def test_remove_id_seq(): conf = ConfigObj(configfi, interactive=False) data_obj = pickle.load(open("tests/data/precooked/tiny_dataobj.p", 'rb')) data_obj.workdir = absworkdir ids = IdDicts(conf, workdir=data_obj.workdir) ids.acc_ncbi_dict = pickle.load( open("tests/data/precooked/tiny_acc_map.p", "rb")) filteredScrape = PhyscraperScrape(data_obj, ids) filteredScrape._blasted = 1 ############################# id_seq = [ "TCGAAACCTGCATAGCAGAACGACCT-GTGAACATGTAAAAACAATTGGG-TGTTCTAAGTATCGGGCTCTTGTTCGATTTCTA-GGATGCCATGTTGACGTGCGTCTTTGGCAAGCCCCTTGGGTGT-CTAAGGACGTCACGTCGACG-CAACAACAAACCCCCGGCACGGCATGTGCCAAGGAAATATAAACTTAAGAAGGGC--TT-GTTCCATGCATT--GCCGTT--CGCGGTGATTGCATTGAAACTTGCTTCTTTATAA-TTCATAAACGACTCTCGG-CAACGGATATCTCGGCTCACGCATCGATGAAGAACGTAGCAAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTTTTTGAACGCAAGTTGCGCCC-GAAGCCTTTTGGTTGAGGGCACGTCTGCCTGGGCGTCACATATCGCGTCGCCC-CCATCAC---ACCTCTT-GACGGGGATGTTTGAATGGGGA-CGGAGATTGGTCTCCCGTTCCT---AAGGTGCGGTTGCCTGAATTTTGAGTCCTCTTCGACGGACGCACGATTAGTGGTGGTTGACAAGACCTTCT--------------TATCGAGTTGTGTG--TTCCAAGAAGTAA-GGAATATCTCTTTAACGACCC-TAAAGTGTTGTCTCATG-ACGATGCTTCGACTGC", "TCGAAACCTGCATAGCAGAACGACCTGTGAACATGTAAAAACAATTGGGTGTTCTAAGTATCGGGCTCTTGTTCGATTTCTAGGATGCCATGTTGACGTGCGTCTTTGGCAAGCCCCTTGGGTGTCTAAGGACGTCACGTCGACGCAACAACAAACCCCCGGCACGGCATGTGCCAAGGAAATATAAACTTAAGAAGGGCTTGTTCCATGCATTGCCGTTCGCGGTGATTGCATTGAAACTTGCTTCTTTATAATTCATAAACGACTCTCGGCAACGGATATCTCGGCTCACGCATCGATGAAGAACGTAGCAAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTTTTTGAACGCAAGTTGCGCCCGAAGCCTTTTGGTTGAGGGCACGTCTGCCTGGGCGTCACATATCGCGTCGCCCCCATCACACCTCTTGACGGGGATGTTTGAATGGGGACGGAGATTGGTCTCCCGTTCCTAAGGTGCGGTTGCCTGAATTTTGAGTCCTCTTCGACGGACGCACGATTAGTGGTGGTTGACAAGACCTTCTTATCGAGTTGTGTGTTCCAAGAAGTAAGGAATATCTCTTTAACGACCCTAAAGTGTTGTCTCATGACGATGCTTCGACTGC", "TCGAAACCTGCATAGCAGAACGACCTGTGAACATGTAAAAACAATTGGGTGTTCTAAGTATCGGGCTCTTGTTCGATTTCTAGGATGCCATGTTGACGTGCGTCTTTGGCAAGCCCCTTGGGTGTCTAAGGACGTCACGTCGACGCAACAACAAACCCCCGGCACGGCATGTGCCAAGGAAATATAAACTTAAGAAGGGCTTGTTCCATGCATTGCCGTTCGCGGTGATTGCATTGAAACTTGCTTCTTTATAATTCATAAACGACTCTCGGCAACGGATATCTCGGCTCACGCATCGATGAAGAACGTAGCAAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTTTTTGAACGCAAGTTGCGCCCGAAGCCTTTTGGTTGAGGGCACGTCTGCCTGGGCGTCACATATCGCGTCGCCCCCATCACACCTCTTGACGGGGATGTTTGAATGGGGACGGAGATTGGTCTCCCGTTCCTAAGGTGCGGTTGCCTGAATTTTGAGTCCTCTTCGACGGACGCACGATTAGTGGTGGTTGACAAGACCTTCTTATCGAGTTGTGTGTTCCAAGAAGTAAGGAATATCTCTTTAACGACCCTAAAGTGTTGTCTCATGACGATGCTTCGACTGCGCGCGCGC", "TCGAAACCTGCATAGCAGAACGACCTGTGAACATGTAAAAACAATTGGGTGTTCTAAGTATCGGGCTCTTGTTCGATTTCTAGGATGCCATGTTGACGTGCGTCTTTGGCAAGCCCCTTGGGTGTCTAAGGACGTCACGTCGACGCAACAACAAACCCCCGGCACGGCATGTGCCAAGGAAATATAAACTTAAGAAGGGCTTGTTCCATGCATTGCCGTTCGCGGTGATTGCATTGAAACTTGCTTCTTTATAATTCATAAACGACTCTCGGCAACGGATATCTCGGCTCACGCATCGATGAAGAACGTAGCAAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTTTTTGAACGCAAGTTGCGCCCGAAGCCTTTTGGTTGAGGGCACGTCTGCCTGGGCGTCACATATCGCGTCGCCCCCATCACACCTCTTGACGGGGATGTTTGAATGGGGACGGAGATTGGTCTCCCGTTCCTAAGGTGCGGTTGCCTGAATTTTGAGTCCTCTTCGACGGACGCACGATTAGTGGTGGTTGACAAGACCTTCTTATCGAGTTGTGTGTTCCAAGAAGTAAGGAATATCTCTTTAACGACCCTAAAGTGTTGTCTCATGACGATGCTTCGACTGCGCGCGCGC" ] # print("start test") tmp_dict = dict( (taxon.label, filteredScrape.data.aln[taxon].symbols_as_string()) for taxon in filteredScrape.data.aln) old_seqs = tmp_dict.keys() avg_seqlen = sum(filteredScrape.data.orig_seqlen) / len( filteredScrape.data.orig_seqlen) assert filteredScrape.config.seq_len_perc <= 1 seq_len_cutoff = avg_seqlen * filteredScrape.config.seq_len_perc count = 1 for item in id_seq: if len(item.replace("-", "").replace("N", "")) > seq_len_cutoff: ott = "OTT_{}".format(count) count += 1 otu_id = ott filteredScrape.data.otu_dict[otu_id] = {} filteredScrape.data.otu_dict[otu_id]['^ncbi:gi'] = 1061375300 filteredScrape.data.otu_dict[otu_id][ '^ncbi:accession'] = "KX494441" filteredScrape.data.otu_dict[otu_id][ '^ncbi:title'] = "some random title" filteredScrape.data.otu_dict[otu_id]['^ncbi:taxon'] = 0101010101 filteredScrape.data.otu_dict[otu_id]['^ot:ottId'] = ott filteredScrape.data.otu_dict[otu_id][ '^physcraper:status'] = "query" filteredScrape.data.otu_dict[otu_id][ '^ot:ottTaxonName'] = "Senecio vulgaris" filteredScrape.data.otu_dict[otu_id][ '^physcraper:last_blasted'] = None filteredScrape.del_superseq = set() filteredScrape.seq_dict_build(item, otu_id, tmp_dict) for tax in old_seqs: try: del tmp_dict[tax] except KeyError: pass filteredScrape.new_seqs_otu_id = tmp_dict expected_add = 1 assert expected_add == len(filteredScrape.new_seqs_otu_id) sys.stdout.write( "todo: add check that newly added seq are checked. they are, but there is no test" )