis;Caenorhabditis remanei\tGGTCGGGATAGACGTTGGAGCGCGGTCAGCCGAGACCCCTGACAGAGGAAAGAGTCTTGAGGAGTCCAACGTTCGGCCAGGCATAATAATTCGTGCCCACTAATCGAATCGGTTTACTCGCCCACCATGTCAGCGCCTTCGGGTTAGTTCTTTATGGAGTTATTTCTTGTTCTTTCTGTCATAACAATTCTCCTTATGGAAGTCCCCCACAAGATTAAGAATGCTTGTTGCCGCGGCTGTCTTGGTTCTTCGTTTAGCTTTCTGGCATATTCTACGGAGCTTTCCACTCTGGAGCTGGCTTTCAGAAAAACCTTCATTCACTAGATGTGAAGCACCCCTATGGGGGAACCCTCTTACCCGCTTTCCTCCCCCCCCGATATGGGGGGCCTCGCTGTCGCCTTTGGCTCGAGCTACTTTTTCTCCTGGAACGGATAGCTTTCTGTCCAAGTCTATCTCCCAAAAGTCAGCCATGTAATTGACTTCTAACGTCTAATTTTCTTTTTCACCGGGGGTCCCTGATCCCCGTTGAATATTCCTTCCTTCTGAAAAAGCTGTGACTCCTAAATTCTTTGATTGAATGAAATGTGGACTTGGTCACGGGGCAATCTTCTTTTTTAGACCCCGCTTCTCTCGGTGTTACCTTTTTCGCCTTCTCGTCTCGCTTCGCGTCGTCNNNNNNNNNNGGTCGGGATAGACGCGCCGCTTCCGTCTGTTTTACCTTGTTAGAATTCTCGGCGCGCTTGGCGTCGTCTTTAGAGTCAATTCTATTGGAATCTCCTTTCCCCTTCTTTTCTTCCCCCACGATGAAAAAAATAAATATTGCAAAAAGAACAATATTTCCCCCCGTGGTCATCATAGTGGTTCCTTCTGATCCTAGAAAACGATTAAAAAGAAGGCAAAAAAAACAAAGGAGGATCTGCTTTTTCATATTAAAGCGCTTTCTTTCTTTTAAAAATACATCATAGTAAAGCGCTTCCTTTTAAAAAAGCATCTGGTTCCATCTTTCTTTCGTTAGTTAACCCACCTTTTTCTAAAAGGGATTGTAGTAATTCTGGTTTTACACTATTTAGAATGGCTCTCTCATATTGAGAGATTCTGTCTAGTGGCATTCGATCACAGAATCCATTGACAGCTGCATAAATGACTAGAATTTGTTTTTCAATTGGAAGTGGTGCATATTGTGGTTGTTTCAGTACTTCTGTAAGCCTTGCACCTCTATTGAGTAATGCCTGAGTCGCAGCATCAAGGTCTGACCCAAATTGAGCAAAGGCCGCCACTTCGCGATACTGTGCCAATTCCAGTTTTAAACTACCGCAGACCTGTTTCATAATTTTCAACTGAGCGGCAGACCCGACGCGACTGACAGATAAGCCGACGTTAATAGCAGGTCTAATTCCGCGATAAAAGAGCTCTGTTTCCAAACAGATTTGTCCATCAGTAATGGAGATTACATTGGTTGGAATATAGGCCGATACGTCTCCAGCTTGTGTTTCAATGACGGGTAAGGCGGTCAAGCTACCTGCACCTGTCTGGTCCGATCGTTTAGCGGCTCTTTCTAAGAGACGGGAATGTAAATAGAAAACATCGCCTGGGAAAGCCTCACGGCCTGGTGGTCGGCGTAACAATAATGACATTTGTCGATATGCCACCGCCTGTTTACTAAGATCATCATAGATTATTAATGCGTGCATTCCATTATCGCGGAAATATTCCCCCATGGCACACCCAGAATATGGGGCCAGAAATTGCAGAGGAGCTGGATCCGAAGCGGTGGCTGCTACAAGAATGGAATATTCCAAAGCATTCGCTTCTGAAAGAATTTGAACTAATTGTGCCACAGTCGAGCGTTTCTGTCCAATTGCTACATAGACACAATACAATGTCTCACTCTCAGAGGTGGCCCTTGAGTTCAGTTGCTTTTGGTTTAATATGGTATCGATAGCAATAGCTGTTTTTCCAGTTTGTCGGTCCCCGATTATAAGTTCTCGTTGACCACGGCCTATAGGAACCAGGCTATCTACCGCTTTTAACCCTGTTTGCATAGGCTCGTGCACAGATTTACGTTCAATAATCCCAGGGGCTTTCACTTCGACACGTCTTCGCTCGTGATCGCTTAGAGCCCCTCTTCCATCAATAGGAACTCCCAACCCGTCGACCACGCGCCCTAGCATAGCCTTTCCCGCAGGAACATCCACAATGGATCCAGTGCGCTTGACAAGATCTCCTTCTTTAATAGCGGTATCACTACCAAAGACAACAATCCCTACATTCTCATTCTCAAGATTCAACGCTATTCCTTTCACACCGCTGGCAAATTCAACCATTTCCCCAGCTTGAATCTCGTTCAATCCATAAACACGTGCAATCCCATCTCCAACTGAGACCACTCGACCGATCTCATCCACTTGAAAATTCGTGTAAAAGTTGGTAATTCTACTTTCTAATAGAGTTGTTAGTTCCGCAGCTCTGGTAGAGAATTCCATAATTTTTTCTTTTAAAGAAAGTCAAGGGAGAATTCCGCTTATTGTTTTTGGCTCGAAATAAAGCTAGGGTCCTGATCGAGCAACTAGTAGTCCTATCTATCCACCTCTCCAGAAGGGCTATTTGGGGTCTAATTTTCTTTCTATCTGACAGGACAAACAAAGAGGAAGGGGTGGTTCTTTCATTGCATTGATAGAAGTCTAACTAGAAAAAGATCTCTCTATTACTTTGAGAAGAGAATCGTTGGTTTGACCGACGAACTACGTGGGAAATATGAGTTGAGAGGACAAGAGGATTCGATCTCCACGAAAGGCTAAAGGAACATAAAAAAAGCTAGAATTTGTTGCAAACAGTGACCGAGATGCCAGGGAAAAACTGTTGTTTCACATTTCCGGAAAGACCACCTATTTGTTCGTTTACCAGGTTCGGTACGAAATCATAAATAAGCTCTACCCCGGGCCATCGCCTTATGGCCTAGGGGCGTCTATCCCGCC\n+TBLASTX\tds2020-328_2\t\t2632\tXR_002602986\tPREDICTED: Momordica charantia uncharacterized LOC111022566 (LOC111022566), ncRNA\tMomordica charantia\t53.7\t1\t100\t6.0\t2.65559e-05\t59.718\t3673\tcellular organisms;Eukaryota;Viridiplantae;Streptophyta;Streptophytina;Embryophyta;Tracheophyta;Euphyllophyta;Spermatophyta;Magnoliopsida;Mesangiospermae;eudicotyledons;Gunneridae;Pentapetalae;rosids;fabids;Cucurbitales;Cucurbitaceae;Momordiceae;Momo'..b'otyledons;Gunneridae;Pentapetalae;asterids;lamiids;Solanales;Solanaceae;Nicotianoideae;Nicotianeae;Nicotiana;Nicotiana attenuata\tCGGTCGGATAGACGATGGTCCTGGTTTGACATGGTTTACGCGTTACTGGTTCCCGGAAGAGTTAATATCTCCATTAGCTAAACCCTTTCTTACCCTGCCCTTGGACTCGTATTTTGTTTGTACACAATCAACGGAGGCCTCCCCGACATATGTTGCAACGTCTTCAATAGCATGCGCTGTTTTCGTCTATCCCGACCGCCATAATTCAGATCGGA\n+TBLASTX\tds2020-328_760\t\t215\t\n+TBLASTX\tds2020-328_762\t\t215\tXM_022823638\tPREDICTED: Setaria italica calcineurin B-like protein 7 (LOC101773532), mRNA\tSetaria italica\t63.2\t3\t100\t5.0\t1.4408199999999998e-08\t100.18979999999999\t4555\tcellular organisms;Eukaryota;Viridiplantae;Streptophyta;Streptophytina;Embryophyta;Tracheophyta;Euphyllophyta;Spermatophyta;Magnoliopsida;Mesangiospermae;Liliopsida;Petrosaviidae;commelinids;Poales;Poaceae;PACMAD clade;Panicoideae;Panicodae;Paniceae;Cenchrinae;Setaria;Setaria italica\tGGTCGGGATAGACGGAACTTCTTGCTCAGCAGGCGTAGCTTGGAGGGGGAGTGTAGCGGGGGTAAGGTAAGGAAGAGCCGCCAGAGAGGAAGCCAAACCGGCCTATTAAGCGCAGCTAAGCTAATATGCGCCGGAGAAAGCCAGGTGCCGGAGGTAAGCTCTATTCGGCCCGGAGCAAAAATTCCCCATAACGAATGGACTCGACTGTCCCGACC\n+TBLASTX\tds2020-328_763\t\t215\tXM_019381544\tPREDICTED: Nicotiana attenuata anthocyanidin 3-O-glucosyltransferase 6-like (LOC109217303), mRNA\tNicotiana attenuata\t61.0\t1\t100\t7.0\t3.09195e-09\t67.0494\t49451\tcellular organisms;Eukaryota;Viridiplantae;Streptophyta;Streptophytina;Embryophyta;Tracheophyta;Euphyllophyta;Spermatophyta;Magnoliopsida;Mesangiospermae;eudicotyledons;Gunneridae;Pentapetalae;asterids;lamiids;Solanales;Solanaceae;Nicotianoideae;Nicotianeae;Nicotiana;Nicotiana attenuata\tCGGTCGGGATAGACGGTGCTCTTCTCTCCAATTCATCCCCAAATACAAACCCATCTTCCTCTCTCTGCACCACAGCAATCGCCATCTCCATTTCCTTCACCAAAATACTCCTATTCATGTGCTGCTCTGCATAGAGCGGCCACGCCACCATCGACACCCCGGCGATCACCGCTTCAAGCACCGAGTTCCAGCCACGTTTATCGTCTATCCCGACC\n+TBLASTX\tds2020-328_766\t\t215\t\n+TBLASTX\tds2020-328_775\t\t214\tXM_017230452\tPREDICTED: Drosophila eugracilis NADH-quinone oxidoreductase subunit M-like (LOC108117906), mRNA\tDrosophila eugracilis\t31.9\t1\t100\t12.0\t0.000539192\t49.6374\t29029\tcellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Protostomia;Ecdysozoa;Panarthropoda;Arthropoda;Mandibulata;Pancrustacea;Hexapoda;Insecta;Dicondylia;Pterygota;Neoptera;Endopterygota;Diptera;Brachycera;Muscomorpha;Eremoneura;Cyclorrhapha;Schizophora;Acalyptratae;Ephydroidea;Drosophilidae;Drosophilinae;Drosophilini;Drosophila;Sophophora;melanogaster group;eugracilis subgroup;Drosophila eugracilis\tCATGTTTTGGCCTTGTGTGTCCATAACTCAAAATAGGTGACCTAACGGCCGCCGCCCGACTAAACATACCAATAGTCACCAGATTCATATGGGCTACTGAGGAGTAAGCAATGATCTTCTTAAGATCGATCTGTCTTGAAGTGGTCAAGGAAGTATATATTATAGCAATCGCGCTTGGAGTATAAATGAAAGAAGTCCCGCGTCTATCCCGACC\n+TBLASTX\tds2020-328_776\t\t214\tXR_002052009\tPREDICTED: Ipomoea nil uncharacterized LOC109168185 (LOC109168185), ncRNA\tIpomoea nil\t85.2\t2\t100\t38.0\t0.000815059\t62.6181\t35883\tcellular organisms;Eukaryota;Viridiplantae;Streptophyta;Streptophytina;Embryophyta;Tracheophyta;Euphyllophyta;Spermatophyta;Magnoliopsida;Mesangiospermae;eudicotyledons;Gunneridae;Pentapetalae;asterids;lamiids;Solanales;Convolvulaceae;Ipomoeeae;Ipomoea;Ipomoea nil\tTATATTAGCGCTCTCCAAGTGTGCTTGTTCCTCCCTTCTTCCTTACCATGGCAAGTCTTTGTGAAATAACTCCGATGAGAAGAAAAAAGAAGGCGTTAAGAGACCCTCCTGGCCCAACCCTAGACACTCTAAGATCCTTTTTCAAACCTGCTCCCATTTCGAGTCAAGAGATAGATAAATAGACACATCCCATTGCACTGACCGGGTTCGTTCG\n+TBLASTX\tds2020-328_826\t\t211\tXM_008367882\tPREDICTED: Malus x domestica F-box/kelch-repeat protein At3g06240-like (LOC103429750), transcript variant X1, mRNA\tMalus domestica\t76.6\t6\t100\t15.0\t0.00013627621933333335\t221.7619\t3750\tcellular organisms;Eukaryota;Viridiplantae;Streptophyta;Streptophytina;Embryophyta;Tracheophyta;Euphyllophyta;Spermatophyta;Magnoliopsida;Mesangiospermae;eudicotyledons;Gunneridae;Pentapetalae;rosids;fabids;Rosales;Rosaceae;Amygdaloideae;Maleae;Malus;Malus domestica\tGGTCGGGATAGACGTTTGGTTTGGTTATGACGAAGATAGACGGGTTTCCAGAGAAGCAATGCTGATCATTCCGTGTTCATAAAAAGGAGAAAAGAGGAAACTACTGTTCTCCTAGTGTACTCAGTTTAGAACTCTAAATTAACAAGTAAAATTTAGATATTAGTAAGATATGCAGCGAGTACGCTCGGCGAGTACGGCGTCTCTCCCGACC\n' |
| b |
| diff -r fd7104249a3c -r d1fd5579469d test-data/input_otu_rps_s1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_otu_rps_s1.tab Sun Sep 08 14:09:07 2024 +0000 |
| b |
| b'@@ -0,0 +1,45 @@\n+#query_id\tquery_length\tcdd_id\thit_id\tevalue\tstartQ\tendQ\tframe\tdescription\tsuperkingdom\n+Query_2\t2436\tpfam02123\tgnl|CDD|280316\t2.04111e-21\t184\t1476\t1\tpfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.\tViruses(1);Riboviria(1);Orthornavirae(1);Duplornaviricota(1)\n+Query_4\t2297\tpfam00680\tgnl|CDD|279070\t3.12197e-05\t995\t1873\t-2\tpfam00680, RdRP_1, RNA dependent RNA polymerase. \tViruses(1);Riboviria(1);Orthornavirae(1);Pisuviricota(1)\n+Query_5\t2029\tpfam00680\tgnl|CDD|279070\t8.86955e-06\t840\t1706\t3\tpfam00680, RdRP_1, RNA dependent RNA polymerase. \tViruses(1);Riboviria(1);Orthornavirae(1);Pisuviricota(1)\n+Query_6\t1860\tpfam02123\tgnl|CDD|280316\t1.27376e-17\t1147\t1764\t-1\tpfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.\tViruses(1);Riboviria(1);Orthornavirae(1);Duplornaviricota(1)\n+Query_8\t1703\tpfam00680\tgnl|CDD|279070\t3.19349e-12\t685\t1458\t-3\tpfam00680, RdRP_1, RNA dependent RNA polymerase. \tViruses(1);Riboviria(1);Orthornavirae(1);Pisuviricota(1)\n+Query_19\t425\tpfam00005\tgnl|CDD|306511\t3.70622e-07\t129\t275\t-1\tpfam00005, ABC_tran, ABC transporter. ABC transporters for a large family of proteins responsible for translocation of a variety of compounds across biological membranes. ABC transporters are the largest family of proteins in many completely sequenced bacteria. ABC transporters are composed of two copies of this domain and two copies of a transmembrane domain pfam00664. These four domains may belong to a single polypeptide as in CFTR, or belong in different polypeptide chains.\tBacteria(2);cellular organisms(1);Terrabacteria group(1)\n+Query_38\t386\tpfam01347\tgnl|CDD|279663\t0.000262768\t129\t275\t-1\tpfam01347, Vitellogenin_N, Lipoprotein amino terminal region. This family contains regions from: Vitellogenin, Microsomal triglyceride transfer protein and apolipoprotein B-100. These proteins are all involved in lipid transport. This family contains the LV1n chain from lipovitellin, that contains two structural domains.\tcellular organisms(1);Eukaryota(1);Opisthokonta(1);Metazoa(1)\n+Query_41\t380\tpfam04879\tgnl|CDD|282703\t2.77416e-08\t125\t274\t-2\tpfam04879, Molybdop_Fe4S4, Molybdopterin oxidoreductase Fe4S4 domain. This domain is found in formate dehydrogenase H for which the structure is known. This first domain (residues 1 to 60) of Structure 1aa6 is an Fe4S4 cluster just below the protein surface.\tBacteria(2);cellular organisms(1);Pseudomonadota(1)\n+Query_42\t379\tpfam16203\tgnl|CDD|318443\t8.05104e-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.\tcellular organisms(2);Bacteria(1);Terrabacteria group(1)\n+Query_44\t376\tpfam00401\tgnl|CDD|306831\t6.62013e-05\t81\t215\t-3\tpfam00401, ATP-synt_DE, ATP synthase, Delta/Epsilon chain, long alpha-helix domain. Part of the ATP synthase CF(1). These subunits are part of the head unit of the ATP synthase. This subunit is called epsilon in bacteria and delta in mitochondria. In bacteria the delta (D) subunit is equivalent to the mitochondrial Oligomycin sensitive subunit, OSCP (pfam00213).\tcellular organisms(2);Eukaryota(1);Viridiplantae(1)\n+Query_58\t347\tpfam00471\tgnl|CDD|306877\t8.86568e-13\t132\t302\t3\tpfam00471, Ribosomal_L33, Ribosomal protein L33. \tcellular organisms(2);Bacteria(1);Eukaryota(1)\n+Query_61\t344\tpfam00252\tgnl|CDD|306711\t1.17482e-22\t107\t295\t2\tpfam00252, Ribosomal_L16, Ribosomal protein L16p/L10e. \tcellular organisms(2);Eukaryota(1);Viridiplantae(1)\n+Query_62\t343\tpfam00421\tgnl|CDD|306845\t7.93928e-41\t92\t337\t-1\tpfam00421, PSII, Photosystem II protein. \tcellular organisms(1);Eukaryota(1);Viridiplantae(1);Streptophyta(1)\n+Query_64\t339\tpfam01333\tgnl|CDD|307480\t0.000362606\t197\t325\t-3\tpfam01333, Apocytochr_F_C, Apocytochrome F, C-terminal. This is a sub-family of cy'..b"8\t126\t1\tpfam03154, Atrophin-1, Atrophin-1 family. Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual 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+Query_203\t235\tpfam00164\tgnl|CDD|278589\t1.83229e-23\t3\t182\t3\tpfam00164, Ribosom_S12_S23, Ribosomal protein S12/S23. This protein is known as S12 in bacteria and archaea and S23 in eukaryotes.\tcellular organisms(2);Eukaryota(1);Viridiplantae(1)\n+Query_211\t234\tpfam00155\tgnl|CDD|306629\t0.000251531\t3\t182\t3\tpfam00155, Aminotran_1_2, Aminotransferase class I and II. \tBacteria(2);cellular organisms(1);Pseudomonadota(1)\n+Query_219\t233\tpfam00680\tgnl|CDD|279070\t0.000703744\t3\t182\t3\tpfam00680, RdRP_1, RNA dependent RNA polymerase. \tViruses(1);Riboviria(1);Orthornavirae(1);Pisuviricota(1)\n+Query_232\t231\tpfam00481\tgnl|CDD|306885\t0.00063843\t3\t182\t3\tpfam00481, PP2C, Protein phosphatase 2C. Protein phosphatase 2C is a Mn++ or Mg++ dependent protein serine/threonine phosphatase.\tEukaryota(2);cellular organisms(1);Viridiplantae(1)\n+Query_241\t230\tpfam00072\tgnl|CDD|306560\t5.30837e-08\t50\t208\t2\tpfam00072, Response_reg, Response regulator receiver domain. This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain.\tBacteria(2);cellular organisms(1);Pseudomonadota(1)\n+Query_246\t230\tpfam00201\tgnl|CDD|278624\t2.93544e-07\t46\t210\t1\tpfam00201, UDPGT, UDP-glucoronosyl and UDP-glucosyl transferase. \tcellular organisms(1);Eukaryota(1);Viridiplantae(1);Streptophytina(1)\n+Query_261\t228\tpfam17035\tgnl|CDD|319097\t3.87403e-09\t108\t203\t3\tpfam17035, BET, Bromodomain extra-terminal - transcription regulation. The BET, or bromodomain extra-terminal domain, is found on bromodomain proteins that play key roles in development, cancer progression and virus-host pathogenesis. It interacts with NSD3, JMJD6, CHD4, GLTSCR1, and ATAD5 all of which are shown to impart a pTEFb-independent transcriptional activation function on the bromodomain proteins.\tcellular organisms(1);Eukaryota(1);Opisthokonta(1);Metazoa(1)\n+Query_280\t207\tpfam04061\tgnl|CDD|309259\t7.30581e-19\t1\t159\t1\tpfam04061, ORMDL, ORMDL family. Evidence form suggests that ORMDLs are involved in protein folding in the ER. Orm proteins have been identified as negative regulators of sphingolipid synthesis that form a conserved complex with serine palmitoyltransferase, the first and rate-limiting enzyme in sphingolipid production. This novel and conserved protein complex, has been termed the SPOTS complex (serine palmitoyltransferase, Orm1/2, Tsc3, and Sac1).\tcellular organisms(1);Eukaryota(1);Opisthokonta(1);Metazoa(1)\n+Query_326\t206\tpfam10775\tgnl|CDD|313884\t0.00091969\t1\t159\t1\tpfam10775, ATP_sub_h, ATP synthase complex subunit h. Subunit h is a component of the yeast mitochondrial F1-F0 ATP synthase. It is essential for the correct assembly and functioning of this enzyme. Subunit h occupies a central place in the peripheral stalk between the F1 sector and the membrane.\tcellular organisms(1);Eukaryota(1);Opisthokonta(1);Fungi(1)\n" |
