def run_dataset(self, case, algorithm): bp = "test/{}/".format(case) test_file = bp + "test.spats.tmp" try: shutil.copyfile(bp + "ds.spats", test_file) db = PairDB(test_file) s = Spats() db.load_run(s.run) if not s.run.cotrans and algorithm == "native": return s.run.writeback_results = True s.run.result_set_name = "test" s.run.algorithm = algorithm s.run.quiet = True s.loadTargets(db) if not s._processor.exists(): # just ignore the native test if it's not available self.assertEqual("native", algorithm) return s.process_pair_db(db, batch_size = 1024) # small batch_size just to exercise multiprocessing code msg = None count = 0 for res in db.differing_results("test", "test_validation"): msg = str([str(x) for x in res]) count += 1 self.assertEqual(0, count, "{} differing results: {} / {} \n{}".format(count, case, algorithm, msg)) finally: if os.path.exists(test_file): os.remove(test_file)
def tmut(): from spats_shape_seq import Spats from spats_shape_seq.db import PairDB from spats_shape_seq.diagram import diagram bp = "/Users/jbrink/mos/tasks/1RwIBa/tmp/mutsl/" pair_db = PairDB(bp + "ds_cmp.spats") if True: print "Parsing to db..." pair_db.wipe() pair_db.add_targets_table(bp + "mut_single.fa") fq_name = "mut2" pair_db.parse(bp + fq_name + "_R1.fastq", bp + fq_name + "_R2.fastq") spatss = [] for alg in [ "find_partial", "lookup" ]: spats = Spats(cotrans = False) spats.run.cotrans_linker = 'CTGACTCGGGCACCAAGGAC' spats.run.count_mutations = True spats.run.algorithm = alg spats.run.allowed_target_errors = 1 spats.run.adapter_b = "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG" spats.run._process_all_pairs = True spats.run.writeback_results = True spats.run.num_workers = 1 spats.run.result_set_name = "mut_" + alg spats.process_pair_db(pair_db) pair_db.store_run(spats.run) pair_db.store_counters(spats.run.result_set_name, spats.counters) spatss.append(spats) rdiff_func(bp + "ds_cmp.spats", "mut_find_partial", "mut_lookup", diag_spats = spatss[0])
def dbrun(): db_path = sys.argv[2] run_name = sys.argv[3] from spats_shape_seq import Spats from spats_shape_seq.db import PairDB db = PairDB(db_path) s = Spats() s.run.writeback_results = True s.run.result_set_name = run_name #s.run.resume_processing = True s.process_pair_db(db)
def d5s_writeback_run(): bp = "/Users/jbrink/mos/tasks/1RwIBa/tmp/" from spats_shape_seq.db import PairDB pair_db = PairDB(bp + "dev_out/pairs.db") pair_db.add_targets_table(bp + "5s/5S.fa") from spats_shape_seq import Spats s = Spats() s.addTargets(bp + "5s/5S.fa") s.writeback_results = True s.result_set_name = "pure_python" s.process_pair_db(pair_db)
def make_test_dataset(): bp = "/Users/jbrink/mos/tasks/1RwIBa/tmp/datasets/cotrans/data/" from spats_shape_seq import Spats from spats_shape_seq.db import PairDB pair_db = PairDB(bp + "ds.spats") pair_db.add_targets_table(bp + "../cotrans_single.fa") pair_db.parse(bp + "med_R1.fq", bp + "med_R2.fq") s = Spats(cotrans = True) s.run.num_workers = 1 s.run.writeback_results = True s.run._process_all_pairs = True s.run.algorithm = "find_partial" s.run.result_set_name = "test_validation" s.process_pair_db(pair_db) pair_db.store_run(s.run) pair_db.store_counters('spats', s.counters)
def make_test_dataset(): bp = "/Users/jbrink/mos/tasks/1RwIBa/tmp/datasets/cotrans/data/" from spats_shape_seq import Spats from spats_shape_seq.db import PairDB pair_db = PairDB(bp + "ds.spats") pair_db.add_targets_table(bp + "../cotrans_single.fa") pair_db.parse(bp + "med_R1.fq", bp + "med_R2.fq") s = Spats(cotrans=True) s.run.num_workers = 1 s.run.writeback_results = True s.run._process_all_pairs = True s.run.algorithm = "find_partial" s.run.result_set_name = "test_validation" s.process_pair_db(pair_db) pair_db.store_run(s.run) pair_db.store_counters('spats', s.counters)