| b |
| diff -r fd7104249a3c -r d1fd5579469d test-data/input_otu_rps_s2.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_otu_rps_s2.tab Sun Sep 08 14:09:07 2024 +0000 |
| b |
| b'@@ -0,0 +1,50 @@\n+#query_id\tquery_length\tcdd_id\thit_id\tevalue\tstartQ\tendQ\tframe\tdescription\tsuperkingdom\n+Query_1\t2975\tpfam02874\tgnl|CDD|308490\t6.56656e-19\t2202\t2405\t-1\tpfam02874, ATP-synt_ab_N, ATP synthase alpha/beta family, beta-barrel domain. This family includes the ATP synthase alpha and beta subunits the ATP synthase associated with flagella.\tcellular organisms(2);Eukaryota(1);Viridiplantae(1)\n+Query_8\t1120\tpfam00146\tgnl|CDD|306623\t6.73934e-18\t936\t1097\t-3\tpfam00146, NADHdh, NADH dehydrogenase. \tcellular organisms(1);Eukaryota(1);Opisthokonta(1);Metazoa(1)\n+Query_19\t872\tpfam01443\tgnl|CDD|307550\t7.69575e-33\t10\t696\t-3\tpfam01443, Viral_helicase1, Viral (Superfamily 1) RNA helicase. Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis.\tViruses(1);Riboviria(1);Orthornavirae(1);Kitrinoviricota(1)\n+Query_22\t847\tpfam13456\tgnl|CDD|316018\t1.2307e-09\t176\t397\t2\tpfam13456, RVT_3, Reverse transcriptase-like. This domain is found in plants and appears to be part of a retrotransposon.\tcellular organisms(1);Eukaryota(1);Viridiplantae(1);Streptophyta(1)\n+Query_30\t681\tpfam00416\tgnl|CDD|306841\t7.7464e-31\t92\t409\t-3\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+Query_36\t644\tpfam00078\tgnl|CDD|306564\t2.13234e-08\t190\t636\t-3\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+Query_40\t623\tpfam00346\tgnl|CDD|306783\t6.5049e-56\t191\t496\t-2\tpfam00346, Complex1_49kDa, Respiratory-chain NADH dehydrogenase, 49 Kd subunit. \tcellular organisms(2);Bacteria(1);Eukaryota(1)\n+Query_43\t620\tpfam00115\tgnl|CDD|306596\t2.19638e-51\t78\t548\t3\tpfam00115, COX1, Cytochrome C and Quinol oxidase polypeptide I. \tcellular organisms(1);Eukaryota(1);Opisthokonta(1);Metazoa(1)\n+Query_45\t598\tpfam00115\tgnl|CDD|306596\t4.78609e-34\t21\t302\t3\tpfam00115, COX1, Cytochrome C and Quinol oxidase polypeptide I. \tcellular organisms(1);Eukaryota(1);Opisthokonta(1);Metazoa(1)\n+Query_50\t458\tpfam02123\tgnl|CDD|280316\t1.82963e-26\t27\t443\t-1\tpfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.\tViruses(1);Riboviria(1);Orthornavirae(1);Duplornaviricota(1)\n+Query_51\t458\tpfam03732\tgnl|CDD|309014\t1.12045e-06\t256\t441\t1\tpfam03732, Retrotrans_gag, Retrotransposon gag protein. Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.\tcellular organisms(1);Eukaryota(1);Viridiplantae(1);Streptophyta(1)\n+Query_53\t454\tpfam14111\tgnl|CDD|316622\t3.40587e-07\t213\t353\t3\tpfam14111, DUF4283, Domain of unknown function (DUF4283). This domain family is found in plants, and is approximately 100 amino acids in length. Considering the very diverse range of other domains it is associated with it is possible that this domain is a binding/guiding region. There are two highly conserved tryptophan residues.\tcellular organisms(1);Eukaryota(1);Streptophytina(1);Viridiplantae(1)\n+Query_58\t446\tpfam01348\tgnl|CDD|279664\t1.01441e-09\t40\t303\t-3\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 '..b'ransferase proteins from both eukaryotes and prokaryotes. Thiopurine S-methyltransferase (TPMT) is a cytosolic enzyme that catalyzes S-methylation of aromatic and heterocyclic sulfhydryl compounds, including anticancer and immunosuppressive thiopurines.\tcellular organisms(2);Bacteria(1);Eukaryota(1)\n+Query_238\t219\tpfam02123\tgnl|CDD|280316\t1.42892e-13\t35\t199\t-3\tpfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.\tViruses(1);Riboviria(1);Orthornavirae(1);Duplornaviricota(1)\n+Query_260\t217\tpfam02123\tgnl|CDD|280316\t4.65988e-13\t13\t210\t-2\tpfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.\tViruses(1);Riboviria(1);Orthornavirae(1);Duplornaviricota(1)\n+Query_264\t216\tpfam02123\tgnl|CDD|280316\t7.05387e-17\t8\t214\t-3\tpfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.\tViruses(1);Riboviria(1);Orthornavirae(1);Duplornaviricota(1)\n+Query_275\t215\tpfam02123\tgnl|CDD|280316\t3.8356e-09\t37\t198\t-3\tpfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.\tViruses(1);Riboviria(1);Orthornavirae(1);Duplornaviricota(1)\n+Query_277\t215\tpfam00201\tgnl|CDD|278624\t5.96981e-07\t113\t193\t-2\tpfam00201, UDPGT, UDP-glucoronosyl and UDP-glucosyl transferase. \tcellular organisms(1);Eukaryota(1);Viridiplantae(1);Streptophytina(1)\n+Query_282\t215\tpfam02123\tgnl|CDD|280316\t4.70874e-08\t33\t209\t3\tpfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.\tViruses(1);Riboviria(1);Orthornavirae(1);Duplornaviricota(1)\n+Query_289\t214\tpfam00361\tgnl|CDD|306795\t1.62395e-10\t59\t196\t-1\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.\tcellular organisms(1);Eukaryota(1);Opisthokonta(1);Metazoa(1)\n+Query_292\t211\tpfam05892\tgnl|CDD|283531\t0.000183874\t59\t196\t-1\tpfam05892, Tricho_coat, Trichovirus coat protein. This family consists of several coat proteins which are specific to the ssRNA positive-strand, no DNA stage viruses such as the Trichovirus and Vitivirus.\tViruses(1);Kitrinoviricota(1);Orthornavirae(1);Tymovirales(1)\n+Query_293\t211\tpfam07727\tgnl|CDD|311594\t9.19953e-05\t43\t120\t1\tpfam07727, RVT_2, 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. This Pfam entry includes reverse transcriptases not recognized by the pfam00078 model.\tcellular organisms(1);Eukaryota(1);Viridiplantae(1);Streptophyta(1)\n+Query_297\t211\tpfam00978\tgnl|CDD|250270\t2.21971e-14\t16\t201\t1\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.\tViruses(1);Riboviria(1);Orthornavirae(1);Kitrinoviricota(1)\n' |
| b |
| diff -r fd7104249a3c -r d1fd5579469d test-data/input_otu_s1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_otu_s1.fasta Sun Sep 08 14:09:07 2024 +0000 |
| b |
| b'@@ -0,0 +1,2368 @@\n+>ds2020-267_1\n+CAGCACGTCCGCAAAAGGTCCTCGCTCCAAAACTGTCTCATCATCTCTATCGTGCCCTGA\n+CCCGTTTTCATCTTTGTACCTAGCTCTACTTCTTCTATCCTTGTTGGCACTTCTATCGCC\n+ATTACCCTCGCTATGTTGCCACGTTGTCCGTTGACCATAGGCCGCCACATCCTATAATGC\n+CTCATGTCTCCAACTACTGCCCCACTCATTGTTATCTCTGTGTATACTGGACATGTTTGC\n+CCTCTGTCTGGCCACAGCAGATTGGCTGCGGCTATAAACTTGTACAGTTTCACCTCGTCG\n+TCATGTGGTGTCAGCACTATGTTCTTATCTATCACGACTCTAGCTTCATGTGGAAAGCAG\n+TTCTCCTGATCTACCGGTATTCTGTGTAGTGAACCATACCCTAGGTGGCAACAGGGCAAC\n+GACATGTGCACCAAATTCACGTGCGTGACTAGAGGCCTCTTGAAGTACATCTTCGCACGG\n+TATTCAAACTCCGTTTGCATCATCCTTCCTTTCACACCTGCCACAATTGGGTTCCTGATG\n+TGAAATTCTCCATATTCTAGTGACATTTCTAGGTTCACTGGCGTCACCAGGAACCCCAGC\n+ATGTTTGACAGCCACGGCACCACTGCGTTGAATGTTGATAGCTCTCCAAGGTGTTGGTGC\n+AGCTCACCAAGTCTGCAGTTCCTGAAGGAGTGTGGCAGTCTAATATCCAACTCCCTCACT\n+TCAGACAGCTCCCAATGCCATATAGGAAAGTCTATGAAACTGCCTCTAATTGTGTTCTTA\n+TCTTTCGTCTGCTTGAAGGAAGTACATCCCAGGCACACACAGTACCTCGTCACATCTCTG\n+AAAGTTGCCTGACCAGGTGCAAACGTGGGTGGAGGCTGTGGTATCTTTGGTTCAATCAAC\n+CTTATTATTTCAGCAGGTGCTATCCTGGTGAACATGTCTGCCTGTTTTGCCAGTTTCAGC\n+AAAGAGTGCTCATCACCCTGCTTCTTGAATAGGCAGAAATGCGGCCCTGTGACATTGTGT\n+TTGTGCCCACAGCTCAGCTTCAGCTGGCTATTCTGTGTAGAGTTGCCAAACCAGTTTATC\n+TTTTCGCCGTAGTACATCCACCTACTTGGGTGCATTTCTTCTTCGTTAAGTGGCATGCCT\n+TTCACCATCCCTTGCATAACCTGGGCCTCGGTATTGATGCCGTGTTCGTGGTCAAAAATA\n+GGGCACTTGCCCTCTGCACCGCATGACATCAACGGCATGCCTTGCCATTTCCCGGTCAGT\n+TCCTGGCAATTTTCAGGTGTCGGTGGTACCAGTGAGGTTCCTCCGCGCTTGAAAGTGTCA\n+TCGTCATCACTCTGCTCTTCCATTATGTGACGTCTTATCCTTCCTAGCTCCTCTCTCGCT\n+CGCTCAGTTCTGTAAGCCTTTTCTTCTTTTCTGTTCATCCATGGCACGTCCCATGATCGT\n+GCGTCTTTTTCCCTTTGTTCCGAACTCGTGTCTGTTTGTGAATCGACAAACTCTTTCGCC\n+TGCCTCAATTTTTCAGCCACATCATCACACTCGATTCTCACTTCTGGCTCTAGCACGACA\n+TGCCCCTCACCTATAAGCAGGTTCTTCATGGTGTCCGCCCCCTCTGTATCTGACTCTGAC\n+GCTTCGTCCTGCGTCTTAACAGGGCTTGGTGTAGGGCCACCATCGAACGTGACGTCAGTT\n+TCTTGCTCTACATCCACCTCAACACTCAGCTTCTTAGAGTGAGCGCTTTTCCGTTCAGTG\n+AACTTGTAGACCAACATGTTTGCGTTGTACATGAGCTGTCCCCTTATGTCTTCCGATTTG\n+TCGCTTGGCCTACGCTGTTTCTGATCGAGCGCCTCGTCAACGTATTCAATGTCTGCTACG\n+TGCTCAGTGCTCATCATCTTGGCGTCTATTACGTCCTCGATTGACGGTGTCCTCTTTAGA\n+GTCTTCACCTCTAGTGTTCCGTCAACCACGACACCTGCCTCTTCGATTGCCTGGTTGCAC\n+AGCGCGCACGACACAAGCTGCTTGCACTTCCTGCACACATGCTGCATTTTTATGTATCCA\n+CAGCAACTTGTTTGGCACGGTGAAGACATCCTGACACACTTCTTGTTCTTCACCCTCGTC\n+TTGGGGGTGCTCATCACTTCATGGACAGACTTGATATTGCGTTGCCCTTTTTGACCGGTT\n+TCAGCCACACATACTTGATACGTGTGCACCAGGCTCAAGTAGTTTGGCCAGTTTGCATCA\n+GCTGCCACCACCAGTGACGCAACATACCTCACACGCGGTGAGTAGTTAGCAAACAAAGTG\n+TGTACCTGCTCCAATCTAGCAGCAGGTGTCATCTCGGTGCTGTTGAGTTTCTCATCCTTG\n+TATTTTAAACCCCTTTTGGTCAAAGTGAGGGCGTAACCGGTGCAGGCGTGCCATACTAGT\n+CTTGAAAGTGACCGTTTTGCGTGCTTGGTCAGTGGCAAGTAATAAACTTGCTTCGCATGT\n+TCGAAAGCCCTCTTACTATGCCAGGTGTACTCGAGTTCACTTTCTTCTGCCAGCAGTGCT\n+GCTGCATCTAGCCATTCTTACATGTCAGACTGATCAACGTACTGGCCTCCTGTTGCGGAC\n+GTGCTGNNNNNNNNNNATCTAAGGAGCAGCACGTCCGCAATGATGGCCCCATACAGTAGT\n+GATTTCTTGTCGAAACCACCAAATTCGAACACTGGCCTGTTGATACTTGAGCTAGTGATC\n+AACATCTTAGCGTTTTCTGTCTCTGCAGTGAAAACAGACCTGTACGTTGCAGCTCCAATA\n+ATGAGCTGTTTCAAATCCATTTGCTTGTCGTGCCATTTGGTCGGTGACACACATATTCCT\n+CTCTTGGTTCTGATGCACATTAGCGCTCTGTACAAGTTTACGACTGACGCTGCTCCTGTC\n+ACGTCGTTGATTGCTGACGTCAGTGACGCAAGGAACATCGATTTTGACGCCTGAGTTCCT\n+ATTGGCCTACCGCTTGACGTCACCGGAACTGCAATCCTGCAGTTGCTATTTGTGGTAACA\n+GCNNNNNNNNNNCAGCACGTCCGCAATTGCCTTCCATTGGGTTGCCAACTCCCAGTACCT\n+TTTCGTCACTCACCCTCAGTTCGAAGCCATATCGCCTGAGTTCTGGTGCGATAGCCATCA\n+CTCTCGCTTCTGCTCCCATTAACTGACCATTTATGATGTTGACATCAGATCTGTCGTTGC\n+CATCAGCAACGCAAGCGTCATCAACCCATGCCATCAGCGAGTTCAATGCTCCTGCCGTTG\n+CCCTCGCTGCTGATACATTAGTCAGCAGCACGCCTGCCTCATTTTGAGGGCCTTGGACAT\n+ACTCATCATGTTGCGATGTCACCGAACAAGCGTAGCTACCTTCAGACTGAACGTCAGTAG\n+TGTACCTGGTGCGCACTGCGCTACCTAGCACACTATCTGAAGTCAAAGCGCTTCTCGAGC\n+TCATTATGCCCGCCCGCATGAAAGGTTCATCTTTGTCAACCACTTCATAAACACCATGAC\n+CCGTCGGAGTTACAACGCTCTCGTCATGCTGCTTGTGTTTGCCACCAAAACCAGCGTATC\n+TGTTGGTGGCGATTATTGGCGTGACTCTTGCTGCGACTGATTTTTCAGCAGAGTTGTATT\n+GAAAAACTGGTACGCCCATCTTGTACAGTTGGCTGCAATGTCCCAA\n+>ds2020-267_2\n+CAGCACGTCCGCAACAGTTGGTCCTTGCTAACAGTAATGGCGACTTGTGGACACGCATGG\n+GCGCCTTGCATGGACAAAGTTCTGCAGTGGCCTGACATAACGAACACGTTTATGTCATCA\n+CTACTACTTGCCATGGCTGCACTACCACCAGAGTTATATGTACTAATGGTGGAGTGG'..b'AGTGACGTAAAATTGCGGACGTGCT\n+GCCTGATTCGATTTGCGGACGTGCTG\n+>ds2020-267_887\n+CAGCACGTCCGCAAACTCAAACCGGTATGATTGCGGACGTGTGAGGCGTACTGCTTTGGG\n+ACGTGCTGGGGGTCTTCCTTTGCGGACGTGCTGCTCCTTAGATTCTGGAAGTAAGGACGT\n+TCGGGCTTCCCTCATGCCCTGGACGTTCGGGCTTACACTCACCCGTGGCGTTCGGCTTCC\n+AAGCAGTATACGAAGCCCGAACGTCC\n+>ds2020-267_888\n+GGACGTTCGGGCTTTCTTACCAACCTACAGAAGCCCAACGTCCAGGGGGGGAGTAAAGCC\n+CGAACGTCCACCAATTCGTGGAAGCCCGAACGTCCTTACTTCCAGATAAGGAGCAGCACG\n+TCCGCAATCACAGTACCCTCAGCACGTCCGCAACAACTGCCCCCTCAGCACGTCCCAACT\n+ACCCTGCCTTTTTTGCGGACGTGCTG\n+>ds2020-267_889\n+CAGCACGTCCGCAATGACAAAGCCCTCAGCACGTCCGCAATCCTAGTCGCCTCAGCACGT\n+CCGCAAAAATGCCGAGCTCGTTGCGGACTCGCTTAAGGCGACGCACTGACCGTTACCAGA\n+GTCATAACGGTCAGGAGTGGCGCTTGGACGGTCAGTGCGTCCCCGAACGGTCAGTGCGTC\n+AGGGGTATATCAACGGTCAGTGCGTC\n+>ds2020-267_890\n+CAGCACGTCCGCAATAAGACCCTATTGTTGCGGACGTGCTGAGCGAGGCGCCTTTGCGGA\n+CGTGCTGCCCATAGCGTATTGCGGACGTGCTGCTCCTTAGACGCTTAAGGCGACGCACTG\n+ACCGTTGGCGAGGGGTTATTACGGTCAGTGCATCAGCAAAACTGGAACGGTCAGTGCGTC\n+AATTGGCCACTTACGGTCAGTGCGTC\n+>ds2020-267_891\n+GCAACTGCGTTACCCTCAGCACGTCCAATGGTACTCGACATCTGTTGCGGACGTGTATCT\n+AAGGAGCAGCACGGCCGCAAGACTGATTCCCTCAGCACGTCGCAAAGCCGCTCAACTCAG\n+CACGTCCGCAACTGCGTTACCCTCAGCACGTCCAATGGTACTCGACATCTGTTGCGGACG\n+TG\n+>ds2020-267_892\n+TCAGCACGTCGCAATCTATCAGTGGTTCATTGCGGACGTGCTATCTAAGGAGCAGCACGT\n+CGCAATCACTCCCCCCAGCACGTCCGCAACAGCATCTAGGTCAGCACGTCCGCAATCTGT\n+AACCGGTCAGCACGTCGCAATCTATCAGTGGTTCATTGCGGACGTGCTATCTAAGGAGCA\n+G\n+>ds2020-267_893\n+AGTGCGTCAGCGTACCCATCACGGTCAGTGCGTCAGCGGCTAAAACACGGTCAGTACGTC\n+GCCTTAAGCGTATCTAAGGAGCAGCACGTCCGCACTGACCGTGTCAATCCTGGTCTGTAC\n+GGTCAGTGCGTCAGCGTACCCATCACGGTCAGTGCGTCAGCGGCTAAAACACGGTCAGT\n+>ds2020-267_894\n+TCTTCCGATCTATCTAAGAGCAGCACGTCCGCAATTATATCCAGGTATATTGCGGAAGTG\n+CTGAGGTTGTCCGCCTTGCGGACGTGCTGACGGATTTAGGCTTGCGGACGTGCTGAGGCG\n+TTATATGTTGCGGACGTGCTGCTCCTTAGATAGATGGGGA\n+>ds2020-267_895\n+CGATCTATCTAAGGAGCAGCACGTCCGCAAAACGCCATGTGTGACATTATTCGCCAACCA\n+ACCATTGTACTTTGGTGCGCTGCTCCACACGCATTTGTGGGCTTTCAGGATGCTGAGGGG\n+TCGGAACTTGCGGACGTGCTGCTCCTTAGATAGATCG\n+>ds2020-267_896\n+TACCTTTGCCGTGTTCACAGGGTTTCTGTGTCCTTTGCCGTGTTCACAGGGTTTCTGTGT\n+CCTTGCCGTGTTCACAGGGTTTCTGTGTCCTTTACCTTACCTTTGCCGTGTTCACAGGGT\n+TTCTGTGTCCTTTGCCGTGTTCACAGGGTTTC\n+>ds2020-267_897\n+ATCGAAGGAGCAGCACGTCCGCAACTGCTCTGCCCTGTCCGCAAAGACCATACGCTGAAA\n+CTTGCGGACGTGCTGAGTCGGTACATATTGCGGACGTGCTGAGTGGCTCCTTTTTGCGGA\n+CGTGCTGCTCCTTAGATAGATCGGAAAGAG\n+>ds2020-267_898\n+CAGCACGTCCGCAATTTTAATCGCCTCAGCACGTCCGAATGATTCGTCCCTCAGCACGTC\n+CGCAACATGAACCCGGTGAGTCTTGCGGACGGGCTGAGGGACGAATCATTCGGACGTGCT\n+GAGGCGATTAAAATTGCGGACGTGCTG\n+>ds2020-267_1259\n+CAGCACGTCCGCAACAGTTGGTCCTTGCTAACAGTAATGGCGACTTGTGGACACGCATGG\n+GCGCCTTGCATGGACAAAGTTCTGCAGTGGCCTGACATAACGAACACGTTTATGTCATCA\n+CTACTACTTGCCATGGCTGCACTACCACCAGAGTTATATGTACTAATGGTGGAGTGGAAC\n+GGCTGGGCAAAGTGTGGCTCTATGGCAGAGTACATCGTAGAGGCAAAAAACCTGACGACT\n+AAGATGAAGGCACTGGACAACCAGGTAACATTGGGTGACTTCGAACTCGACTTATCGCCT\n+TTATTCGAGTGGGAAGTGCTAAATCACAGAGCGGTCTTGAAAGGCATCTATGACAAGGAA\n+GTCACAGAGCGTAGAGATCAGAAACAGAGCATCAAGCTATCTGCTGCCGATCTGGAGGAA\n+GAAATAGACAGCGTGTTTCAGGACGTGGGTTCCGTTCTAGACGCCAGGACAAAAGAGGGT\n+GAAAAATCACCTCTGTATGCAACGTGGGATGATTGGTACGTTGACAGGGTGCAAACCACA\n+CCAGCTGGGTCTGCATTCACAGTCAACAAGGACATGATGGAGGCAAGAAACATGCTGAAA\n+GCCAATGGGGTCCAAAATCTGACCAAGACGCAAGTGATGGCGCAGATGAGGGACAAGCTC\n+CCGCTGGCGTCTATCTTGGGTAGCGAGCCAATGATATTGGCCCAGATGTCATGGAAGTTG\n+GAATGGTCAAAACTGAGGGCACTATTTTTAACGCGTTTTTTGCTGCTAGCATGGAGCACT\n+TTCGCCCTGGGGCAGATAGAAGAGTATCTACCCAGTGACTGCCCCATAGGTAAAGCTGCC\n+GATGCGCACAACGTGTGCAGGCGCGTGATGGAAATGTCAACGCAAGGAGTGGTAGCATGC\n+ATAGATGCAAAGAACTTCAACATCTTGCACACCCACGAGATAATGTCAGCAATACTGAAA\n+TCCGCATCAAAGATGCTAGGAGATAGGCTGTCTAGTGAGCAACATGACTGCCTAAAGTGG\n+CTGGCGAAAGCGGAGCTGAACCAGAAAGTGCTGGTCAAGACAGGTGAAGTAACTGAACAG\n+TTGCTCCAGGTCGGCAGGAGAGACGGGTGGATTAACAAGCTAACTAAAGGTGACGGCACA\n+GTGGTAGAAGCGGCTGACGTGACGGTTGGAATGTTTTCAGGTACTAGGTTCACGATGCTG\n+TACAACACAGTGCTAAACAGGGCGTACTACAAAGTGGCGGAGAAACGTGCGAAGATAAAG\n+ACTTTATCACTTCATTCGGGTGATGACGTGTATGCTGTTTTCGCTAACTATATAGACGTG\n+TACAAGATGAAGCGTGAGATGGCGTTAATCGGCTACACACTGCAGTTAGGCAAGTGCTTC\n+TTGCAGGGAGTCCGAGAATTCTTGAGAATATCTCATAAGAATGCAAACACTTCTCAATAC\n+CTAGGATGCCATCGGCA\n' |
| b |
| diff -r fd7104249a3c -r d1fd5579469d test-data/input_otu_s2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_otu_s2.fasta Sun Sep 08 14:09:07 2024 +0000 |
| b |
| b'@@ -0,0 +1,2288 @@\n+>ds2020-328_1\n+GGTCGGGATAGACGTTGGAGCGCGGTCAGCCGAGACCCCTGACAGAGGAAAGAGTCTTGA\n+GGAGTCCAACGTTCGGCCAGGCATAATAATTCGTGCCCACTAATCGAATCGGTTTACTCG\n+CCCACCATGTCAGCGCCTTCGGGTTAGTTCTTTATGGAGTTATTTCTTGTTCTTTCTGTC\n+ATAACAATTCTCCTTATGGAAGTCCCCCACAAGATTAAGAATGCTTGTTGCCGCGGCTGT\n+CTTGGTTCTTCGTTTAGCTTTCTGGCATATTCTACGGAGCTTTCCACTCTGGAGCTGGCT\n+TTCAGAAAAACCTTCATTCACTAGATGTGAAGCACCCCTATGGGGGAACCCTCTTACCCG\n+CTTTCCTCCCCCCCCGATATGGGGGGCCTCGCTGTCGCCTTTGGCTCGAGCTACTTTTTC\n+TCCTGGAACGGATAGCTTTCTGTCCAAGTCTATCTCCCAAAAGTCAGCCATGTAATTGAC\n+TTCTAACGTCTAATTTTCTTTTTCACCGGGGGTCCCTGATCCCCGTTGAATATTCCTTCC\n+TTCTGAAAAAGCTGTGACTCCTAAATTCTTTGATTGAATGAAATGTGGACTTGGTCACGG\n+GGCAATCTTCTTTTTTAGACCCCGCTTCTCTCGGTGTTACCTTTTTCGCCTTCTCGTCTC\n+GCTTCGCGTCGTCNNNNNNNNNNGGTCGGGATAGACGCGCCGCTTCCGTCTGTTTTACCT\n+TGTTAGAATTCTCGGCGCGCTTGGCGTCGTCTTTAGAGTCAATTCTATTGGAATCTCCTT\n+TCCCCTTCTTTTCTTCCCCCACGATGAAAAAAATAAATATTGCAAAAAGAACAATATTTC\n+CCCCCGTGGTCATCATAGTGGTTCCTTCTGATCCTAGAAAACGATTAAAAAGAAGGCAAA\n+AAAAACAAAGGAGGATCTGCTTTTTCATATTAAAGCGCTTTCTTTCTTTTAAAAATACAT\n+CATAGTAAAGCGCTTCCTTTTAAAAAAGCATCTGGTTCCATCTTTCTTTCGTTAGTTAAC\n+CCACCTTTTTCTAAAAGGGATTGTAGTAATTCTGGTTTTACACTATTTAGAATGGCTCTC\n+TCATATTGAGAGATTCTGTCTAGTGGCATTCGATCACAGAATCCATTGACAGCTGCATAA\n+ATGACTAGAATTTGTTTTTCAATTGGAAGTGGTGCATATTGTGGTTGTTTCAGTACTTCT\n+GTAAGCCTTGCACCTCTATTGAGTAATGCCTGAGTCGCAGCATCAAGGTCTGACCCAAAT\n+TGAGCAAAGGCCGCCACTTCGCGATACTGTGCCAATTCCAGTTTTAAACTACCGCAGACC\n+TGTTTCATAATTTTCAACTGAGCGGCAGACCCGACGCGACTGACAGATAAGCCGACGTTA\n+ATAGCAGGTCTAATTCCGCGATAAAAGAGCTCTGTTTCCAAACAGATTTGTCCATCAGTA\n+ATGGAGATTACATTGGTTGGAATATAGGCCGATACGTCTCCAGCTTGTGTTTCAATGACG\n+GGTAAGGCGGTCAAGCTACCTGCACCTGTCTGGTCCGATCGTTTAGCGGCTCTTTCTAAG\n+AGACGGGAATGTAAATAGAAAACATCGCCTGGGAAAGCCTCACGGCCTGGTGGTCGGCGT\n+AACAATAATGACATTTGTCGATATGCCACCGCCTGTTTACTAAGATCATCATAGATTATT\n+AATGCGTGCATTCCATTATCGCGGAAATATTCCCCCATGGCACACCCAGAATATGGGGCC\n+AGAAATTGCAGAGGAGCTGGATCCGAAGCGGTGGCTGCTACAAGAATGGAATATTCCAAA\n+GCATTCGCTTCTGAAAGAATTTGAACTAATTGTGCCACAGTCGAGCGTTTCTGTCCAATT\n+GCTACATAGACACAATACAATGTCTCACTCTCAGAGGTGGCCCTTGAGTTCAGTTGCTTT\n+TGGTTTAATATGGTATCGATAGCAATAGCTGTTTTTCCAGTTTGTCGGTCCCCGATTATA\n+AGTTCTCGTTGACCACGGCCTATAGGAACCAGGCTATCTACCGCTTTTAACCCTGTTTGC\n+ATAGGCTCGTGCACAGATTTACGTTCAATAATCCCAGGGGCTTTCACTTCGACACGTCTT\n+CGCTCGTGATCGCTTAGAGCCCCTCTTCCATCAATAGGAACTCCCAACCCGTCGACCACG\n+CGCCCTAGCATAGCCTTTCCCGCAGGAACATCCACAATGGATCCAGTGCGCTTGACAAGA\n+TCTCCTTCTTTAATAGCGGTATCACTACCAAAGACAACAATCCCTACATTCTCATTCTCA\n+AGATTCAACGCTATTCCTTTCACACCGCTGGCAAATTCAACCATTTCCCCAGCTTGAATC\n+TCGTTCAATCCATAAACACGTGCAATCCCATCTCCAACTGAGACCACTCGACCGATCTCA\n+TCCACTTGAAAATTCGTGTAAAAGTTGGTAATTCTACTTTCTAATAGAGTTGTTAGTTCC\n+GCAGCTCTGGTAGAGAATTCCATAATTTTTTCTTTTAAAGAAAGTCAAGGGAGAATTCCG\n+CTTATTGTTTTTGGCTCGAAATAAAGCTAGGGTCCTGATCGAGCAACTAGTAGTCCTATC\n+TATCCACCTCTCCAGAAGGGCTATTTGGGGTCTAATTTTCTTTCTATCTGACAGGACAAA\n+CAAAGAGGAAGGGGTGGTTCTTTCATTGCATTGATAGAAGTCTAACTAGAAAAAGATCTC\n+TCTATTACTTTGAGAAGAGAATCGTTGGTTTGACCGACGAACTACGTGGGAAATATGAGT\n+TGAGAGGACAAGAGGATTCGATCTCCACGAAAGGCTAAAGGAACATAAAAAAAGCTAGAA\n+TTTGTTGCAAACAGTGACCGAGATGCCAGGGAAAAACTGTTGTTTCACATTTCCGGAAAG\n+ACCACCTATTTGTTCGTTTACCAGGTTCGGTACGAAATCATAAATAAGCTCTACCCCGGG\n+CCATCGCCTTATGGCCTAGGGGCGTCTATCCCGCC\n+>ds2020-328_2\n+CCCCCCCTTTCGCCCTTTTTTATGCAGACGATTCCCCGATCGGGGAATCGTCTGCTTCCC\n+TACGTATTAATCTTCTTCTTTTCTCCTTTTTCGCGTTTTCCTCTTATTCCTCTTTCGTTT\n+TCCTCTTATTCTTTTTATACGCAATTTCTTTTTTAATTTCTTACTGGTCTAAGTCCCACT\n+CCTCTTTCTCCCCGTTTTGCGTTAAGAATATTTCACATGGCATCGGTTTATAGCCTTTTT\n+CCCTTGTCATCTCCTCTACAATCTTTTCTATTTTTTCATATTTCTTCTTATAAAATTCTT\n+CCTCTTCTCTTCTCTTGCTTACTTGTATGGTTGCCGGAAATACTCTTGTTTCGCCTATTT\n+GTATTTGTAGAGGCCATGTAGCATAGTCGTTTCCTTGTTGAGCCCCCTTACTTCTTTTAA\n+CTTCCATGTAGCTTCTTGCTGTCCAATCCCTTTTATCGTAGAATATCCTTTTAATTTTCT\n+TTGTTTCTGAGTTTTCGTCTTGCTCTCTCTCTCCTTCATTTTCCTCGTCGCTTCCCTCCT\n+GGTTTTCCTCCTCATATTCTTCCTTACTCTTAAATAGCTGCAAGAATCTCCTTCTTTTTT\n+TCTCCTCTTTTTCTTCTTTCTTTTTTACGGGTATACACGCAAAATCTAACAGTGCCATTT\n+CCTTCTCTTGTTCGCCCCATGTGTAGCATTCCTCACCATCGATTGTTTGTAATTCAAACA\n+TCAAATAACTTCCTCCCGCTGTGGTTTTAATCTTTTTTATTTTTACTTCATATATTTTTC\n+CTTTTTTTGTTATAAAGATAACTTCTTTCTTTAGAATGTATTCTGCGGCCTCTGGGTTCA\n+ACTCCC'..b'ACGAGGCAGCTTAATGGGAATGGTAAATGGAGTTTTTGAGGGTGACATC\n+AATGTTTGTGTCTACGGTAATTTGATAAAGGCGTACGTGGCTCCGATGCCAGGGAACAGG\n+TCAGCAGTCTACTATGACGTTAGTCAGCGAACTTGGGGAATACGTAAAGAAATACTCTCG\n+CAGATGACGAGGCACAGCAACCGTCTATCCCGACC\n+>ds2020-328_774\n+TTTCTTATTATTTGACAGTGCAGAATGTTATTGATGACCATCAGCCATCATGCGCAAAAG\n+CTTCACAAAGCCCCACTAAGAACATCATGATGACATCCTGAAAATGGTCCCAGCTACTAT\n+TGCCGAAGGTCTGAACACCCGGCTCCTATTTTCAAACCAAGTCCTAGGTTCCAGCTACAA\n+AAAAAGAGAGTAGGCAGCGTCGTCTATCCCGACC\n+>ds2020-328_775\n+CATGTTTTGGCCTTGTGTGTCCATAACTCAAAATAGGTGACCTAACGGCCGCCGCCCGAC\n+TAAACATACCAATAGTCACCAGATTCATATGGGCTACTGAGGAGTAAGCAATGATCTTCT\n+TAAGATCGATCTGTCTTGAAGTGGTCAAGGAAGTATATATTATAGCAATCGCGCTTGGAG\n+TATAAATGAAAGAAGTCCCGCGTCTATCCCGACC\n+>ds2020-328_776\n+TATATTAGCGCTCTCCAAGTGTGCTTGTTCCTCCCTTCTTCCTTACCATGGCAAGTCTTT\n+GTGAAATAACTCCGATGAGAAGAAAAAAGAAGGCGTTAAGAGACCCTCCTGGCCCAACCC\n+TAGACACTCTAAGATCCTTTTTCAAACCTGCTCCCATTTCGAGTCAAGAGATAGATAAAT\n+AGACACATCCCATTGCACTGACCGGGTTCGTTCG\n+>ds2020-328_777\n+TAACGGCCTATTTGCCAGATGAGACCACGCCAACAACAGCTTGTTTCTCAACGGTTCCTG\n+ATGTTTCAGCCCATGATCCCTAAGTATACCATTGTACCTTGGGTCTGTGCGTACATCTGA\n+CCCCTTAGTGCATGTACTGTCACCTAATCCGCCCGTTGCTTCAACAAGATTAGCAGCTTC\n+CATCTTGTACAGCGAGCCGACGTCTATCCCGACC\n+>ds2020-328_825\n+CTTACATCAATTGCCCAGCTGTTGTCTTTGACTTCAATAAGGGACTACCCTTGACAATAA\n+TTAAGATTGGAAAGAACGCTAACGCAATCTCCGCTTGCAATCAAAGGCTTTTCAATAGGG\n+AGGGGATAGACGGCATGCGTTCTTAACGTCTTCCCGACCAGGCGCCCGAGACGTCTATCC\n+CGACCAGAGCTTACATGCGTCTATCCCGACC\n+>ds2020-328_826\n+GGTCGGGATAGACGTTTGGTTTGGTTATGACGAAGATAGACGGGTTTCCAGAGAAGCAAT\n+GCTGATCATTCCGTGTTCATAAAAAGGAGAAAAGAGGAAACTACTGTTCTCCTAGTGTAC\n+TCAGTTTAGAACTCTAAATTAACAAGTAAAATTTAGATATTAGTAAGATATGCAGCGAGT\n+ACGCTCGGCGAGTACGGCGTCTCTCCCGACC\n+>ds2020-328_827\n+GGTCGGGATAGACGGGCCCCTCCCCTAATCTACTATCAAAACGTTTAACTATATATACGT\n+AAAGAAACACATGCACAGACGATATAGCCAGTCACCGAACCTCTTCCCCGAATGAGTCGA\n+AATTGCTACAGCCCTAAACCCGACAGAACTGAACCGGATGTGTGTCGACGACGAGTCTCA\n+GGACGATGAGTGACATGCGTCTATCCCGACC\n+>ds2020-328_828\n+GGTCGGGATAGACGTTACCTAGCCCTGGAGTAATGTATTCTATGAATAATAAATAAAGGA\n+GTAATGTATTCTATGAATAATAAATATGAAGAATACTCTTTCAATCAAAGAAATATTTCA\n+ACTATTTCCGTGTTCGTATTTCGAAAGTAAAAAAACGTAATAGGAATACAAAAGATAGGA\n+AATTTATTACAGATGAATTCTTCATAAATTT\n+>ds2020-328_829\n+GGTCGGGATGACGGCTTAGGGGACTAGGGACTGCCCTACGGCTCCCACTGAACCTGGAAT\n+GCTCGGTCCTGATTCCACAAAAATTCACAAGTTCCCAACCCAGAAGTCACTTCTTGACAG\n+CGAACTTGGGGGACTACTGTTTACACCATAATCAACCAAACATATCCAGCATCAAAACAA\n+CTCGCACTGGCAAAATACGTCTATCCCGACC\n+>ds2020-328_830\n+GGTCGGGATAGACGCTTACCTTCCCATGGTGAGGTTAATTACTTTTCTGAGTACTTGAAA\n+GGTAAAGCGATCGATGATGATGATCTATACGTTGATCCTATTTGTTTAGTTTCTATGGAT\n+AAGTATAGACATATGATAAAATCCCAACTTACACCAGTTGAAGATAACAGTATGATGTTT\n+GAGAGGCCTCTGGCAGCCGTCTATCCCGGCC\n+>ds2020-328_831\n+GCCGTGGACCTAGTCTGATATCCCCTGCCGTGACTAGTTTCCCACCGTCTTAGGCACTAG\n+GTCCACGGCAGGACACGACGAACTAGGTCCACGGCAGAGTTCGCAGCACTAGGTCCACGG\n+CTCTCTGTCCGTGAATTACGGCGGTCGGGATAGACGACATTCCTGCCTGGTCGGGATAGA\n+CGTACAACCACCATGCTCGTCTATCCCGACC\n+>ds2020-328_832\n+GGTCGGGATAGACGAACTGTTCCACTGGTCGGGATAGACGTAAAGGTGGTTTGTCCGTCT\n+ATCCCGACCGCCGTAATTCACGGACAAGAGCCGTGGACCTAGTCCGAACCCCCCTGCCGT\n+GGACCTAGTTCTAAACTTCCTGCCGTGGACCTAGTTTTAGTGCACCTGCCGTGACCTAGT\n+TCAGCACCGTCTTTGATACTAGGTCCACGGC\n+>ds2020-328_833\n+GGTCGGGATAGACGATACATACCCCTGGTCGGGATAGACGACACGATGGGGTGTTTGCGT\n+CTATCCGACCGCCGTAATTCACGGACAGAGAGCCGTGGACCTAGTTCATAGAGCCGTGCC\n+GTGGACCTAGTGTCTTTCCTGCTGCCGTGGACCTAGTGTCCACCACGGGCCGTGGCCTAG\n+TTCCTATCGCACTTATAACTAGGTCCACGGC\n+>ds2020-328_834\n+GGTCGGATAGACGTACGGGCCTTGTCGGGATAGACGTGACGAATGCCTGGTCGGGATAGA\n+CGGACTAGCCCCCGAACACGTCTATCCCGGACAGAGAGCCGTGGACCTAGTCATACATTA\n+CTTGGTCCACGGCAGCCAGCTTGACACTAGGTCCACGGCAGGGGAAATGTCACTAGGTCC\n+ACGGCAGGTCGAATGGCACTAGGTCCACGGC\n+>ds2020-328_835\n+GGTCGGGATAGACGGAGACCACGTATATCCCGACCAGGAACCACCAACGTCTATCCCGAC\n+CAGGTGAGGCCGGCGTCTATCCCGACCCGGACAGAGAGCCGTGGACCTAGTGTGAGGGGT\n+ATTAGGTCCACGGCAGAGAGTAGCAAACTAGGTCCACGGCAGGCTACATAGTACTAGGTC\n+CACGGCCCCGCATGTTTACTAGGTCCACGGC\n+>ds2020-328_836\n+GGTCGGAAGACGGTCCATTTCGGTGGTCGGGATAGACGAGTTCGCTGCACCGTCTATCCT\n+CGGACAGAGAGCCGTGGACCTAGTATTCTCTAACATGCCGTGGACCTAGTGCGCTCTCAC\n+CTGCCGTGGACCTAGTTCCGTATCCTCTGCCGTGGACCTAGTGTTCTACCCCTGCCGTGG\n+ACTAGAGGTCTTGAATTACTAGGTCCACGGC\n' |
| b |
| diff -r fd7104249a3c -r d1fd5579469d test-data/otu_s1.fa --- a/test-data/otu_s1.fa Wed Aug 21 13:13:28 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,6856 +0,0 @@\n->ds2020-267_1\n-CAGCACGTCCGCAAAAGGTCCTCGCTCCAAAACTGTCTCATCATCTCTATCGTGCCCTGA\n-CCCGTTTTCATCTTTGTACCTAGCTCTACTTCTTCTATCCTTGTTGGCACTTCTATCGCC\n-ATTACCCTCGCTATGTTGCCACGTTGTCCGTTGACCATAGGCCGCCACATCCTATAATGC\n-CTCATGTCTCCAACTACTGCCCCACTCATTGTTATCTCTGTGTATACTGGACATGTTTGC\n-CCTCTGTCTGGCCACAGCAGATTGGCTGCGGCTATAAACTTGTACAGTTTCACCTCGTCG\n-TCATGTGGTGTCAGCACTATGTTCTTATCTATCACGACTCTAGCTTCATGTGGAAAGCAG\n-TTCTCCTGATCTACCGGTATTCTGTGTAGTGAACCATACCCTAGGTGGCAACAGGGCAAC\n-GACATGTGCACCAAATTCACGTGCGTGACTAGAGGCCTCTTGAAGTACATCTTCGCACGG\n-TATTCAAACTCCGTTTGCATCATCCTTCCTTTCACACCTGCCACAATTGGGTTCCTGATG\n-TGAAATTCTCCATATTCTAGTGACATTTCTAGGTTCACTGGCGTCACCAGGAACCCCAGC\n-ATGTTTGACAGCCACGGCACCACTGCGTTGAATGTTGATAGCTCTCCAAGGTGTTGGTGC\n-AGCTCACCAAGTCTGCAGTTCCTGAAGGAGTGTGGCAGTCTAATATCCAACTCCCTCACT\n-TCAGACAGCTCCCAATGCCATATAGGAAAGTCTATGAAACTGCCTCTAATTGTGTTCTTA\n-TCTTTCGTCTGCTTGAAGGAAGTACATCCCAGGCACACACAGTACCTCGTCACATCTCTG\n-AAAGTTGCCTGACCAGGTGCAAACGTGGGTGGAGGCTGTGGTATCTTTGGTTCAATCAAC\n-CTTATTATTTCAGCAGGTGCTATCCTGGTGAACATGTCTGCCTGTTTTGCCAGTTTCAGC\n-AAAGAGTGCTCATCACCCTGCTTCTTGAATAGGCAGAAATGCGGCCCTGTGACATTGTGT\n-TTGTGCCCACAGCTCAGCTTCAGCTGGCTATTCTGTGTAGAGTTGCCAAACCAGTTTATC\n-TTTTCGCCGTAGTACATCCACCTACTTGGGTGCATTTCTTCTTCGTTAAGTGGCATGCCT\n-TTCACCATCCCTTGCATAACCTGGGCCTCGGTATTGATGCCGTGTTCGTGGTCAAAAATA\n-GGGCACTTGCCCTCTGCACCGCATGACATCAACGGCATGCCTTGCCATTTCCCGGTCAGT\n-TCCTGGCAATTTTCAGGTGTCGGTGGTACCAGTGAGGTTCCTCCGCGCTTGAAAGTGTCA\n-TCGTCATCACTCTGCTCTTCCATTATGTGACGTCTTATCCTTCCTAGCTCCTCTCTCGCT\n-CGCTCAGTTCTGTAAGCCTTTTCTTCTTTTCTGTTCATCCATGGCACGTCCCATGATCGT\n-GCGTCTTTTTCCCTTTGTTCCGAACTCGTGTCTGTTTGTGAATCGACAAACTCTTTCGCC\n-TGCCTCAATTTTTCAGCCACATCATCACACTCGATTCTCACTTCTGGCTCTAGCACGACA\n-TGCCCCTCACCTATAAGCAGGTTCTTCATGGTGTCCGCCCCCTCTGTATCTGACTCTGAC\n-GCTTCGTCCTGCGTCTTAACAGGGCTTGGTGTAGGGCCACCATCGAACGTGACGTCAGTT\n-TCTTGCTCTACATCCACCTCAACACTCAGCTTCTTAGAGTGAGCGCTTTTCCGTTCAGTG\n-AACTTGTAGACCAACATGTTTGCGTTGTACATGAGCTGTCCCCTTATGTCTTCCGATTTG\n-TCGCTTGGCCTACGCTGTTTCTGATCGAGCGCCTCGTCAACGTATTCAATGTCTGCTACG\n-TGCTCAGTGCTCATCATCTTGGCGTCTATTACGTCCTCGATTGACGGTGTCCTCTTTAGA\n-GTCTTCACCTCTAGTGTTCCGTCAACCACGACACCTGCCTCTTCGATTGCCTGGTTGCAC\n-AGCGCGCACGACACAAGCTGCTTGCACTTCCTGCACACATGCTGCATTTTTATGTATCCA\n-CAGCAACTTGTTTGGCACGGTGAAGACATCCTGACACACTTCTTGTTCTTCACCCTCGTC\n-TTGGGGGTGCTCATCACTTCATGGACAGACTTGATATTGCGTTGCCCTTTTTGACCGGTT\n-TCAGCCACACATACTTGATACGTGTGCACCAGGCTCAAGTAGTTTGGCCAGTTTGCATCA\n-GCTGCCACCACCAGTGACGCAACATACCTCACACGCGGTGAGTAGTTAGCAAACAAAGTG\n-TGTACCTGCTCCAATCTAGCAGCAGGTGTCATCTCGGTGCTGTTGAGTTTCTCATCCTTG\n-TATTTTAAACCCCTTTTGGTCAAAGTGAGGGCGTAACCGGTGCAGGCGTGCCATACTAGT\n-CTTGAAAGTGACCGTTTTGCGTGCTTGGTCAGTGGCAAGTAATAAACTTGCTTCGCATGT\n-TCGAAAGCCCTCTTACTATGCCAGGTGTACTCGAGTTCACTTTCTTCTGCCAGCAGTGCT\n-GCTGCATCTAGCCATTCTTACATGTCAGACTGATCAACGTACTGGCCTCCTGTTGCGGAC\n-GTGCTGNNNNNNNNNNATCTAAGGAGCAGCACGTCCGCAATGATGGCCCCATACAGTAGT\n-GATTTCTTGTCGAAACCACCAAATTCGAACACTGGCCTGTTGATACTTGAGCTAGTGATC\n-AACATCTTAGCGTTTTCTGTCTCTGCAGTGAAAACAGACCTGTACGTTGCAGCTCCAATA\n-ATGAGCTGTTTCAAATCCATTTGCTTGTCGTGCCATTTGGTCGGTGACACACATATTCCT\n-CTCTTGGTTCTGATGCACATTAGCGCTCTGTACAAGTTTACGACTGACGCTGCTCCTGTC\n-ACGTCGTTGATTGCTGACGTCAGTGACGCAAGGAACATCGATTTTGACGCCTGAGTTCCT\n-ATTGGCCTACCGCTTGACGTCACCGGAACTGCAATCCTGCAGTTGCTATTTGTGGTAACA\n-GCNNNNNNNNNNCAGCACGTCCGCAATTGCCTTCCATTGGGTTGCCAACTCCCAGTACCT\n-TTTCGTCACTCACCCTCAGTTCGAAGCCATATCGCCTGAGTTCTGGTGCGATAGCCATCA\n-CTCTCGCTTCTGCTCCCATTAACTGACCATTTATGATGTTGACATCAGATCTGTCGTTGC\n-CATCAGCAACGCAAGCGTCATCAACCCATGCCATCAGCGAGTTCAATGCTCCTGCCGTTG\n-CCCTCGCTGCTGATACATTAGTCAGCAGCACGCCTGCCTCATTTTGAGGGCCTTGGACAT\n-ACTCATCATGTTGCGATGTCACCGAACAAGCGTAGCTACCTTCAGACTGAACGTCAGTAG\n-TGTACCTGGTGCGCACTGCGCTACCTAGCACACTATCTGAAGTCAAAGCGCTTCTCGAGC\n-TCATTATGCCCGCCCGCATGAAAGGTTCATCTTTGTCAACCACTTCATAAACACCATGAC\n-CCGTCGGAGTTACAACGCTCTCGTCATGCTGCTTGTGTTTGCCACCAAAACCAGCGTATC\n-TGTTGGTGGCGATTATTGGCGTGACTCTTGCTGCGACTGATTTTTCAGCAGAGTTGTATT\n-GAAAAACTGGTACGCCCATCTTGTACAGTTGGCTGCAATGTCCCAA\n->ds2020-267_2\n-CAGCACGTCCGCAACAGTTGGTCCTTGCTAACAGTAATGGCGACTTGTGGACACGCATGG\n-GCGCCTTGCATGGACAAAGTTCTGCAGTGGCCTGACATAACGAACACGTTTATGTCATCA\n-CTACTACTTGCCATGGCTGCACTACCACCAGAGTTATATGTACTAATGGTGGAGTGG'..b'TGCGGACGTGCTGCTCCTTAGATAGATCGGAAG\n-A\n->ds2020-267_1209\n-CTTGCGGACGTGCTGAGTACAATATCTTTGCGGACGTGCTGCTCCTTAGATAGATCGGAA\n-G\n->ds2020-267_1210\n-TTGCGGACGTGCTGACCGGATCTAAGTTGCGGACGTGCTGCTCCTTAGATAGATCGTAAG\n-A\n->ds2020-267_1211\n-TTGCGGACGTGCTGAGGGGATTCGCTTTGCGGACGTGCTGCTCCTTAGATAGATCGGAAG\n-A\n->ds2020-267_1212\n-CAGCACGTCCGCAAACGATAGGCGTTAGCACGTCCGCAAGTTTATACGCCTCAGCACGTC\n->ds2020-267_1213\n-CAGCACGTCCGCAATGCAGACCCTTTAGCACGTCCGCAATTCGGCACTCTCAGCACGTCC\n->ds2020-267_1214\n-TTGCGGACGCGCTGGACGTGCTGATCAAGGCGCATTTGCGGACGTGCTGCTCCTTAGATA\n->ds2020-267_1215\n-TCTCCGATCTATCTAAGGAGCAGCACGTCCGCAATTACACCCACCTCAGCACGTCCGCAA\n->ds2020-267_1216\n-CTTCCGATCTATCTAAGGAGCAGCACGTCCGCAAGTGATGATCTCTCAGCACGTCCGCAA\n->ds2020-267_1217\n-GCAGCCGTCCGCAACCAACTGCTGCTCAGCACGTCGCAAGTCATATGGCCTCAGCACGTC\n->ds2020-267_1218\n-GGACGTGCTGAGGACTGCTACATTGGGACGTGCTAAGCGAGCATGGTTGCGGACGTGCTG\n->ds2020-267_1219\n-TTGCGGACGTGCTGAGGTATGGTAGATTGCGGACTGCTGCTCCTTAGATAGATCGGAAGA\n->ds2020-267_1220\n-TTGCGGACGTGCTGAGGGATCCGCAGTTGCGGACGTGCTGCTCCTTAGATAGATCGGAAG\n->ds2020-267_1221\n-TTGCGGACGTGCTGAGGGGCGTGCTATTGCGGACGTGCTGCTCCTTAGATAGATCGGAAG\n->ds2020-267_1222\n-TTGCGGACGTGCTGAGCCATGCACACTTGCGGACTGCTGCTCCTTAGATAGATCGGAAGA\n->ds2020-267_1223\n-TTGCGGACGTGCTGAGTCCCGACCACTTGCGGACGTGCTGCTCCTTAGATAGATCGGAAG\n->ds2020-267_1224\n-CTTCCGATCTATCTAAGGAGCAGCACGTCCGCAAATCAAAGTACCTCAGCACGTCCGCAA\n->ds2020-267_1225\n-TCTCCGATCTATCTAAGGAGCAGCACGTCCGCAACGTAGGATCTGTCAGCACGTCCGCAA\n->ds2020-267_1226\n-TTGCGGACGTGCTGAGGATTCCACATTTGCGGACGTGCTGCTCCTTAGATAGATCGGAAG\n->ds2020-267_1227\n-TTGCGGACGTGCTGAGGTAAGGAGCATTGCGGACGTGCTGCTCCTTAGATAGATCGGGAG\n->ds2020-267_1228\n-CTCTCCGATCTATCTAAGGAGCAGCACGTCCGCAAGCGTTATCCCTCAGCACGTCCGCAA\n->ds2020-267_1229\n-TTGCGGACGTGCTGCCCGGATAACATTGCGGACGTGCTGCTCCTTAGATAGATCGGAAGA\n->ds2020-267_1230\n-TTGCGGACGTGCTGCCGAGATAACATTGCGGACGTGCTGCTCCTTAGATAGATCGGAAGA\n->ds2020-267_1231\n-TTGCGGACGTGCTGAGAGAATCAAGTTGCGGACGTGCTGCTCCTTAGATAGATCGGGAAG\n->ds2020-267_1232\n-TTGCGGACGTGCTACCCCGTGATACTTGCGGACGTGCTGCTCCTTAGATAGATCGAAAGA\n->ds2020-267_1233\n-TTGCGGACGTGCTGAGGGGATCCTTATTGCGGACGTGCTGCTCCTTAGATAGATCGGAAG\n->ds2020-267_1234\n-TCCGATCTATCTAAGGAGCAGCACGTCCGCAACCTGCTATCCGTCAGCACGTCCGCAACT\n->ds2020-267_1235\n-TGAGTGAGTGAGTGAGTGAGTGAGTGAGTGAGTGAGTGAGTGAGTGAGTGAGTGAGTGA\n->ds2020-267_1236\n-CCACTGCCACTGCCACTGTTGAGACTATCCCCCAAGCCAAAGGTATTGCGGACGTGCTG\n->ds2020-267_1237\n-TTGCGGACGTGCTGACTGAGAGGGCATTGCGGAAGTGATCACGTATTGCGGACGTGCTG\n->ds2020-267_1238\n-TTCCGATCTATCTAAGGAGCAGCACGTCCGCAAATTCATTCTGGTCAGCACGTCCGCAA\n->ds2020-267_1239\n-ATTGCGGACGTGCTGAGGCACTGTTCGTTGCGGACGTGCTGCTCCTTAGATAGATCGGA\n->ds2020-267_1240\n-TTGCGGACGTGCTGATGGGTTTCGTCTTGCGGACGTGCTGCTCCTTAGATAGATCGGAA\n->ds2020-267_1241\n-CTTCCGATCTATCTAAGGAGCAGCACGTCCGCAACGTGCTATGCCTCACACGTCCGCAA\n->ds2020-267_1242\n-TTGCGGACGTGCTGAGGGAACCGGCTTTGCGGACGTGCTGCTCCTTAGATAGATCGGAA\n->ds2020-267_1243\n-TTCCGATCTATCTAAGGAGCAGCACGTCCGCAATCCGATTGCCCTCAGCACGTCCGCAA\n->ds2020-267_1244\n-CTTCGATCTATCTAAGGAGCAGCACGTCCGCAAGAGATTACTCCTCAGCACGTCCGCAA\n->ds2020-267_1245\n-TTGCGGACGTGCTGGGGAGTATTGCTTGCGGACGTGCTGCTCCTTAGATAGATCGGGAG\n->ds2020-267_1246\n-TTAGAGGGACTATCGGCTCAAGCCGATGGAAGTTTGAGGCAATAACAGGTCTGTGCTG\n->ds2020-267_1247\n-TTGCGGACGTGCTGAGGCGATACCTCTTGCGGACGTGCTGCTCCTTAGATAGATCGGA\n->ds2020-267_1248\n-GTAAAAGCTCACTGGTAACCGGTCCAAAACGAAACTCTTAAAACAGTGGATACCCTCC\n->ds2020-267_1249\n-CGGACGTGCTGAGACAATGGCGCTTGCGGACGTGCTGCTCCTTAGATAGATCGGAAGA\n->ds2020-267_1250\n-CCCGATCTATCTAAGGAGCAGCACGCCCGCAAATGTACACCGGTCAGCACGTCCGCAA\n->ds2020-267_1251\n-TCCGATCTATCTAAGGAGCAGCACGTCCGCAAGGTAGACGCCCTCAGCACGTCCGCAA\n->ds2020-267_1252\n-GTGCTGAGCCAGACTACTTGCGGACGTGCTGAGGGAGCCTAAATTGCGGACGTGCTG\n->ds2020-267_1253\n-TTGCGGACGTGCTGAGTGTTTACAATTTGCGGACGTGCTGCTCCTTAGATAGATCGG\n->ds2020-267_1254\n-TGCTGAGCGACTATAAATTGCGGACGTGCTGAGGGATTCACCGTTGCGGACGTGCTG\n->ds2020-267_1255\n-TTGCGGACGTGCTGACGGACGACTATTTGCGGACGTGCTGCTCCTTAGATAGATCGG\n->ds2020-267_1256\n-GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\n->ds2020-267_1257\n-GCTGAGGGCAGTGGGCTTGCGGACGTGCTGACGGATACGTCATTGCGGGCGTGCTG\n->ds2020-267_1258\n-CTCACTCCTCAGCACGTCCGCAAACTGCTTCGGGTTGGGACGTGCTGAGGAGTGAC\n' |
| b |
| diff -r fd7104249a3c -r d1fd5579469d test-data/otu_s1_rps.tab --- a/test-data/otu_s1_rps.tab Wed Aug 21 13:13:28 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,109 +0,0 @@\n-#query_id\tquery_length\tcdd_id\thit_id\tevalue\tstartQ\tendQ\tframe\tdescription\tsuperkingdom\tno rank\tfamily\tgenus\n-"ds2020-267_100"\t"376"\t"pfam02823"\t"gnl|CDD|376940"\t"3.06167e-09"\t"228"\t"347"\t"-3"\t"pfam02823, ATP-synt_DE_N, ATP synthase, Delta/Epsilon chain, beta-sandwich domain. Part of the ATP synthase CF(1). These subunits are part of the head unit of the ATP synthase. The subunit is called epsilon in bacteria and delta in mitochondria. In bacteria the delta (D) subunit is equivalent to the mitochondrial Oligomycin sensitive subunit, OSCP (pfam00213)."\t"Bacteria(0.97);Eukaryota(0.03);"\t"(1.00);"\t"Lactobacillaceae(0.05);Rhodobacteraceae(0.04);Streptococcaceae(0.03);Bacillaceae(0.03);Burkholderiaceae(0.02);"\t"Lactobacillus(0.04);Streptococcus(0.03);Bacillus(0.02);Mycoplasma(0.02);Synechococcus(0.01);"\n-"ds2020-267_100"\t"376"\t"pfam00401"\t"gnl|CDD|366077"\t"8.90041e-05"\t"87"\t"218"\t"-3"\t"pfam00401, ATP-synt_DE, ATP synthase, Delta/Epsilon chain, long alpha-helix domain. Part of the ATP synthase CF(1). These subunits are part of the head unit of the ATP synthase. This subunit is called epsilon in bacteria and delta in mitochondria. In bacteria the delta (D) subunit is equivalent to the mitochondrial Oligomycin sensitive subunit, OSCP (pfam00213)."\t"Bacteria(0.97);Eukaryota(0.03);"\t"(1.00);"\t"(0.06);Clostridiaceae(0.05);Lachnospiraceae(0.05);Bacillaceae(0.04);Peptococcaceae(0.04);"\t"(0.06);Clostridium(0.05);Lactobacillus(0.03);Bacillus(0.03);Eubacterium(0.02);"\n-"ds2020-267_114"\t"347"\t"pfam00471"\t"gnl|CDD|376336"\t"8.05888e-12"\t"132"\t"302"\t"3"\t"pfam00471, Ribosomal_L33, Ribosomal protein L33. "\t"Bacteria(0.86);Eukaryota(0.14);"\t"(1.00);"\t"(0.07);Mycoplasmataceae(0.07);Clostridiaceae(0.06);Bacillaceae(0.03);Lactobacillaceae(0.03);"\t"Mycoplasma(0.06);Clostridium(0.05);(0.04);Lactobacillus(0.02);Bacillus(0.02);"\n-"ds2020-267_117"\t"344"\t"pfam00252"\t"gnl|CDD|376306"\t"7.27175e-23"\t"107"\t"295"\t"2"\t"pfam00252, Ribosomal_L16, Ribosomal protein L16p/L10e. "\t"Bacteria(0.58);Eukaryota(0.29);Archaea(0.13);"\t"(1.00);"\t"(0.08);Clostridiaceae(0.03);Mycoplasmataceae(0.03);Spirochaetaceae(0.02);"\t"(0.04);Clostridium(0.03);Mycoplasma(0.02);"\n-"ds2020-267_118"\t"343"\t"pfam00421"\t"gnl|CDD|366090"\t"7.68219e-41"\t"92"\t"337"\t"-1"\t"pfam00421, PSII, Photosystem II protein. "\t"Bacteria(0.79);Eukaryota(0.21);"\t"(1.00);"\t"Gloeobacteraceae(0.14);Synechococcaceae(0.14);Prochloraceae(0.14);Acaryochloridaceae(0.14);Nostocaceae(0.07);"\t"Acaryochloris(0.14);Gloeobacter(0.14);Prochlorococcus(0.14);Synechococcus(0.14);Nostoc(0.07);"\n-"ds2020-267_120"\t"339"\t"pfam16639"\t"gnl|CDD|374695"\t"2.20279e-25"\t"197"\t"325"\t"-3"\t"pfam16639, Apocytochr_F_N, Apocytochrome F, N-terminal. This is the N-terminal domain of cytochrome f. It is a soluble lumen-side domain."\t"Bacteria(0.75);Eukaryota(0.25);"\t"(1.00);"\t"Synechococcaceae(0.25);Gloeobacteraceae(0.07);Prochloraceae(0.07);Aphanothecaceae(0.07);(0.07);"\t"Synechococcus(0.21);Prochlorococcus(0.07);Gloeobacter(0.07);Oscillatoria(0.04);Aureococcus(0.04);"\n-"ds2020-267_130"\t"330"\t"pfam00680"\t"gnl|CDD|366242"\t"7.64962e-05"\t"124"\t"282"\t"1"\t"pfam00680, RdRP_1, RNA dependent RNA polymerase. "\t"Viruses(1.00);"\t"Riboviria(1.00);"\t"Caliciviridae(0.30);Picornaviridae(0.30);Secoviridae(0.20);Potyviridae(0.20);"\t"Vesivirus(0.20);Aphthovirus(0.10);Sequivirus(0.10);Bymovirus(0.10);Potyvirus(0.10);"\n-"ds2020-267_139"\t"320"\t"pfam05860"\t"gnl|CDD|368641"\t"1.34887e-13"\t"167"\t"298"\t"2"\t"pfam05860, Haemagg_act, haemagglutination activity domain. This domain is suggested to be a carbohydrate- dependent haemagglutination activity site. It is found in a range of haemagglutinins and haemolysins."\t"Bacteria(1.00);"\t"(1.00);"\t"Nostocaceae(0.36);Burkholderiaceae(0.14);Pasteurellaceae(0.14);Pseudomonadaceae(0.12);Neisseriaceae(0.07);"\t"Nostoc(0.36);Ralstonia(0.14);Pseudomonas(0.12);Haemophilus(0.10);Neisseria(0.07);"\n-"ds2020-267_145"\t"315"\t"pfam02626"\t"gnl|CDD|376868"\t"3.97676e-05"\t"140"\t"256"\t"-3"\t"pfam02626, CT_A_B, Carboxyltransferase do'..b' 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."\t"Bacteria(0.79);Eukaryota(0.16);Archaea(0.05);"\t"(1.00);"\t"Flavobacteriaceae(0.05);(0.04);Saccharomycetaceae(0.02);Vibrionaceae(0.01);Spirochaetaceae(0.01);"\t"(0.02);Mycoplasma(0.01);Vibrio(0.01);Corynebacterium(0.01);"\n-"ds2020-267_8"\t"1703"\t"pfam00680"\t"gnl|CDD|366242"\t"2.85682e-13"\t"685"\t"1458"\t"-3"\t"pfam00680, RdRP_1, RNA dependent RNA polymerase. "\t"Viruses(1.00);"\t"Riboviria(1.00);"\t"Caliciviridae(0.30);Picornaviridae(0.30);Secoviridae(0.20);Potyviridae(0.20);"\t"Vesivirus(0.20);Aphthovirus(0.10);Sequivirus(0.10);Bymovirus(0.10);Potyvirus(0.10);"\n-"ds2020-267_811"\t"208"\t"pfam07991"\t"gnl|CDD|285265"\t"1.80927e-08"\t"20"\t"190"\t"-1"\t"pfam07991, IlvN, Acetohydroxy acid isomeroreductase, NADPH-binding domain. Acetohydroxy acid isomeroreductase catalyzes the conversion of acetohydroxy acids into dihydroxy valerates. This reaction is the second in the synthetic pathway of the essential branched side chain amino acids valine and isoleucine. This N-terminal region of the enzyme carries the binding-site for NADPH. The active-site for enzymatic activity lies in the C-terminal part, IlvC, pfam01450."\t"Bacteria(0.76);Archaea(0.24);"\t"(1.00);"\t"Bacillaceae(0.07);Helicobacteraceae(0.05);Sulfolobaceae(0.05);Bartonellaceae(0.02);Leptospiraceae(0.02);"\t"Bacillus(0.07);Thermus(0.02);Tropheryma(0.02);Corynebacterium(0.02);Pyrococcus(0.02);"\n-"ds2020-267_817"\t"208"\t"pfam05656"\t"gnl|CDD|377540"\t"3.45664e-06"\t"86"\t"190"\t"-1"\t"pfam05656, DUF805, Protein of unknown function (DUF805). This family consists of several bacterial proteins of unknown function."\t"Bacteria(1.00);"\t"(1.00);"\t"Veillonellaceae(0.07);Sutterellaceae(0.06);Sphingomonadaceae(0.05);Rhodobacteraceae(0.04);Caulobacteraceae(0.04);"\t"Veillonella(0.04);Sphingomonas(0.04);Asticcacaulis(0.03);Dakarella(0.03);Prevotella(0.03);"\n-"ds2020-267_837"\t"207"\t"pfam04061"\t"gnl|CDD|367791"\t"2.43363e-18"\t"1"\t"159"\t"1"\t"pfam04061, ORMDL, ORMDL family. Evidence form suggests that ORMDLs are involved in protein folding in the ER. Orm proteins have been identified as negative regulators of sphingolipid synthesis that form a conserved complex with serine palmitoyltransferase, the first and rate-limiting enzyme in sphingolipid production. This novel and conserved protein complex, has been termed the SPOTS complex (serine palmitoyltransferase, Orm1/2, Tsc3, and Sac1)."\t"Eukaryota(1.00);"\t"(1.00);"\t"Saccharomycetaceae(0.15);Nosematidae(0.04);(0.04);Phaffomycetaceae(0.03);Salpingoecidae(0.03);"\t"Kazachstania(0.04);Thalassiosira(0.03);Trichomonas(0.03);Nosema(0.03);Nakaseomyces(0.03);"\n-"ds2020-267_94"\tno_hit\n-"ds2020-267_97"\t"380"\t"pfam04879"\t"gnl|CDD|368171"\t"1.9903e-08"\t"125"\t"274"\t"-2"\t"pfam04879, Molybdop_Fe4S4, Molybdopterin oxidoreductase Fe4S4 domain. This domain is found in formate dehydrogenase H for which the structure is known. This first domain (residues 1 to 60) of Structure 1aa6 is an Fe4S4 cluster just below the protein surface."\t"Bacteria(0.75);Archaea(0.25);"\t"(1.00);"\t"Enterobacteriaceae(0.11);Bacillaceae(0.09);Pseudomonadaceae(0.08);Methanobacteriaceae(0.06);Phyllobacteriaceae(0.06);"\t"Bacillus(0.09);Escherichia(0.09);Pseudomonas(0.08);Mesorhizobium(0.06);Synechococcus(0.06);"\n-"ds2020-267_98"\t"379"\t"pfam16203"\t"gnl|CDD|374428"\t"1.33948e-30"\t"131"\t"280"\t"-1"\t"pfam16203, ERCC3_RAD25_C, ERCC3/RAD25/XPB C-terminal helicase. This is the C-terminal helicase domain of ERCC3, RAD25 and XPB helicases."\t"Eukaryota(1.00);"\t"(1.00);"\t"Cryptosporidiidae(0.06);Vahlkampfiidae(0.06);(0.03);Opisthorchiidae(0.03);Chaetomiaceae(0.03);"\t"Naegleria(0.06);Cryptosporidium(0.06);Micromonas(0.03);Batrachochytrium(0.03);Caenorhabditis(0.03);"\n' |
| b |
| diff -r fd7104249a3c -r d1fd5579469d test-data/otu_s1_tblastx.tab --- a/test-data/otu_s1_tblastx.tab Wed Aug 21 13:13:28 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,57 +0,0 @@\n-#algo\tquery_id\tnb_reads\tquery_length\taccession\tdescription\torganism\tpercentIdentity\tnb_hsps\tqueryOverlap\thitOverlap\tevalue\tscore\ttax_id\ttaxonomy\tsequence\n-TBLASTX\tds2020-267_392\t26\t240\tNC_005979\tHelminthosporium victoriae 145S virus\tHelminthosporium victoriae 145S virus\t40.0\t1\t100\t6.0\t1.12512e-11\t66.1329\t164750\tViruses;Orthornavirae;Duplornaviricota;Chrymotiviricetes;Ghabrivirales;Chrysoviridae;Chrysovirus;Helminthosporium victoriae 145S virus\tCAGCACGTCCGCAAGTTGTCCGGCTTAAATCTTTAGCCCCTAACTTAAGTGCCGCTACAGCTCCATTTTCTATTACTTTTTTTGTTCTATCACATAACCACATTCCTTCGAAGACTGATAGTTGTGAAATTTCATATATGTTGTCTTCATCTAAGTAATATAGAAATTTGAAACTTGGTGTTGCGTCCGTTAAACGTAGATCAGTGAAGTACGCACCCATTCGTAGTTGCGGACGTGCTG\n-TBLASTX\tds2020-267_268\t14\t259\tNC_001963\tSphaeropsis sapinea RNA virus 1, complete genome\tSphaeropsis sapinea RNA virus 1\t62.0\t1\t100\t5.0\t1.78772e-31\t132.115\t73497\tViruses;Orthornavirae;Duplornaviricota;Chrymotiviricetes;Ghabrivirales;Totiviridae;Victorivirus;Sphaeropsis sapinea RNA virus 1\tCAGCACGTCCGCAATGCATGGCCTCTGAGTTTGTGGAAACGAACCCTCTGCCAACCTGGGACGGCACGACCCACGTCTCTAAGTCTGCCAAGTTAGAACACGGGAAGACCCGCGCAATATTCGCCTGCGACACCCGGTCGTATTTTGGGTTTTCGTGGATCCTAGATGCGACCCAACAGGCCTGGAAGAACGAACGGGTTGTCATGGATCCGGGCAAAGGTGGGAAGTGTGGGATGACGCAACGATTGCGGACGTGCTG\n-TBLASTX\tds2020-267_4\t1434\t2297\tNC_038699\tXanthophyllomyces dendrorhous virus L1b capsid protein (CP) and RNA-dependent RNA polymerase (RdRp) genes, complete cds\tXanthophyllomyces dendrorhous virus L1B\t44.3\t8\t100\t64.0\t1.9240409540575e-07\t928.6219\t1167691\tViruses;Orthornavirae;Duplornaviricota;Chrymotiviricetes;Ghabrivirales;Totiviridae;Totivirus;Xanthophyllomyces dendrorhous virus L1B\tCTTCCGATCTATCTAAGGAGCAGCACGTCCGCAATTCAGCTACTCTCAGCACGTCCGCAATACTAACAGCTCAGCGCGTCCGCAACACGACTGGGGCACACGTCCGCAACGTCCACGACTTATCACTTGCGGACGTGCTGCTCCTTAGATTCTGGAAGTAAGGACGTTCGGGCTTCCTATTCCGCTTTATTAAGGTACACTAAGTAACTATTCCTATTAACTCCATCGGGTCCTTAGATCCTTTGAGTAGGTGTAGTAGTGGGCCGCTTTTATTGGTCCCATTCAACACGTCCATCAGGAAGCCGGTCATTTTGGCTTTTCCGTAATTGACTATGTCTGTTTCTTCTTTGTGTACCTTGAATAACGCTCGCAAAATCTCGTACCGCTTGATGTTACCATTCCTTGAAACGTTTATGTTCCTTTCTTTTGGTATCACCGCGTCGTATGTTGCGCGCATTATTCGTGAAATGAAATCCTGCAAAGGTCTTTCAAGTTGTAGTGATGCTTTCACCATCCTGGAGTAGTCCACCACTCCCGGTAACACGCCTATCTGCGTGGCACCCTTCCTGAAGCCCGACGACCGTATCATCCACTTTACGTCCGATCTCTTGTCTTCACTTATGCCCCCCACACACCTGTGGGAGGTCTTTATTTTATAACAGTCTGAAACTGTCATGTGCAATCGCTCACATTGTCTCGAGTAGTATTTGTTCCTCAATGACGCCGCTAACCACATTGGCATTCCCCTAGACACTGAATCGTCCAGACGCGACTCCAGCGCTTCCAAAAGGTCCCTCATATCGCTTGAAGGTTTTGACTCTATCCTCGAGTGTACCAAGGTTGCCATAGCTCTAGATAGATACTGTCCCTTAGACCCACGTTTGTGATCTACGCGTAGAAACTCTGCTATGGCCCCATACGCACATTTGCTCATCTGCAGGCGTATGTTGTGCTTCTTGGCATTTTTGCCAGCTAGCAACACGTCCTCGAGCGAATTACTTCCCAGTAGCACGTCGTCACCGTTGTGGAGGCTGTTTTGCGATTGTACCACGTCAGGTACTATCAGTTGAGTGTAAATGTAGTTAAGCACGCTGTTCATGAACGTAGTGAGTCGCCACCCCGATAACAGGGTCCCCTTAGCGTTGTACTCCATTTTCAAGCCTTGATTGTCGTGTACTATTACCCTATCCAGTGAAAGCCGAGTCCACTCCACAGCTGCTAGTTGCTCCTGAGTCAGGAAGTGTCCGAAAGTATCTCTGTACGCATCTATTACTGCTTTCATAGATTGTACACTGTGTTGACTGTTGAAATCCTCGAAATCTACACAATACTGAGTCCTGCCTTCTAAGACTGACCTTACTCTACTGCGGACGTTCTCATCGTTGGCTGCTTTTCCCACCGGGAACGGCGAGGGCAATACGTCCTCGCAGTTATAGAAGGCGAAATGTGCCAATACGTAACTAGTGACATCTGTCCCGTAGATAGCGCGGAGTTTGCTCCATTCATACTTCGTGGATGACCATGCGTGAAGTTCAGGATCTCTTTCGCGCCACGAGTCCATATTCATATCCGGCATGGCCAGTATTGATATGAACTTGTTCTTGAGGTATATGTCTTTGAATATGTATTTATCGTCTTCTGAATATTGCGAGTGTATGCTGCCGGCCGCACTCCACTGCCACCTACTCTGCCAGTACTCCCGCCAATCAAACTTCCTCGGTCTCTTACCCGCTGAGATCGATCTACTGAAGAGCTGCGAGGCCCTTTCATAAACCAATCCCTCCGGCATCTCGGCCAAGTTAGGGGACACCCTGTTCTTGTGCTCCTCCTCCCAGTTGACCAGTCTTGATTTGCGGACGTGCTGCTCCTTAGATANNNNNNNNNNGGACGTTCGGGCTTTGCGCTGGCAATGGAGAACAGTCCTGACCCTCTAGCGAGCTGCATCTCCTCGGGGGTGAGACCAGCTGCCCACAGTGCCACGCCCGTAAGGAATGAGTTAGTAGCTTCTCTGGTTATTGATAAGGCCAGAGCTACGCTGTCAGAGTTGACTCCCAAAATGTCTACCACCTCCTTGAACGAAAAGTGAACATGATGCGACGCCGTTATCTTGGTGTGTTTTGCCGACATTGCTTCATGTAACTGCCACCCTCTGCCTTGCTGTCCATTTACTTTCCTCAATAATCGCTTCGGAGACACAGGGTCCTCAAAGTCGATAGAATCGTAAAGACCTGAGGTGTGCCTGGTCATTTGAGAAAGTATTTCTTTGCGTATACCCCAAGATCTTTGCGGACGTGCTG\n-TBLASTX\tds2020-267_18\t840\t1037\tNC_016760\tRosellinia ne'..b'a;Chrymotiviricetes;Ghabrivirales;Quadriviridae;Quadrivirus;Rosellinia necatrix quadrivirus 1\tCAGCACGTCCGCAACTACGACACGTTTTTGTAGCGCTCCCTGGCCGTGTCTGCGTTCTGCATTGCTCGCGGCAAACACAGCAGGTTGTGTGCATGATCAAGTTGCAGACGCGTAACGTCCTCATCTTTTAGACACATTTGTGACCGCTGTGCCACGTGCACCTCTGCCATCGCTCTACCGCTGCCCAACATCTGGATGCTCGAGCAGATCATGCTGACCATCTCATCACCGTTGATTGACGAATTCTCACTGATCTTGTTAAACTGAGGGCTGTTAGATGATGAAAACAGCCTGTCAACCGTTGGCTCGCAAAAGGGTTGTACCACTTTGTACACCCCTGCGTAAAACACGTCAGCATAGTCGTGGTGGGACAAGGCTGCAGGCTGGTAGGTAGACGCCACAGCTAGCGACGCCATTAACATCACGTTTTTAGAAGCCATGAAGTGCCTGGTCGTGACGTGTCCAATGAGGTCCAACATGTCGTTGATCGAGAAACCAACACTGTTGAACCAGTCTCTGTCGAGGTGGGGCGCTGACGACCCTACACCTGCAATGAAGGACACATTGCACTCACTTGCCACCGCCATCAACTTCTGATGCCCCACAGCAGCCTCAATGGAAGGCGAGAACCCCGTATTTGCGGACGTGCTG\n-TBLASTX\tds2020-267_5\t37987\t2029\tNC_023684\tRhizoctonia solani dsRNA virus 2 segment 1, complete sequence\tRhizoctonia solani dsRNA virus 2\t47.6\t8\t100\t100\t3.1306275000000004e-37\t1379.9565000000002\t1411681\tViruses;Orthornavirae;Pisuviricota;Duplopiviricetes;Durnavirales;Partitiviridae;Rhizoctonia solani dsRNA virus 2\tATCGCACATGATAAAGCCCGATATCTAAGGAGCAGCACGTCCGCAACCCTCTGCCTCCAACAATAAAGCAGATTTCTTTGCTCTTCTAACAGCTATTACTTACCACAATGGACCACCTCACTTCCCTTTTCGAGCTTTTTGCTATCACACCGAAAACACAAAACAATCTACAGTTTGTTGGGATCTACCACAGACCTCCACACTCCGTTCGAGCAAACCTCCGCAACGTTGAAAAACACAAAATCACAGTCGCTCACGCCATGCACAAGTACCTTTACCCGCATGAAATCGACTTTGTTATCAACCAAATGCGACGCTCAGACGTCACTGAAGATGCCATACTTGCTGACTTTTTCGACAACAACGTCGAACCACTTGAACCTGTTCTTGACGAACACTTCGAACGTGGACTCTCCGCAATGCTGGACGCTTTTCGCCCTCCGCAGAAATGCCTACCTGCCCACATCTATGATGTGCAGCACCACTACCCATATAAATGGCAAGTGAACGCTGAAGCCCCCTTCTCCACCGATTCCTATTTCTTAGCGAATCGACCAACCTTCCGCGCAGTGTTTGAACGACTCGAATCGCTCTACACACACCTCGCAACCGATTGGCACCGCCGATACGGAAACAAAACCGACAATGATGATTTTATGAATGATCATGTCCCTGCGAAATTTGGCCCTATGAAAGAAACAGTCTTCTCATGGACTCACCGATGGCACCACGTCATCAAATCCAACTTCACCGACACAGCTGGATTGTCTAAAGACTATTACTTCAAAAACCGATACATCTTCCCAATGCTACTTCACACGAAGACAGCGATTGTCAAGAAAGACGACCCGAATAAGATGCGAACCATCTGGGGCTGTTCAAAGCCTTGGATCATCGCAGACACCATGCTATGGTGGGAATACGTCGCGTACGCTAAGTTACAACCTGGAGCCACACCAATGCTCTGGAGTTACGAAACCTTCACAGGTGGCTGGCTTAGACTCAACCACGCACTTTTCTCTTCATACATACGGCACTCGTACATCACACTCGACTGGAAACGCTTCGACAAGAAAGCGTATTTCTGCATCATCGACAAAATTTTCGATGGCGTTGAAACATTCCTCGACTTTGACAACGGCTATTTGCCTACGAAAGATTATCCCGATACCAAATCGACTTGGACACAAGAACGTTCCACCCGCCTCAAACGCCTGTTTGACTGGACAAAAGAGAACTTCTACCATGCACCAATTGTCCTACCCAATGGGCACATGTACGTCCGAAAATTCGCTGGAATACCCTCTGGCCTATTTATCACTCAACTGATCGATTCCTGGTACAACTACACCATGCTCGCAACCATCCTATCCGCGATGGGCTTCGACCCTCGGTCCTGTATTATTAAAGTCCAAGGTGATGACTCAATCATCCGCCTCAGTGCACTCATCCCTCCGGATGCTCACGATTCTTTTTTAACTAAGGTCCAAGAACTCGCCGACTACTACTTTCAATCAGTAGTCTCCGTGAACAAGTCTGAAGTACGCAACGAGCTCAACGGATGCGAAGTTTTATCGTACCGACACAGACACGGTTTACCATACCGCGATGAACTAGCTATGCTAGCTCAACTGTATCACACGAAAGCACGCAACCCAAGTCCCGAAATCACAATGGCACAATCCATCGGCTTCGCCTACGCTTCCTTCGGAAATCATGAAAGAGTACGTCTCGTACTACATGATATCTACGAATATTACAAGCATCAAGGCTACACACCCAACCGAGCCGGACTCAGCCTCGTCTTCGGAAACTCTCCTGACCTCATGATCCCGCACTACACACTTGATCACTTTCCCTCAATCAGGGAAATAAAAATGTTCCTGACTAATGCAAAATATGCCAATGAAGAAACCAACTCACGAACGTGGCCTTTAACCCACTTTCTCCATCTTCCTTGTCATCGCACTTAGTATTTGAGCAATTGCAATTACAACATAATTACAAAAAAAGGATTGCGGACGTGCTG\n-TBLASTX\tds2020-267_43\t465\t563\tNC_021222\tCryphonectria parasitica bipartite mycovirus 1 strain 09269 segment RNA1, complete sequence\tCryphonectria parasitica bipartite mycovirus 1\t57.9\t2\t100\t21.0\t5.04473e-43\t192.2912\t1329781\tViruses;Cryphonectria parasitica bipartite mycovirus 1\tCAGCACGTCCGCAACTACTCTCCCTTGCATCAGGCGGTGAAATGCGCTCTCTGCGTCGGCTTGTGCCAGGGGATTCGCCTCTTCCCTGGTCTTAAGTCCCATTGTAGCGTACTCAATGCCGGCGAACTTCTTGGGGTAGAACTTAACGGTGGCGAGATCTTCCACTGCCGGGAAGAAGAGGAAGTCGGGAAGGTCGAGTAACTTTGCCACTACATAGGCGGCCTTCTCTATGGAGTCGGTGTAGCGGGGGTCAGGGGTGTGATTTGGCCGATCGAAGTGGCGAAGGTGTGCCATCTCAACTGGGGTGCAGGCCTTGACGAATGTGAATTCCTCCGGCTTGAAATTGTTGATGGGGGGGGGATGGAGGAGGGTGTAGGCGACAACTTCGGGGTCGGGTGGCGCAATGTCGAGTTCCTTGTTTAGCTTCCCATAGGCTTCAACCCTACCGAGGATTCGTATATGTTGGAACATGTTGGTGAGTTCCATCACTTCGCGGGTCGCGGCCTCTTTGGACCTCATGGATCGCATACGCGTCCTACGCTTGATAGATTGCGGACGTGCTG\n-TBLASTX\tds2020-267_453\t17\t232\t\n-TBLASTX\tds2020-267_352\t4\t245\t\n' |
| b |
| diff -r fd7104249a3c -r d1fd5579469d test-data/otu_s2.fa --- a/test-data/otu_s2.fa Wed Aug 21 13:13:28 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,6446 +0,0 @@\n->ds2020-328_1\n-GGTCGGGATAGACGTTGGAGCGCGGTCAGCCGAGACCCCTGACAGAGGAAAGAGTCTTGA\n-GGAGTCCAACGTTCGGCCAGGCATAATAATTCGTGCCCACTAATCGAATCGGTTTACTCG\n-CCCACCATGTCAGCGCCTTCGGGTTAGTTCTTTATGGAGTTATTTCTTGTTCTTTCTGTC\n-ATAACAATTCTCCTTATGGAAGTCCCCCACAAGATTAAGAATGCTTGTTGCCGCGGCTGT\n-CTTGGTTCTTCGTTTAGCTTTCTGGCATATTCTACGGAGCTTTCCACTCTGGAGCTGGCT\n-TTCAGAAAAACCTTCATTCACTAGATGTGAAGCACCCCTATGGGGGAACCCTCTTACCCG\n-CTTTCCTCCCCCCCCGATATGGGGGGCCTCGCTGTCGCCTTTGGCTCGAGCTACTTTTTC\n-TCCTGGAACGGATAGCTTTCTGTCCAAGTCTATCTCCCAAAAGTCAGCCATGTAATTGAC\n-TTCTAACGTCTAATTTTCTTTTTCACCGGGGGTCCCTGATCCCCGTTGAATATTCCTTCC\n-TTCTGAAAAAGCTGTGACTCCTAAATTCTTTGATTGAATGAAATGTGGACTTGGTCACGG\n-GGCAATCTTCTTTTTTAGACCCCGCTTCTCTCGGTGTTACCTTTTTCGCCTTCTCGTCTC\n-GCTTCGCGTCGTCNNNNNNNNNNGGTCGGGATAGACGCGCCGCTTCCGTCTGTTTTACCT\n-TGTTAGAATTCTCGGCGCGCTTGGCGTCGTCTTTAGAGTCAATTCTATTGGAATCTCCTT\n-TCCCCTTCTTTTCTTCCCCCACGATGAAAAAAATAAATATTGCAAAAAGAACAATATTTC\n-CCCCCGTGGTCATCATAGTGGTTCCTTCTGATCCTAGAAAACGATTAAAAAGAAGGCAAA\n-AAAAACAAAGGAGGATCTGCTTTTTCATATTAAAGCGCTTTCTTTCTTTTAAAAATACAT\n-CATAGTAAAGCGCTTCCTTTTAAAAAAGCATCTGGTTCCATCTTTCTTTCGTTAGTTAAC\n-CCACCTTTTTCTAAAAGGGATTGTAGTAATTCTGGTTTTACACTATTTAGAATGGCTCTC\n-TCATATTGAGAGATTCTGTCTAGTGGCATTCGATCACAGAATCCATTGACAGCTGCATAA\n-ATGACTAGAATTTGTTTTTCAATTGGAAGTGGTGCATATTGTGGTTGTTTCAGTACTTCT\n-GTAAGCCTTGCACCTCTATTGAGTAATGCCTGAGTCGCAGCATCAAGGTCTGACCCAAAT\n-TGAGCAAAGGCCGCCACTTCGCGATACTGTGCCAATTCCAGTTTTAAACTACCGCAGACC\n-TGTTTCATAATTTTCAACTGAGCGGCAGACCCGACGCGACTGACAGATAAGCCGACGTTA\n-ATAGCAGGTCTAATTCCGCGATAAAAGAGCTCTGTTTCCAAACAGATTTGTCCATCAGTA\n-ATGGAGATTACATTGGTTGGAATATAGGCCGATACGTCTCCAGCTTGTGTTTCAATGACG\n-GGTAAGGCGGTCAAGCTACCTGCACCTGTCTGGTCCGATCGTTTAGCGGCTCTTTCTAAG\n-AGACGGGAATGTAAATAGAAAACATCGCCTGGGAAAGCCTCACGGCCTGGTGGTCGGCGT\n-AACAATAATGACATTTGTCGATATGCCACCGCCTGTTTACTAAGATCATCATAGATTATT\n-AATGCGTGCATTCCATTATCGCGGAAATATTCCCCCATGGCACACCCAGAATATGGGGCC\n-AGAAATTGCAGAGGAGCTGGATCCGAAGCGGTGGCTGCTACAAGAATGGAATATTCCAAA\n-GCATTCGCTTCTGAAAGAATTTGAACTAATTGTGCCACAGTCGAGCGTTTCTGTCCAATT\n-GCTACATAGACACAATACAATGTCTCACTCTCAGAGGTGGCCCTTGAGTTCAGTTGCTTT\n-TGGTTTAATATGGTATCGATAGCAATAGCTGTTTTTCCAGTTTGTCGGTCCCCGATTATA\n-AGTTCTCGTTGACCACGGCCTATAGGAACCAGGCTATCTACCGCTTTTAACCCTGTTTGC\n-ATAGGCTCGTGCACAGATTTACGTTCAATAATCCCAGGGGCTTTCACTTCGACACGTCTT\n-CGCTCGTGATCGCTTAGAGCCCCTCTTCCATCAATAGGAACTCCCAACCCGTCGACCACG\n-CGCCCTAGCATAGCCTTTCCCGCAGGAACATCCACAATGGATCCAGTGCGCTTGACAAGA\n-TCTCCTTCTTTAATAGCGGTATCACTACCAAAGACAACAATCCCTACATTCTCATTCTCA\n-AGATTCAACGCTATTCCTTTCACACCGCTGGCAAATTCAACCATTTCCCCAGCTTGAATC\n-TCGTTCAATCCATAAACACGTGCAATCCCATCTCCAACTGAGACCACTCGACCGATCTCA\n-TCCACTTGAAAATTCGTGTAAAAGTTGGTAATTCTACTTTCTAATAGAGTTGTTAGTTCC\n-GCAGCTCTGGTAGAGAATTCCATAATTTTTTCTTTTAAAGAAAGTCAAGGGAGAATTCCG\n-CTTATTGTTTTTGGCTCGAAATAAAGCTAGGGTCCTGATCGAGCAACTAGTAGTCCTATC\n-TATCCACCTCTCCAGAAGGGCTATTTGGGGTCTAATTTTCTTTCTATCTGACAGGACAAA\n-CAAAGAGGAAGGGGTGGTTCTTTCATTGCATTGATAGAAGTCTAACTAGAAAAAGATCTC\n-TCTATTACTTTGAGAAGAGAATCGTTGGTTTGACCGACGAACTACGTGGGAAATATGAGT\n-TGAGAGGACAAGAGGATTCGATCTCCACGAAAGGCTAAAGGAACATAAAAAAAGCTAGAA\n-TTTGTTGCAAACAGTGACCGAGATGCCAGGGAAAAACTGTTGTTTCACATTTCCGGAAAG\n-ACCACCTATTTGTTCGTTTACCAGGTTCGGTACGAAATCATAAATAAGCTCTACCCCGGG\n-CCATCGCCTTATGGCCTAGGGGCGTCTATCCCGCC\n->ds2020-328_2\n-CCCCCCCTTTCGCCCTTTTTTATGCAGACGATTCCCCGATCGGGGAATCGTCTGCTTCCC\n-TACGTATTAATCTTCTTCTTTTCTCCTTTTTCGCGTTTTCCTCTTATTCCTCTTTCGTTT\n-TCCTCTTATTCTTTTTATACGCAATTTCTTTTTTAATTTCTTACTGGTCTAAGTCCCACT\n-CCTCTTTCTCCCCGTTTTGCGTTAAGAATATTTCACATGGCATCGGTTTATAGCCTTTTT\n-CCCTTGTCATCTCCTCTACAATCTTTTCTATTTTTTCATATTTCTTCTTATAAAATTCTT\n-CCTCTTCTCTTCTCTTGCTTACTTGTATGGTTGCCGGAAATACTCTTGTTTCGCCTATTT\n-GTATTTGTAGAGGCCATGTAGCATAGTCGTTTCCTTGTTGAGCCCCCTTACTTCTTTTAA\n-CTTCCATGTAGCTTCTTGCTGTCCAATCCCTTTTATCGTAGAATATCCTTTTAATTTTCT\n-TTGTTTCTGAGTTTTCGTCTTGCTCTCTCTCTCCTTCATTTTCCTCGTCGCTTCCCTCCT\n-GGTTTTCCTCCTCATATTCTTCCTTACTCTTAAATAGCTGCAAGAATCTCCTTCTTTTTT\n-TCTCCTCTTTTTCTTCTTTCTTTTTTACGGGTATACACGCAAAATCTAACAGTGCCATTT\n-CCTTCTCTTGTTCGCCCCATGTGTAGCATTCCTCACCATCGATTGTTTGTAATTCAAACA\n-TCAAATAACTTCCTCCCGCTGTGGTTTTAATCTTTTTTATTTTTACTTCATATATTTTTC\n-CTTTTTTTGTTATAAAGATAACTTCTTTCTTTAGAATGTATTCTGCGGCCTCTGGGTTCA\n-ACTCCC'..b'AGTTCCTTTCCACCTGCCGTGGACCTAGTAGAGTTGCCCCTGCCG\n-TGGACCTAGTTCCTTTCCACCTGCCGTGGACCTAGTAGAGTTGCCCC\n->ds2020-328_950\n-TTCTTCGATGATGCGCAAATTGAAGCTTCGGTACCCTTGTTTTTTCCAATCGCCCAATTT\n-CTCTTCTTTCTTTTTTATTTCGGGTTTCTTTATTTTTTCAGGGGGG\n->ds2020-328_951\n-AACCAAGAGCGCTTTTTCTTTCCATTCGCCTGGGACAAGGCCTCCCATCACGCTTCCATT\n-GAAGAGTTAATCCTTCAAGTAGCGGTGGTGCACCCTGCCTGTACT\n->ds2020-328_952\n-TGGAGTGATGGTGGCTTGTATGGTTTCTTAGGTGGTAGGGGTGGTGAGTAAACTGGTGGC\n-TTGTAGACTGGTGTGGGTGGTGGGGGAGACTTGTAGTGGTA\n->ds2020-328_953\n-AGCTTGGAGTGTGGTGAGGAACAGGCAGGAGAGAAGCTTGGAGTGTGGTGAGGAACAGGC\n-AGGAGAGAAGCTTGGAGTGTGGTGAGGAA\n->ds2020-328_954\n-GCTTAGGTGGTGAAGGTGATGGTGGTGGTGGAGACTTGTAGTGGTATGGGTGCTTAGGTG\n-GTGAAGGTGATGGTGGTGGTGGAG\n->ds2020-328_955\n-GATTGATTTCTTGTTTATTGGCGTCAGTGGTGAGGTTTGACACCATGTGTTTGAAGGAGG\n-GATCGTGTGCGTCTATCCCGACC\n->ds2020-328_956\n-CGTCTATCCCGACCAGCGATTGTGACCGTCTATCCCGACCAGGGCACTGCCACGTCTATC\n-CCGACCGCCGTAATTCAGATC\n->ds2020-328_957\n-TCGAAGAGGGGCTTGCTAAAGAGGCTCGAAGAGGGGCTTGCTAAAGAGGCTCGAAGAGGG\n-GCTTGCTAAAGAGGCTCGAA\n->ds2020-328_958\n-TGAATTACGGCGGTCGGGATAGACGAGCTAAACGCCTGGTCGGGATAGACGAACGTATTC\n-TCTGGTCGGGATAGACG\n->ds2020-328_959\n-GGAACACCAGTGGCGAAGGAAGGAACACCAGTGGCGAAGGAAGGAACACCAGTGGCGAAG\n-GAAGGAACACCAGTGG\n->ds2020-328_960\n-GAATTACGGCGGTCGGGATAGACGCGAAGCACCGGTGGTCGGGATAGACGGCCGACCCCC\n-TTGGTCGGGATAGACG\n->ds2020-328_961\n-TGGATTACGGCGGTCGGGATAGACGTTGACCGTGCCTGGTCGGGATAGACGAGTGAACCG\n-CTGGTCGGGATAGACG\n->ds2020-328_962\n-TGAATTACGGCGGTCGGGATAGACGCCAATCGCCCCTGGTCGGGATAGACGCAATACCAC\n-CCTTCGGGATAGACG\n->ds2020-328_963\n-CGTCTATCCCGACCAGGTCCCATTTTCGTCTATCCCGACCAAGGCTAAATGACGTCTATC\n-CGCCGCCGTAATTCA\n->ds2020-328_964\n-GAATTCGGCGGTCGGGATAGACGAAAGGAGCGGGGGTCGGGATAGACGATTGCTTGCCTT\n-GGTCGGGATAGACG\n->ds2020-328_965\n-TTAGACGTCTAGTGTCCCTGGTCGGGATAAACGGGGCAAATCGTCTATCCCGACCAGGGA\n-CACTAGACGTCTAT\n->ds2020-328_966\n-TCTATCCCGACCAGGGAAATACACCGTCTATCCCGACCAGGAGCGGGGTTCGTCTATCCG\n-ACCGCCGAATTCA\n->ds2020-328_967\n-AGGTAGTTTACTTGCTTACTTGTTAGAGTAAGGAAGAGAGGAAAAGGGTGCTGTCGTCTA\n-TCCCGACCC\n->ds2020-328_968\n-GTGATGGTGGTGGTGGAGACTTGTAGTGGTAGGGGTGCTTGGGTGGTGAAGGTGATGGTG\n-GTGGTGGAG\n->ds2020-328_969\n-CGTCTATCCCGACCAACGTCTATCCCGACCAGTGGTATTAATCGTCTATCCCGACCGCCG\n-TAATTCA\n->ds2020-328_970\n-GGTCGGGATAGACGCCGCGGTATCCTGGTCGGGATAGACGGTAATATTGCCTGGTCGGGA\n-TAGACG\n->ds2020-328_971\n-GGTCGGGATAGACGAGATAATTACCTGGTCGGGATAGACGTCATGAGTCCCTGGTCGGGA\n-TAGACG\n->ds2020-328_972\n-CGTCTATCCCGACCAGGCGGTGTATACGCCAATCCCGACCAGGGGGTTAGGGCGTCTATC\n-CCGACC\n->ds2020-328_973\n-GGTCGGGATAGACGGAACATGACGCTGGTCGGGATAGACGACATAGACCCCTGGTCGGGA\n-TAGAC\n->ds2020-328_974\n-TTCGAGCCTCTTTAGCAAGCCCCTCTTCGAGCCTCTTTAGCAAGCCCCTCTTCGAAAGAT\n-TCTTT\n->ds2020-328_975\n-GGTCGGGATAGACGATCACACCCTGGTCGGGATAGACGCACGAACAGGCTGGTCGGGATA\n-GACG\n->ds2020-328_976\n-AGTGATGTCAGTGATGTCAGTGATGTCAGTGATGTCAGTGATGTCAGTGATGTCAGTGAT\n-GTCA\n->ds2020-328_977\n-CGTCTATCCCGACCAGGGGCAAATTGCGTCTATCCCGACCAAATCCTTCGTCTATCCCGA\n-CCG\n->ds2020-328_978\n-GTAGGTCCGTAGGTCCGTAGGTCCGTAGGTCCGTAGGTCCGTAGGTCCGTAGGTCCGTAG\n-GTC\n->ds2020-328_979\n-GGTCGGGATAGACGGATGGACTCGTGGTCGTGATAGACGTTTCCCAGTCTGTCGGGATAG\n-ACG\n->ds2020-328_980\n-TCACTTTTCACTTTTCACTTTTCACTTTTCACTTTTCACTTTTCACTTTTCACTTTTCAC\n-TT\n->ds2020-328_981\n-CATACGTCATACGTCATACGTCATACGTCATACGTCATACGTCATACGTCATACGTCATA\n-CG\n->ds2020-328_982\n-GGTCGGGATAGACGAACAAAGACACTGGTCGGGATAGACGCTCGATACTACTGGTCGGGA\n-TA\n->ds2020-328_983\n-TTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGG\n-T\n->ds2020-328_984\n-GTGGTGGAGACTTGTAGTGGTATGGGTGCTTGGGTGGTGAAGGTGATGGTGGTGGGGGAG\n->ds2020-328_985\n-CATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCAT\n->ds2020-328_986\n-TTCCGATCTGAATTACGGCGGTCGGGATAGACGATAGCCACCACTGGTCGGGATAGACG\n->ds2020-328_987\n-GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG\n->ds2020-328_988\n-GGTCGGGATAGACGCATGCATTGTCTGGTCGGGATAGACGGCGCGCTGCACTGTCGG\n->ds2020-328_989\n-GGTCGGGATAGACGTTAGCACCCACTGGTCGGGATAGACGAGACAGTTAGCTGGTCG\n->ds2020-328_990\n-GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\n->ds2020-328_991\n-GGTCGGGATAGACGTAGACAGCCCCCGGTCGGGATAGACGTTAATTTCTGCTGGTC\n->ds2020-328_992\n-GGTCGGGATAGACGATTATGCTCTCTGGTCGGGATAGACGTGTGACTCCCCTGGTC\n' |
| b |
| diff -r fd7104249a3c -r d1fd5579469d test-data/otu_s2_rps.tab --- a/test-data/otu_s2_rps.tab Wed Aug 21 13:13:28 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,149 +0,0 @@\n-#query_id\tquery_length\tcdd_id\thit_id\tevalue\tstartQ\tendQ\tframe\tdescription\tsuperkingdom\tno rank\tfamily\tgenus\n-"ds2020-328_1"\t"2975"\t"pfam00006"\t"gnl|CDD|376291"\t"6.25354e-106"\t"1359"\t"2033"\t"-1"\t"pfam00006, ATP-synt_ab, ATP synthase alpha/beta family, nucleotide-binding domain. This entry includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho."\t"Bacteria(0.88);Archaea(0.07);Eukaryota(0.05);"\t"(1.00);"\t"(0.07);Mycoplasmataceae(0.06);Clostridiaceae(0.04);Spirochaetaceae(0.03);Rhodobacteraceae(0.02);"\t"Mycoplasma(0.06);(0.03);Clostridium(0.03);Treponema(0.01);Persephonella(0.01);"\n-"ds2020-328_1"\t"2975"\t"pfam00306"\t"gnl|CDD|366015"\t"1.33353e-53"\t"1008"\t"1340"\t"-1"\t"pfam00306, ATP-synt_ab_C, ATP synthase alpha/beta chain, C terminal domain. "\t"Bacteria(0.94);Eukaryota(0.06);"\t"(1.00);"\t"(0.08);Mycoplasmataceae(0.08);Clostridiaceae(0.06);Ruminococcaceae(0.03);Eubacteriaceae(0.02);"\t"Mycoplasma(0.07);(0.07);Clostridium(0.05);Eubacterium(0.02);Faecalibacterium(0.01);"\n-"ds2020-328_1"\t"2975"\t"pfam02874"\t"gnl|CDD|367225"\t"8.80807e-19"\t"2202"\t"2405"\t"-1"\t"pfam02874, ATP-synt_ab_N, ATP synthase alpha/beta family, beta-barrel domain. This family includes the ATP synthase alpha and beta subunits the ATP synthase associated with flagella."\t"Bacteria(0.60);Eukaryota(0.28);Archaea(0.13);"\t"(1.00);"\t"Spirochaetaceae(0.04);Bacillaceae(0.04);Schizosaccharomycetaceae(0.03);Chlamydomonadaceae(0.03);Sulfolobaceae(0.03);"\t"Treponema(0.04);Schizosaccharomyces(0.03);Chlamydomonas(0.03);Bacillus(0.03);Thermotoga(0.02);"\n-"ds2020-328_10"\t"1434"\t"pfam17917"\t"gnl|CDD|375428"\t"1.68574e-20"\t"187"\t"453"\t"-1"\t"pfam17917, RT_RNaseH, RNase H-like domain found in reverse transcriptase. DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection. This entry represents the RNase H like domain."\t"unknown"\t"unknown"\t"unknown"\t"unknown"\n-"ds2020-328_10"\t"1434"\t"pfam00078"\t"gnl|CDD|365856"\t"1.48081e-05"\t"920"\t"1051"\t"-3"\t"pfam00078, 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."\t"Eukaryota(0.62);Viruses(0.23);Bacteria(0.15);"\t"(0.77);Ortervirales(0.21);Poxviridae(0.02);"\t"Retroviridae(0.15);Drosophilidae(0.15);Brassicaceae(0.12);Enterobacteriaceae(0.09);Caulimoviridae(0.06);"\t"Drosophila(0.15);Arabidopsis(0.12);Lentivirus(0.08);Escherichia(0.08);Bombyx(0.05);"\n-"ds2020-328_101"\t"454"\t"pfam14111"\t"gnl|CDD|372914"\t"8.33283e-09"\t"213"\t"353"\t"3"\t"pfam14111, DUF4283, Domain of unknown function (DUF4283). This domain family is found in plants, and is approximately 100 amino acids in length. Considering the very diverse range of other domains it is associated with it is possible that this domain is a binding/guiding region. There are two highly conserved tryptophan residues."\t"Eukaryota(1.00);"\t"(1.00);"\t"Salicaceae(0.35);Brassicaceae(0.27);Poaceae(0.13);Vitaceae(0.08);Solanaceae(0.06);"\t"Populus(0.35);Brassica(0.13);Arabidopsis(0.11);Brachypodium(0.10);Vitis(0.08);"\n-"ds2020-328_106"\t"446"\t"pfam01348"\t"gnl|CDD|279664"\t"1.08017e-09"\t"40"\t"303"\t"-3"\t"pfam01348, 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."\t"Eukar'..b'ns 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"Eukaryota(0.54);Bacteria(0.46);"\t"(1.00);"\t"Culicidae(0.23);Rhodobacteraceae(0.23);Poaceae(0.15);Enterobacteriaceae(0.15);Phasianidae(0.08);"\t"Paracoccus(0.23);Anopheles(0.23);Escherichia(0.15);Zea(0.15);Aspergillus(0.08);"\n-"ds2020-328_90"\t"476"\t"pfam01578"\t"gnl|CDD|307628"\t"6.70073e-11"\t"145"\t"399"\t"-3"\t"pfam01578, Cytochrom_C_asm, Cytochrome C assembly protein. This family consists of various proteins involved in cytochrome c assembly from mitochondria and bacteria; CycK from Rhizobium, CcmC from E. coli and Paracoccus denitrificans and orf240 from wheat mitochondria. The members of this family are probably integral membrane proteins with six predicted transmembrane helices. It has been proposed that members of this family comprise a membrane component of an ABC (ATP binding cassette) transporter complex. It is also proposed that this transporter is necessary for transport of some component needed for cytochrome c assembly. One member CycK contains a putative heme-binding motif, orf240 also contains a putative heme-binding motif and is a proposed ABC transporter with c-type heme as its proposed substrate. However it seems unlikely that all members of this family transport heme nor c-type apocytochromes because CcmC in the putative CcmABC transporter transports neither. CcmF forms a working module with CcmH and CcmI, CcmFHI, and itself is unlikely to bind haem directly."\t"Bacteria(0.56);Eukaryota(0.38);Archaea(0.05);"\t"(1.00);"\t"Enterobacteriaceae(0.10);Pasteurellaceae(0.08);Histionidae(0.05);Marchantiaceae(0.05);Archaeoglobaceae(0.05);"\t"Escherichia(0.08);Reclinomonas(0.05);Archaeoglobus(0.05);Marchantia(0.05);Bradyrhizobium(0.05);"\n-"ds2020-328_904"\tno_hit\n-"ds2020-328_908"\t"207"\t"pfam02123"\t"gnl|CDD|280316"\t"5.3529e-06"\t"4"\t"207"\t"-1"\t"pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus."\t"Viruses(1.00);"\t"Riboviria(1.00);"\t"Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);"\t"Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);"\n-"ds2020-328_921"\tno_hit\n-"ds2020-328_97"\t"461"\t"pfam02123"\t"gnl|CDD|280316"\t"5.16988e-30"\t"39"\t"461"\t"-1"\t"pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus."\t"Viruses(1.00);"\t"Riboviria(1.00);"\t"Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);"\t"Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);"\n-"ds2020-328_98"\t"458"\t"pfam02123"\t"gnl|CDD|280316"\t"1.94825e-26"\t"27"\t"443"\t"-1"\t"pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus."\t"Viruses(1.00);"\t"Riboviria(1.00);"\t"Totiviridae(0.44);Solemoviridae(0.19);Luteoviridae(0.15);Reoviridae(0.15);Chrysoviridae(0.07);"\t"Sobemovirus(0.19);Rotavirus(0.15);Victorivirus(0.15);Polerovirus(0.11);Totivirus(0.11);"\n-"ds2020-328_99"\t"458"\t"pfam03732"\t"gnl|CDD|367628"\t"7.72961e-07"\t"256"\t"441"\t"1"\t"pfam03732, Retrotrans_gag, Retrotransposon gag protein. Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved."\t"Eukaryota(1.00);"\t"(1.00);"\t"Brassicaceae(0.58);Poaceae(0.29);Tetraodontidae(0.04);Solanaceae(0.02);Plantaginaceae(0.02);"\t"Arabidopsis(0.58);Oryza(0.18);Sorghum(0.05);Takifugu(0.04);Zea(0.04);"\n' |
| b |
| diff -r fd7104249a3c -r d1fd5579469d test-data/otu_s2_tblastx.tab --- a/test-data/otu_s2_tblastx.tab Wed Aug 21 13:13:28 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,139 +0,0 @@\n-#algo\tquery_id\tnb_reads\tquery_length\taccession\tdescription\torganism\tpercentIdentity\tnb_hsps\tqueryOverlap\thitOverlap\tevalue\tscore\ttax_id\ttaxonomy\tsequence\n-TBLASTX\tds2020-328_275\t16\t279\t\n-TBLASTX\tds2020-328_625\t13\t226\tNC_008039\tPrune dwarf virus RNA 1, complete sequence\tPrune dwarf virus\t90.7\t3\t100\t17.0\t1.9242059400026399e-29\t420.172\t33760\tViruses;Orthornavirae;Kitrinoviricota;Alsuviricetes;Martellivirales;Bromoviridae;Ilarvirus;Prune dwarf virus\tGGTCGGGATAGACGGCCGCCCGCCATACTGAGCGTCTCATGCAGTACACTACCTACAAGACTAGTAGACCTGATGAAGTTCATGAACCGAACTTTTGTGAAAACACATTCCAGGACTGCTCCTTGCAAGGTAAGTATGCCATGGCAATCCATTCCACTTCGGATTTACCCTTAGGTGAGCTCTGTGAGAGCTTAAGGAAGAAGGGAGTGATTCGTCTATCCCGACC\n-TBLASTX\tds2020-328_196\t14\t318\tNC_033468\tWuhan insect virus 27 strain WHZM10130 hypothetical protein 1 and hypothetical protein 2 genes, complete cds\tWuhan insect virus 27\t45.3\t1\t100\t6.0\t2.90542e-27\t118.644\t1923731\tViruses;Wuhan insect virus 27\tGGTCGGGATAGACGTTTAGCAGCCTTAAACTCTTCATCTTCAGGGTATTGTGAGTGATATGCTCCCGTAGGTGCCCACTGCCACCTCTTATTCCAATAACTTTTCCACTTTATGTTATCTGGTTTACTCCCGAGGTTTTTCAATCTAGTGAACATTTCTCCACTAGCCCTGTATATCTGCTCTCTAGTGAAAGAAGCGACGTTGGGTTTGGTTCTGTGCTCTTTCTCGGCTTTCCAATCCACTTCTCCTATACCTCTGTTGACTAAAACTTCCATTTCAAAGAATGGTTTTAAGTTGAGCGGTGCGTCTATCCCGACC\n-TBLASTX\tds2020-328_638\t4\t225\tNC_030890\tArabidopsis halleri partitivirus 1 gene for capsid protein, complete cds\tArabidopsis halleri partitivirus 1\t48.2\t1\t100\t10.0\t1.45353e-08\t55.5941\t1849335\tViruses;Orthornavirae;Pisuviricota;Duplopiviricetes;Durnavirales;Partitiviridae;Arabidopsis halleri partitivirus 1\tGTCGGGATAGACGTACCAGTCAACTTTTTGCAATTTTCTTCATACATCACATGGTATGACTTGGTTTGCCCAAGTCCGCGATGTAGCCGCAGCCGAAGCCTCGTCTTTCGAAGGCTCAGGCACCCTGGCTGATTGTCCCCCATTCGGGATAACGTCAAACCAGGTAGTTGTTAACTACTTGGCCCCAGCCACACTGCCAACGTCCCCTATTCGTCTATCCCGACC\n-TBLASTX\tds2020-328_858\t2\t210\t\n-TBLASTX\tds2020-328_761\t8\t215\t\n-TBLASTX\tds2020-328_553\t2\t234\t\n-TBLASTX\tds2020-328_845\t11\t210\tNC_003689\tCherry virus A, complete genome\tCherry virus A\t75.0\t2\t100\t5.0\t5.449000000000025e-19\t225.74040000000002\t42882\tViruses;Orthornavirae;Kitrinoviricota;Alsuviricetes;Tymovirales;Betaflexiviridae;Capillovirus;Cherry virus A\tGCCGTGGACCTAGTTAGGAGAGTAATTTCGGATGGTGTTCTTTACTGCTCTCTGATTTTCTGATAAGATTATCGCCGGCGTGGCTGCTACTCCCTCTGAAGCCTCTACTGCTGGCTTCGCAGTCAGGTGCAATAGATCCCTTGGATCTATCATATTCTCCCAGATATAATTTACAAGGCCCCTTCTTATCACGTTGTAATTCTTATACAC\n-TBLASTX\tds2020-328_483\t8\t242\tNC_033495\tBotryosphaeria dothidea virus 1 strain YZN115 segment RNA4 hypothetical protein gene, complete cds\tBotryosphaeria dothidea virus 1\t50.0\t1\t100\t13.0\t1.155e-07\t52.8449\t1516075\tViruses;Orthornavirae;Pisuviricota;Duplopiviricetes;Durnavirales;Partitiviridae;Botryosphaeria dothidea virus 1\tGGTCGGGATAGACGGAATTAACCCATGTAATGGCACAATCGAAGGCTCTAGCCGTGGCCGTTGCACGGATAACGAGAGGGAAGGGGCGGCACGACGCATCTGTAGAAGATTTCATCTTCTACATAGCCTCAAACGGGCGTGCCGTCTCCGCTTCGGATATACCATCCGGAGTCCATAGCTTGGCTTGCGGTCCTCGTGACCATGTGGAACCCTCTGAGCGTTTACCAGCGTCTATCCCGACC\n-TBLASTX\tds2020-328_910\t2\t207\t\n-TBLASTX\tds2020-328_531\t10\t236\t\n-TBLASTX\tds2020-328_893\t4\t208\t\n-TBLASTX\tds2020-328_507\t26\t238\t\n-TBLASTX\tds2020-328_594\t8\t229\t\n-TBLASTX\tds2020-328_600\t4\t229\tNC_014823\tTolypocladium cylindrosporum virus 1, complete genome\tTolypocladium cylindrosporum virus 1\t55.8\t2\t100\t7.0\t8.34655e-06\t145.07119999999998\t939923\tViruses;Orthornavirae;Duplornaviricota;Chrymotiviricetes;Ghabrivirales;Totiviridae;Victorivirus;Tolypocladium cylindrosporum virus 1\tGGTGGGGATAGACGTTTTGGTTCCTTCTAAAGGCCGCGCCCTCTCCCGCCCAATTGATGGTTCCCTGCTTGTTGAAGCGGGATACCCTACTGCTCATGCCTTGGCTGAGGATTTTGTTGGACTTTCTAAGAAGTACACTAATTTCTATGCCACGTCCGAGTACGCGTCCCTGGCTGACCTGGTTGAACACCTCATCCATGGTTTAGCTCCAACCTCCGTATATCCCGAC\n-TBLASTX\tds2020-328_765\t8\t215\t\n-TBLASTX\tds2020-328_575\t4\t231\tNC_003710\tDiscula destructiva virus 2 segment 1, complete genome\tDiscula destructiva virus 2\t69.0\t4\t100\t20.0\t0.00012443\t208.6303\t160484\tViruses;Orthornavirae;Pisuviricota;Duplopiviricetes;Durnavirales;Partitiviridae;Gammapartitivirus;Discula destructiva virus 2\tGGTCGGGATAGACGTACGTCTGGCATGAGTATGGGTGTATTAATGAAA'..b'nd RNA-dependent RNA polymerase (RdRp) genes, complete cds\tXanthophyllomyces dendrorhous virus L1B\t47.3\t1\t100\t6.0\t3.23633e-27\t118.369\t1167691\tViruses;Orthornavirae;Duplornaviricota;Chrymotiviricetes;Ghabrivirales;Totiviridae;Totivirus;Xanthophyllomyces dendrorhous virus L1B\tGGTCGGGATAGACGCTATCGAGATAAATTTATTCTTCAACCTTATATCTGATTTATGTATAAATTGTTCGTCAGTTTTATATTGTGAATGGATACTCCCAGAAGCACTCCACTGCCATCTGTTGGTCCAAAATTTTTCCCAAGACATCACCATAGGAGTTCTCCCGCTAACTGCTGCACTCGCGAAGATTTTAAGTGCTTCATTCTGGATATAATCAGCACTTAGCTTGACTGTTGACGCTTTTGTTCTATGTGTGAACTCAGCTTCCCAATCGAGCGCGCCGTAACGTCTATCCCGACC\n-TBLASTX\tds2020-328_159\t47\t348\tNC_008039\tPrune dwarf virus RNA 1, complete sequence\tPrune dwarf virus\t97.0\t3\t100\t27.0\t2.5280226430549335e-55\t668.0630000000001\t33760\tViruses;Orthornavirae;Kitrinoviricota;Alsuviricetes;Martellivirales;Bromoviridae;Ilarvirus;Prune dwarf virus\tGGGTCGGGATAGACGGCAGATACCACTCGAACGTGGTTGTTCGTATTTTAAATCAATCATGACTTCTTCCGAGATCACTGCTGCCAATGTCCATGAACTTTTGGTTAAAGTTCTGGAAAAGCAATGCGCTGACGAGACCACTACCGTCGGTAAGGCTTTCTCTGAGAAAGCAAAACAGTCTTTGAATAAGACATTCGGACTAAATGACGAGTCCAAGCAACTGAAGATTTCTTTTGATTTGACGGCTGAACAGCAGGCGTTACTCAAGAGACATTTTCCGGGTCGATCGGTGATTTTTTCAAATTCATCGAGTTCCTCACACAGTTATGCAGCGCGTCTATCCCGACC\n-TBLASTX\tds2020-328_166\t24\t346\tNC_005980\tHelminthosporium victoriae 145S virus\tHelminthosporium victoriae 145S virus\t26.8\t1\t100\t8.0\t1.12841e-07\t53.7613\t164750\tViruses;Orthornavirae;Duplornaviricota;Chrymotiviricetes;Ghabrivirales;Chrysoviridae;Chrysovirus;Helminthosporium victoriae 145S virus\tGGGTCGGGATAGACGTTAACTGCCCATACCAACCATGTTTGCTAGCCTTGCAACGTCAGCTATTTCCTGCCAAGTGTCGACAGCTGCCTCATCTCGCAGCCTATTGTATATCACTGCCTCATCTGCGGTTGTGCAATAACCACGTATACGTAAGTTCTGCACTAATGCATGTATTCCACAAGTACCATCTCCTTTTGTGTTAACTTCTGTCACTATTATTTTGTCCTCCTCTACTGGCATTGGCTCATCTTTGACCAACTTTGACTCTGTGCCTTTGTCTTTCAGTTCATATGAACTACCTAGCATTTCCTCACCATTTACGCCTTTGACATAAACTGGCGATGGT\n-TBLASTX\tds2020-328_97\t31\t461\tNC_020903\tXanthophyllomyces dendrorhous virus L1A capsid protein (CP) and RNA-dependent RNA polymerase (RdRp) genes, complete cds\tXanthophyllomyces dendrorhous virus L1A\t52.1\t2\t100\t14.0\t1.888695e-05\t241.7778\t1167690\tViruses;Orthornavirae;Duplornaviricota;Chrymotiviricetes;Ghabrivirales;Totiviridae;Totivirus;Xanthophyllomyces dendrorhous virus L1A\tAACGGCCGCCACTAAATTGTCCCCTTAGATCCGCGCTTGTGATCCACTCGTAGGAACTCCGCTATAGCTCCGTACGCGCACTTGCTCATTTGTAGTCGTATATTGTGCTTCTTCGCGTTTCGGCCGGCTAGTAACACGTCCCCGAGCGAGTTACTGCCCAGCAGCACGTCGTCGCCGTTATGAAGACTGTTTTGTGACTTCACGACATCTGGCACTATTAATTGAGTGTAAATGTAGTTCAGGACGCTATTCATGAATGTGGTGAGCCTCCACCCCGACAGTAAAGTTCCTTTAGCACTATACTCCATCTTCAAGCCTTGGTTGTCATGTACTATCACTCTGTTCAGCGACAGTCGAGTCCATTCCACCGCCGCCAGCTGCTCTTGCGTTAGGAAGGGCCTGAAGGTGTCTCTGTACGCATCTATCACTGTTTTCATTGACTGTACACTATGTTGACTGTT\n-TBLASTX\tds2020-328_750\t10\t216\t\n-TBLASTX\tds2020-328_92\t33\t472\tNC_033465\tWuhan insect virus 26 strain WHZM10161 hypothetical protein 1 and hypothetical protein 2 genes, complete cds\tWuhan insect virus 26\t38.6\t1\t100\t10.0\t6.24209e-27\t118.369\t1923730\tViruses;Wuhan insect virus 26\tCGTCATTGAGGAACAAATACTACTCGAGACAATGCGAGCGATTGCACATGACAGTTTCGGACTGTTATAAAATAAAGACCTCCCACAGGTGTGTGGGGGGCATAAGTGAAGACAAGAGATCGGACGTAAAGTGGATGATACGGTCGTCGGGCTTCAGGAAGGGTGCCACGCAGATAGGCGTGTTACCGGGAGTGGTGGACTACTCCAGGATGGTGAAAGCATCACTACAACTTGAAAGACCTTTGCAGGATTTCATTTCACGAATAATGCGCGCAACATACGACGCGGTGATACCAAAAGAAAGGAACATAAACGTTTCAAGGAATGGTAACATCAAGCGGTACGAGATTTTGCGAGCGTTATTCAAGGTACACAAAGAAGAAACAGACATAGTCAATTACGGAAAAGCCAAAATGACCGGCTTCCTGATGGACGTGTTGAATGGGACCAATTATTCATAGTGGCGGCCGTT\n-TBLASTX\tds2020-328_825\t7\t211\t\n-TBLASTX\tds2020-328_896\t2\t208\tNC_033476\tBotryosphaeria dothidea virus 1 strain YZN115 RNA-dependent RNA polymerase (RdRp) gene, complete cds\tBotryosphaeria dothidea virus 1\t41.8\t1\t100\t7.0\t8.29721e-08\t52.8449\t1516075\tViruses;Orthornavirae;Pisuviricota;Duplopiviricetes;Durnavirales;Partitiviridae;Botryosphaeria dothidea virus 1\tGGTCGGGATAGACGGGGGGCCTTCTTTCACTCCACACCCCCCATGCACAGGCAACAAAGAAAAAGATGAGACTGGGAACATCGACGACCATCGGTGGAACTCTTTTCGGAGGTCCACTTACCCCGGCGGCGGCTTGGGCCCACGACCAGACAAGGTCTACCTGGGCAAAGTACCTCAAAGAAACGGACGCCAGTCGTCTATCCCGACC\n' |
| b |
| diff -r fd7104249a3c -r d1fd5579469d test-data/rps_s1_out.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rps_s1_out.tab Sun Sep 08 14:09:07 2024 +0000 |
| b |
| b'@@ -0,0 +1,46 @@\n+#query_id\tquery_length\tcdd_id\thit_id\tevalue\tstartQ\tendQ\tframe\tdescription\tsuperkingdom\n+ds2020-267_2\t2436\tpfam02123\tgnl|CDD|280316\t2.04111e-21\t184\t1476\t1\tpfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.\tViruses(1);Riboviria(1);Orthornavirae(1);Duplornaviricota(1)\n+ds2020-267_4\t2297\tpfam00680\tgnl|CDD|279070\t3.12197e-05\t995\t1873\t-2\tpfam00680, RdRP_1, RNA dependent RNA polymerase. \tViruses(1);Riboviria(1);Orthornavirae(1);Pisuviricota(1)\n+ds2020-267_5\t2029\tpfam00680\tgnl|CDD|279070\t8.86955e-06\t840\t1706\t3\tpfam00680, RdRP_1, RNA dependent RNA polymerase. \tViruses(1);Riboviria(1);Orthornavirae(1);Pisuviricota(1)\n+ds2020-267_6\t1860\tpfam02123\tgnl|CDD|280316\t1.27376e-17\t1147\t1764\t-1\tpfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.\tViruses(1);Riboviria(1);Orthornavirae(1);Duplornaviricota(1)\n+ds2020-267_8\t1703\tpfam00680\tgnl|CDD|279070\t3.19349e-12\t685\t1458\t-3\tpfam00680, RdRP_1, RNA dependent RNA polymerase. \tViruses(1);Riboviria(1);Orthornavirae(1);Pisuviricota(1)\n+ds2020-267_75\t425\tpfam00005\tgnl|CDD|306511\t3.70622e-07\t129\t275\t-1\tpfam00005, ABC_tran, ABC transporter. ABC transporters for a large family of proteins responsible for translocation of a variety of compounds across biological membranes. ABC transporters are the largest family of proteins in many completely sequenced bacteria. ABC transporters are composed of two copies of this domain and two copies of a transmembrane domain pfam00664. These four domains may belong to a single polypeptide as in CFTR, or belong in different polypeptide chains.\tBacteria(2);cellular organisms(1);Terrabacteria group(1)\n+ds2020-267_94\t386\tpfam01347\tgnl|CDD|279663\t0.000262768\t129\t275\t-1\tpfam01347, Vitellogenin_N, Lipoprotein amino terminal region. This family contains regions from: Vitellogenin, Microsomal triglyceride transfer protein and apolipoprotein B-100. These proteins are all involved in lipid transport. This family contains the LV1n chain from lipovitellin, that contains two structural domains.\tcellular organisms(1);Eukaryota(1);Opisthokonta(1);Metazoa(1)\n+ds2020-267_97\t380\tpfam04879\tgnl|CDD|282703\t2.77416e-08\t125\t274\t-2\tpfam04879, Molybdop_Fe4S4, Molybdopterin oxidoreductase Fe4S4 domain. This domain is found in formate dehydrogenase H for which the structure is known. This first domain (residues 1 to 60) of Structure 1aa6 is an Fe4S4 cluster just below the protein surface.\tBacteria(2);cellular organisms(1);Pseudomonadota(1)\n+ds2020-267_98\t379\tpfam16203\tgnl|CDD|318443\t8.05104e-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.\tcellular organisms(2);Bacteria(1);Terrabacteria group(1)\n+ds2020-267_100\t376\tpfam00401\tgnl|CDD|306831\t6.62013e-05\t81\t215\t-3\tpfam00401, ATP-synt_DE, ATP synthase, Delta/Epsilon chain, long alpha-helix domain. Part of the ATP synthase CF(1). These subunits are part of the head unit of the ATP synthase. This subunit is called epsilon in bacteria and delta in mitochondria. In bacteria the delta (D) subunit is equivalent to the mitochondrial Oligomycin sensitive subunit, OSCP (pfam00213).\tcellular organisms(2);Eukaryota(1);Viridiplantae(1)\n+ds2020-267_114\t347\tpfam00471\tgnl|CDD|306877\t8.86568e-13\t132\t302\t3\tpfam00471, Ribosomal_L33, Ribosomal protein L33. \tcellular organisms(2);Bacteria(1);Eukaryota(1)\n+ds2020-267_117\t344\tpfam00252\tgnl|CDD|306711\t1.17482e-22\t107\t295\t2\tpfam00252, Ribosomal_L16, Ribosomal protein L16p/L10e. \tcellular organisms(2);Eukaryota(1);Viridiplantae(1)\n+ds2020-267_118\t343\tpfam00421\tgnl|CDD|306845\t7.93928e-41\t92\t337\t-1\tpfam00421, PSII, Photosystem II protein. \tcellular organisms(1);Eukaryota(1);Viridiplantae(1);Streptophyta(1)\n+ds2020-267_120\t339\tpfam01333\tgnl|CDD|307480\t0.000362606\t197\t325\t-3\tpfam0133'..b"n extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual 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_428\t235\tpfam00164\tgnl|CDD|278589\t1.83229e-23\t3\t182\t3\tpfam00164, Ribosom_S12_S23, Ribosomal protein S12/S23. This protein is known as S12 in bacteria and archaea and S23 in eukaryotes.\tcellular organisms(2);Eukaryota(1);Viridiplantae(1)\n+ds2020-267_436\t234\tpfam00155\tgnl|CDD|306629\t0.000251531\t3\t182\t3\tpfam00155, Aminotran_1_2, Aminotransferase class I and II. \tBacteria(2);cellular organisms(1);Pseudomonadota(1)\n+ds2020-267_444\t233\tpfam00680\tgnl|CDD|279070\t0.000703744\t3\t182\t3\tpfam00680, RdRP_1, RNA dependent RNA polymerase. \tViruses(1);Riboviria(1);Orthornavirae(1);Pisuviricota(1)\n+ds2020-267_457\t231\tpfam00481\tgnl|CDD|306885\t0.00063843\t3\t182\t3\tpfam00481, PP2C, Protein phosphatase 2C. Protein phosphatase 2C is a Mn++ or Mg++ dependent protein serine/threonine phosphatase.\tEukaryota(2);cellular organisms(1);Viridiplantae(1)\n+ds2020-267_466\t230\tpfam00072\tgnl|CDD|306560\t5.30837e-08\t50\t208\t2\tpfam00072, Response_reg, Response regulator receiver domain. This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain.\tBacteria(2);cellular organisms(1);Pseudomonadota(1)\n+ds2020-267_471\t230\tpfam00201\tgnl|CDD|278624\t2.93544e-07\t46\t210\t1\tpfam00201, UDPGT, UDP-glucoronosyl and UDP-glucosyl transferase. \tcellular organisms(1);Eukaryota(1);Viridiplantae(1);Streptophytina(1)\n+ds2020-267_486\t228\tpfam17035\tgnl|CDD|319097\t3.87403e-09\t108\t203\t3\tpfam17035, BET, Bromodomain extra-terminal - transcription regulation. The BET, or bromodomain extra-terminal domain, is found on bromodomain proteins that play key roles in development, cancer progression and virus-host pathogenesis. It interacts with NSD3, JMJD6, CHD4, GLTSCR1, and ATAD5 all of which are shown to impart a pTEFb-independent transcriptional activation function on the bromodomain proteins.\tcellular organisms(1);Eukaryota(1);Opisthokonta(1);Metazoa(1)\n+ds2020-267_837\t207\tpfam04061\tgnl|CDD|309259\t7.30581e-19\t1\t159\t1\tpfam04061, ORMDL, ORMDL family. Evidence form suggests that ORMDLs are involved in protein folding in the ER. Orm proteins have been identified as negative regulators of sphingolipid synthesis that form a conserved complex with serine palmitoyltransferase, the first and rate-limiting enzyme in sphingolipid production. This novel and conserved protein complex, has been termed the SPOTS complex (serine palmitoyltransferase, Orm1/2, Tsc3, and Sac1).\tcellular organisms(1);Eukaryota(1);Opisthokonta(1);Metazoa(1)\n+ds2020-267_883\t206\tpfam10775\tgnl|CDD|313884\t0.00091969\t1\t159\t1\tpfam10775, ATP_sub_h, ATP synthase complex subunit h. Subunit h is a component of the yeast mitochondrial F1-F0 ATP synthase. It is essential for the correct assembly and functioning of this enzyme. Subunit h occupies a central place in the peripheral stalk between the F1 sector and the membrane.\tcellular organisms(1);Eukaryota(1);Opisthokonta(1);Fungi(1)\n+ds2020-267_1259\t1481\tpfam02123\tgnl|CDD|280316\t2.17343e-21\t184\t1476\t1\tpfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.\tEukaryota(1)\xc2\xa0;Viruses(1);\n" |
| b |
| diff -r fd7104249a3c -r d1fd5579469d test-data/rps_s2_out.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rps_s2_out.tab Sun Sep 08 14:09:07 2024 +0000 |
| b |
| b'@@ -0,0 +1,50 @@\n+#query_id\tquery_length\tcdd_id\thit_id\tevalue\tstartQ\tendQ\tframe\tdescription\tsuperkingdom\n+ds2020-328_1\t2975\tpfam02874\tgnl|CDD|308490\t6.56656e-19\t2202\t2405\t-1\tpfam02874, ATP-synt_ab_N, ATP synthase alpha/beta family, beta-barrel domain. This family includes the ATP synthase alpha and beta subunits the ATP synthase associated with flagella.\tcellular organisms(2);Eukaryota(1);Viridiplantae(1)\n+ds2020-328_15\t1120\tpfam00146\tgnl|CDD|306623\t6.73934e-18\t936\t1097\t-3\tpfam00146, NADHdh, NADH dehydrogenase. \tcellular organisms(1);Eukaryota(1);Opisthokonta(1);Metazoa(1)\n+ds2020-328_26\t872\tpfam01443\tgnl|CDD|307550\t7.69575e-33\t10\t696\t-3\tpfam01443, Viral_helicase1, Viral (Superfamily 1) RNA helicase. Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis.\tViruses(1);Riboviria(1);Orthornavirae(1);Kitrinoviricota(1)\n+ds2020-328_29\t847\tpfam13456\tgnl|CDD|316018\t1.2307e-09\t176\t397\t2\tpfam13456, RVT_3, Reverse transcriptase-like. This domain is found in plants and appears to be part of a retrotransposon.\tcellular organisms(1);Eukaryota(1);Viridiplantae(1);Streptophyta(1)\n+ds2020-328_37\t681\tpfam00416\tgnl|CDD|306841\t7.7464e-31\t92\t409\t-3\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+ds2020-328_43\t644\tpfam00078\tgnl|CDD|306564\t2.13234e-08\t190\t636\t-3\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+ds2020-328_47\t623\tpfam00346\tgnl|CDD|306783\t6.5049e-56\t191\t496\t-2\tpfam00346, Complex1_49kDa, Respiratory-chain NADH dehydrogenase, 49 Kd subunit. \tcellular organisms(2);Bacteria(1);Eukaryota(1)\n+ds2020-328_50\t620\tpfam00115\tgnl|CDD|306596\t2.19638e-51\t78\t548\t3\tpfam00115, COX1, Cytochrome C and Quinol oxidase polypeptide I. \tcellular organisms(1);Eukaryota(1);Opisthokonta(1);Metazoa(1)\n+ds2020-328_52\t598\tpfam00115\tgnl|CDD|306596\t4.78609e-34\t21\t302\t3\tpfam00115, COX1, Cytochrome C and Quinol oxidase polypeptide I. \tcellular organisms(1);Eukaryota(1);Opisthokonta(1);Metazoa(1)\n+ds2020-328_98\t458\tpfam02123\tgnl|CDD|280316\t1.82963e-26\t27\t443\t-1\tpfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.\tViruses(1);Riboviria(1);Orthornavirae(1);Duplornaviricota(1)\n+ds2020-328_99\t458\tpfam03732\tgnl|CDD|309014\t1.12045e-06\t256\t441\t1\tpfam03732, Retrotrans_gag, Retrotransposon gag protein. Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.\tcellular organisms(1);Eukaryota(1);Viridiplantae(1);Streptophyta(1)\n+ds2020-328_101\t454\tpfam14111\tgnl|CDD|316622\t3.40587e-07\t213\t353\t3\tpfam14111, DUF4283, Domain of unknown function (DUF4283). This domain family is found in plants, and is approximately 100 amino acids in length. Considering the very diverse range of other domains it is associated with it is possible that this domain is a binding/guiding region. There are two highly conserved tryptophan residues.\tcellular organisms(1);Eukaryota(1);Streptophytina(1);Viridiplantae(1)\n+ds2020-328_106\t446\tpfam01348\tgnl|CDD|279664\t1.01441e-09\t40\t303\t-3\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 sp'..b'ryotes. Thiopurine S-methyltransferase (TPMT) is a cytosolic enzyme that catalyzes S-methylation of aromatic and heterocyclic sulfhydryl compounds, including anticancer and immunosuppressive thiopurines.\tcellular organisms(2);Bacteria(1);Eukaryota(1)\n+ds2020-328_724\t219\tpfam02123\tgnl|CDD|280316\t1.42892e-13\t35\t199\t-3\tpfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.\tViruses(1);Riboviria(1);Orthornavirae(1);Duplornaviricota(1)\n+ds2020-328_746\t217\tpfam02123\tgnl|CDD|280316\t4.65988e-13\t13\t210\t-2\tpfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.\tViruses(1);Riboviria(1);Orthornavirae(1);Duplornaviricota(1)\n+ds2020-328_750\t216\tpfam02123\tgnl|CDD|280316\t7.05387e-17\t8\t214\t-3\tpfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.\tViruses(1);Riboviria(1);Orthornavirae(1);Duplornaviricota(1)\n+ds2020-328_761\t215\tpfam02123\tgnl|CDD|280316\t3.8356e-09\t37\t198\t-3\tpfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.\tViruses(1);Riboviria(1);Orthornavirae(1);Duplornaviricota(1)\n+ds2020-328_763\t215\tpfam00201\tgnl|CDD|278624\t5.96981e-07\t113\t193\t-2\tpfam00201, UDPGT, UDP-glucoronosyl and UDP-glucosyl transferase. \tcellular organisms(1);Eukaryota(1);Viridiplantae(1);Streptophytina(1)\n+ds2020-328_768\t215\tpfam02123\tgnl|CDD|280316\t4.70874e-08\t33\t209\t3\tpfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.\tViruses(1);Riboviria(1);Orthornavirae(1);Duplornaviricota(1)\n+ds2020-328_775\t214\tpfam00361\tgnl|CDD|306795\t1.62395e-10\t59\t196\t-1\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.\tcellular organisms(1);Eukaryota(1);Opisthokonta(1);Metazoa(1)\n+ds2020-328_825\t211\tpfam05892\tgnl|CDD|283531\t0.000183874\t59\t196\t-1\tpfam05892, Tricho_coat, Trichovirus coat protein. This family consists of several coat proteins which are specific to the ssRNA positive-strand, no DNA stage viruses such as the Trichovirus and Vitivirus.\tViruses(1);Kitrinoviricota(1);Orthornavirae(1);Tymovirales(1)\n+ds2020-328_826\t211\tpfam07727\tgnl|CDD|311594\t9.19953e-05\t43\t120\t1\tpfam07727, RVT_2, 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. This Pfam entry includes reverse transcriptases not recognized by the pfam00078 model.\tcellular organisms(1);Eukaryota(1);Viridiplantae(1);Streptophyta(1)\n+ds2020-328_830\t211\tpfam00978\tgnl|CDD|250270\t2.21971e-14\t16\t201\t1\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.\tViruses(1);Riboviria(1);Orthornavirae(1);Kitrinoviricota(1)\n' |
| b |
| diff -r fd7104249a3c -r d1fd5579469d test-data/rps_test.tab --- a/test-data/rps_test.tab Wed Aug 21 13:13:28 2024 +0000 +++ b/test-data/rps_test.tab Sun Sep 08 14:09:07 2024 +0000 |
| b |
| b'@@ -1,26 +1,5 @@\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.\tcellular organisms(1);Eukaryota(1);Viridiplantae(1);Streptophyta(1)\n-ds2020-267_374\t242\tpfam00124\tgnl|CDD|365890\t5.09126e-07\t21\t125\t3\tpfam00124, Photo_RC, Photosynthetic reaction centre protein. \tcellular organisms(1);Eukaryota(1);Viridiplantae(1);Streptophyta(1)\n-ds2020-267_471\t230\tpfam00201\tgnl|CDD|278624\t3.12575e-07\t46\t210\t1\tpfam00201, UDPGT, UDP-glucoronosyl and UDP-glucosyl transferase. \tcellular organisms(1);Eukaryota(1);Viridiplantae(1);Streptophytina(1)\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(2);cellular organisms(1);Pseudomonadota(1)\n-ds2020-267_692\t214\tpfam00680\tgnl|CDD|366242\t4.79875e-05\t70\t180\t1\tpfam00680, RdRP_1, RNA dependent RNA polymerase. \tViruses(1);Riboviria(1);Orthornavirae(1);Pisuviricota(1)\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(2);cellular organisms(1);Pseudomonadota(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.\tcellular organisms(2);Bacteria(1);Terrabacteria group(1)\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.\tcellular organisms(1);Bacteria(1);Pseudomonadota(1);Gammaproteobacteria(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(2);cellular organisms(1);Pseudomonadota(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. \tcellular organisms(1);Eukaryota(1);Opisthokonta(1);Metazoa(1)\n-ds2020-267_139\t320\tpfam05860\tgnl|CDD|368641\t1.34887e-13\t167\t298\t'..b'(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+No definition line\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+ds2020-267_4\t2297\tpfam00680\tgnl|CDD|279070\t3.12197e-05\t995\t1873\t-2\tpfam00680, RdRP_1, RNA dependent RNA polymerase. \tViruses(1);Riboviria(1);Orthornavirae(1);Pisuviricota(1)\n+ds2020-267_5\t2029\tpfam00680\tgnl|CDD|279070\t8.86955e-06\t840\t1706\t3\tpfam00680, RdRP_1, RNA dependent RNA polymerase. \tViruses(1);Riboviria(1);Orthornavirae(1);Pisuviricota(1)\n+ds2020-267_6\t1860\tpfam02123\tgnl|CDD|280316\t1.27376e-17\t1147\t1764\t-1\tpfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.\tViruses(1);Riboviria(1);Orthornavirae(1);Duplornaviricota(1)\n' |
| b |
| diff -r fd7104249a3c -r d1fd5579469d test-data/rps_test.xml --- a/test-data/rps_test.xml Wed Aug 21 13:13:28 2024 +0000 +++ b/test-data/rps_test.xml Sun Sep 08 14:09:07 2024 +0000 |
| b |
| b'@@ -194,6 +194,175 @@\n </Iteration_stat>\n </Iteration>\n <Iteration>\n+ <Iteration_iter-num>4</Iteration_iter-num>\n+ <Iteration_query-ID>Query_4</Iteration_query-ID>\n+ <Iteration_query-def>ds2020-267_4</Iteration_query-def>\n+ <Iteration_query-len>2297</Iteration_query-len>\n+<Iteration_hits>\n+<Hit>\n+ <Hit_num>1</Hit_num>\n+ <Hit_id>gnl|CDD|280316</Hit_id>\n+ <Hit_def>pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.</Hit_def>\n+ <Hit_accession>280316</Hit_accession>\n+ <Hit_len>465</Hit_len>\n+ <Hit_hsps>\n+ <Hsp>\n+ <Hsp_num>1</Hsp_num>\n+ <Hsp_bit-score>187.283</Hsp_bit-score>\n+ <Hsp_score>476</Hsp_score>\n+ <Hsp_evalue>1.84305e-52</Hsp_evalue>\n+ <Hsp_query-from>824</Hsp_query-from>\n+ <Hsp_query-to>1858</Hsp_query-to>\n+ <Hsp_hit-from>121</Hsp_hit-from>\n+ <Hsp_hit-to>464</Hsp_hit-to>\n+ <Hsp_query-frame>-2</Hsp_query-frame>\n+ <Hsp_hit-frame>0</Hsp_hit-frame>\n+ <Hsp_identity>94</Hsp_identity>\n+ <Hsp_positive>136</Hsp_positive>\n+ <Hsp_gaps>19</Hsp_gaps>\n+ <Hsp_align-len>354</Hsp_align-len>\n+ <Hsp_qseq>VRKSRLVNWEEEHKNRVSPNLAEMPEGLVYERASQLFSRSISAGKRPR-KFD-WREYWQSRWQWSAAGSIHSQYSEDDKYIFKDIYLKNKFISILAMPDMNMDSWRER----DPELHAWSSTKYEWSKLRAIYGTDVTSYVLAHFAFYNCEDVLPSPFPVGKAANDEN--VRSRVRSVLEGRTQYCVDFEDFNSQHSVQSMKAVIDAYRDTFGHFLTQEQLAAVEWTRLSLDRVIVHDNQGLKMEYNAKGTLLSGWRLTTFMNSVLNYIYTQLIVPDVVQSQNSLHNGDDVLLGSNSLEDVLLAGKNAKKHNIRLQMSK-CAYGAIAEFLRVDHKRGSKGQYLSRAMATLVHSR</Hsp_qseq>\n+ <Hsp_hseq>GRGVTNVDWEEEAKNRVDLAVVCRLVLLPMEELRAHIDAVLDELVVRRGLCDPIRLFVKNEPLWCVNGHPDHKLRE---GRLRLLSSVSLVDQLVRR--MLFEPQNNNEIAWWGSVPSKPSMKLEHGKSRAIYACDTRSYLAFEYLLAPVEKAWANKSVILNPGEGDISGFDWSVQDWKRGGVSLMLDYDDFNSQHSTESMRAVFERLR----RRLPDEPAEAADWLVCSMDSMYQLSD-GTLLAQRVPGTLKSGHRATTFINSVLNCAYAELAGAPWADVPTSIHMGDDVLEGLRTPADATSLLDKYARLGFKVNPSKQSVGHTIAEFLRVAFCSHEVRGYLARAIASLVSGN</Hsp_hseq>\n+ <Hsp_midline> R V+WEEE KNRV + L E + R D R + ++ W G + E + + + ++ M + + + S K E K RAIY D SY+ + E + + + V+ G +D++DFNSQHS +SM+AV + R L E A +W S+D + + G + GTL SG R TTF+NSVLN Y +L S+H GDDVL G + D + ++ SK IAEFLRV YL+RA+A+LV </Hsp_midline>\n+ </Hsp>\n+ </Hit_hsps>\n+</Hit>\n+<Hit>\n+ <Hit_num>2</Hit_num>\n+ <Hit_id>gnl|CDD|279070</Hit_id>\n+ <Hit_def>pfam00680, RdRP_1, RNA dependent RNA polymerase. </Hit_def>\n+ <Hit_accession>279070</Hit_accession>\n+ <Hit_len>475</Hit_len>\n+ <Hit_hsps>\n+ <Hsp>\n+ <Hsp_num>1</Hsp_num>\n+ <Hsp_bit-score>45.0546</Hsp_bit-score>\n+ <Hsp_score>107</Hsp_score>\n+ <Hsp_evalue>3.12197e-05</Hsp_evalue>\n+ <Hsp_query-from>995</Hsp_query-from>\n+ <Hsp_query-to>1873</Hsp_query-to>\n+ <Hsp_hit-from>4</Hsp_hit-from>\n+ <Hsp_hit-to>344</Hsp_hit-to>\n+ <Hsp_query-frame>-2</Hsp_query-frame>\n+ <Hsp_hit-frame>0</Hsp_hit-frame>\n+ <Hsp_identity>62</Hsp_identity>\n+ <Hsp_positive>102</Hsp_positive>\n+ <Hsp_gaps>96</Hsp_gaps>\n+ <Hsp_align-len>365</Hsp_align-len>\n+ <Hsp_qseq>SKEQHVRKSRLVNWEEEHKNRVSP-NLA----EMPEGLVYERASQL-----FSRSISAGKRPRKFDWREYWQSRWQWSAAGSIHSQYSEDDKYIFKDIYLKNKFISILAMPDMNMDS----------WRERDPE-------------LHAWSST----------------------KYEWSKLRAIYGTDVTSYVLAHFAFYNCEDVLPSPFPVGKAANDENVRSRVRSVLEGRTQ-----YCVDFEDFNSQHSVQSMKAVIDAYRDTFGHFLTQEQLAAVEW--TRLSL-DRVIVHDNQGLKMEYNAKGTLLSGWRLTTFMNSVLNYIYTQ--LI-------VPDVVQSQNSLHNGDDVLLGSN</Hsp_qseq>\n+ <Hsp_hseq>MTKTALVPS-VIEGYIDTVEDYEPAALGFKDPRLDAYLGLSRVAISKDSLKPYGQEEVLGVPREF---------LHDAAKGLT----SMLEGADLGDLSVSEAINGADGFDALNMDTSPGFPYILNGGKKRDLVKDEEADKVLLKAAYEALRLAEGGEGLPGVYTTCLKDELRPLEKVLKGKTRLFWGCPVEVNLVARAAFGPFNNKIYANGIKLGIAVGINPFSRDWERLAALIRKGSDVLDVDYSAFDSTLSPFVFDLVIDIRSEFCEDKLKLTRLALLELLSNPIHIFNGTIIKVEGGLP----------SGQPATSVINSINNNIYVLYALIKHTGESELDDLFETIRFFSYGDDNLVAVN</Hsp_hseq>\n+ <Hsp_midline> + + S ++ + P L '..b'TLDWKRFDKKAYFCIIDKIFDGVETFLDFDNGYLPTKD-YPDTKSTWTQERSTRLKRLFDWTKENFYHAPIVLPNGHMYVRKFAGIPSGLFITQLIDSWYN-YTMLATILSAMGFDPRSCIIK-----VQGDDSIIRLSALIPPDAHDSFLTKVQELADYYFQSVVSVNKSEVRNELNGCEVLSYRHRHGLP----YRDEL---AMLAQLYHTKARNPSPEITMAQ---SIGFAYAS</Hsp_qseq>\n+ <Hsp_hseq>KVLKGKTRLFWGCPVEVNLVARAAFGPFNNKIYANGIKLGIAVGINPFSRDWERL-AALIRKG--SDVLDVDYSAFDSTLSPFVFDLVIDIRSEF--CEDKLKLTRLALLELLSN-----------------------PIHIFNG-TIIKVEGGLPSGQPATSVINSINNNIYVLYALIKHTGESELDDLFETIRFFSYGDDNLVAVNPDVDSVGQKLK----EHLKDLG-LTPTRADKTSEFSPIKPIEEVVFLKRTFSRTEGGVRPRLDRKSIERQLYWIRAGNTSEEARGQQLENALGEAYHH</Hsp_hseq>\n+ <Hsp_midline>K K R WGC + + + + F+ W RL AL + +D+ FD + D + D F ++ T+ + S PI + NG ++ G+PSG T +I+S N +L ++ G + + GDD+++ ++ + + L D + +K+ + + E + + R R L ++ QLY +A N S E Q ++G AY </Hsp_midline>\n+ </Hsp>\n+ </Hit_hsps>\n+</Hit>\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>92</Statistics_hsp-len>\n+ <Statistics_eff-space>771811480</Statistics_eff-space>\n+ <Statistics_kappa>0.0625983</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>6</Iteration_iter-num>\n+ <Iteration_query-ID>Query_6</Iteration_query-ID>\n+ <Iteration_query-def>ds2020-267_6</Iteration_query-def>\n+ <Iteration_query-len>1860</Iteration_query-len>\n+<Iteration_hits>\n+<Hit>\n+ <Hit_num>1</Hit_num>\n+ <Hit_id>gnl|CDD|280316</Hit_id>\n+ <Hit_def>pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.</Hit_def>\n+ <Hit_accession>280316</Hit_accession>\n+ <Hit_len>465</Hit_len>\n+ <Hit_hsps>\n+ <Hsp>\n+ <Hsp_num>1</Hsp_num>\n+ <Hsp_bit-score>83.6639</Hsp_bit-score>\n+ <Hsp_score>207</Hsp_score>\n+ <Hsp_evalue>1.27376e-17</Hsp_evalue>\n+ <Hsp_query-from>1147</Hsp_query-from>\n+ <Hsp_query-to>1764</Hsp_query-to>\n+ <Hsp_hit-from>288</Hsp_hit-from>\n+ <Hsp_hit-to>464</Hsp_hit-to>\n+ <Hsp_query-frame>-1</Hsp_query-frame>\n+ <Hsp_hit-frame>0</Hsp_hit-frame>\n+ <Hsp_identity>49</Hsp_identity>\n+ <Hsp_positive>81</Hsp_positive>\n+ <Hsp_gaps>31</Hsp_gaps>\n+ <Hsp_align-len>207</Hsp_align-len>\n+ <Hsp_qseq>RRVMEMSTQGVVACIDARNFNILHTQEVMASILESASVMLGSRLSEEQHKCLKWLSKAELNQKVLVKKGEVTEELLSAGRQEGWINQMMKGDGTMVEAATVTVGMFSGTRFTMLYNTILNRAYYKVAEELAGIKTLSLHSGDDVYSAFASYIDVYKMKKAMAFIGYTLQLAK-CFLQGVREFLRISHKNANTSQYLARSAATAIHGR</Hsp_qseq>\n+ <Hsp_hseq>WSVQDWKRGGVSLMLDYDDFNSQHSTESMRAVFER----LRRRLPDEPAEAADWLVCS--------------------------MDSMYQLSDGTLLAQRVPGTLKSGHRATTFINSVLNCAYAELAGAPWADVPTSIHMGDDVLEGLRTPADATSLLDKYARLGFKVNPSKQSVGHTIAEFLRVAFCSHEVRGYLARAIASLVSGN</Hsp_hseq>\n+ <Hsp_midline> V + GV +D +FN H+ E M ++ E L RL +E + WL + ++ M + + A V + SG R T N++LN AY ++A S+H GDDV + D + A +G+ + +K + EFLR++ + YLAR+ A+ + G </Hsp_midline>\n+ </Hsp>\n+ </Hit_hsps>\n+</Hit>\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>92</Statistics_hsp-len>\n+ <Statistics_eff-space>697802160</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>7</Iteration_iter-num>\n <Iteration_query-ID>ds2020-267_374</Iteration_query-ID>\n <Iteration_query-def>No definition line</Iteration_query-def>\n' |
| b |
| diff -r fd7104249a3c -r d1fd5579469d virAnnot_rps2tsv.xml --- a/virAnnot_rps2tsv.xml Wed Aug 21 13:13:28 2024 +0000 +++ b/virAnnot_rps2tsv.xml Sun Sep 08 14:09:07 2024 +0000 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="virAnnot_rps2tsv" name="virAnnot Rps2tsv" version="1.0.1+galaxy0" profile="21.05"> +<tool id="virAnnot_rps2tsv" name="virAnnot Rps2tsv" version="1.1.0+galaxy0" profile="21.05"> <description>Convert xml rpstblast results to tab file with taxonomic informations</description> <macros> <import>macros.xml</import> @@ -31,7 +31,7 @@ <output name="output" file="rps_test.tab"> <assert_contents> <has_n_columns n="10" /> - <has_n_lines n="26" /> + <has_n_lines n="5" /> <has_text text="pfam00680, RdRP_1" /> </assert_contents> </output> |