def tags(): bp = "/Users/jbrink/mos/tasks/1RwIBa/tmp/datasets/cotrans/" from spats_shape_seq.db import PairDB pair_db = PairDB(bp + "db/pairs.db") if True: print "Parsing to db..." pair_db.wipe() pair_db.add_targets_table(bp + "cotrans_single.fa") pair_db.parse(bp + "data/EJS_6_F_10mM_NaF_Rep1_GCCAAT_R1.fastq", bp + "data/EJS_6_F_10mM_NaF_Rep1_GCCAAT_R2.fastq", sample_size=100000) from spats_shape_seq import Spats from spats_shape_seq.tag import TagProcessor from spats_shape_seq.util import reverse_complement s = Spats() s.run._processor_class = TagProcessor s.run.writeback_results = True s.run.result_set_name = "tags" s.run.num_workers = 1 s.run.cotrans = True s.run.cotrans_linker = 'CTGACTCGGGCACCAAGGAC' s.loadTargets(pair_db) s.run.allow_indeterminate = True s.run.allowed_target_errors = 2 s.run.allowed_adapter_errors = 2 p = s._processor for target in pair_db.targets(): p.addTagTarget(target[0], target[1]) p.addTagTarget(target[0] + "_rc", reverse_complement(target[1])) p.addTagTarget("adapter_t_rc", reverse_complement(s.run.adapter_t)) p.addTagTarget("adapter_b", s.run.adapter_b) if s.run.cotrans: p.addTagTarget("linker_cotrans", s.run.cotrans_linker) p.addTagTarget("linker_cotrans_rc", reverse_complement(s.run.cotrans_linker)) s.process_pair_db(pair_db) rsid = pair_db.result_set_id_for_name(s.run.result_set_name) pair_db.count_tags(rsid) print pair_db.tag_counts(rsid)
def tags(): bp = "/Users/jbrink/mos/tasks/1RwIBa/tmp/datasets/cotrans/" from spats_shape_seq.db import PairDB pair_db = PairDB(bp + "db/pairs.db") if True: print "Parsing to db..." pair_db.wipe() pair_db.add_targets_table(bp + "cotrans_single.fa") pair_db.parse(bp + "data/EJS_6_F_10mM_NaF_Rep1_GCCAAT_R1.fastq", bp + "data/EJS_6_F_10mM_NaF_Rep1_GCCAAT_R2.fastq", sample_size = 100000) from spats_shape_seq import Spats from spats_shape_seq.tag import TagProcessor from spats_shape_seq.util import reverse_complement s = Spats() s.run._processor_class = TagProcessor s.run.writeback_results = True s.run.result_set_name = "tags" s.run.num_workers = 1 s.run.cotrans = True s.run.cotrans_linker = 'CTGACTCGGGCACCAAGGAC' s.loadTargets(pair_db) s.run.allow_indeterminate = True s.run.allowed_target_errors = 2 s.run.allowed_adapter_errors = 2 p = s._processor for target in pair_db.targets(): p.addTagTarget(target[0], target[1]) p.addTagTarget(target[0] + "_rc", reverse_complement(target[1])) p.addTagTarget("adapter_t_rc", reverse_complement(s.run.adapter_t)) p.addTagTarget("adapter_b", s.run.adapter_b) if s.run.cotrans: p.addTagTarget("linker_cotrans", s.run.cotrans_linker) p.addTagTarget("linker_cotrans_rc", reverse_complement(s.run.cotrans_linker)) s.process_pair_db(pair_db) rsid = pair_db.result_set_id_for_name(s.run.result_set_name) pair_db.count_tags(rsid) print pair_db.tag_counts(rsid)
def tmut(): from spats_shape_seq import Spats from spats_shape_seq.db import PairDB from spats_shape_seq.diagram import diagram bp = "/Users/jbrink/mos/tasks/1RwIBa/tmp/mutsl/" pair_db = PairDB(bp + "ds_cmp.spats") if True: print "Parsing to db..." pair_db.wipe() pair_db.add_targets_table(bp + "mut_single.fa") fq_name = "mut2" pair_db.parse(bp + fq_name + "_R1.fastq", bp + fq_name + "_R2.fastq") spatss = [] for alg in ["find_partial", "lookup"]: spats = Spats(cotrans=False) spats.run.cotrans_linker = 'CTGACTCGGGCACCAAGGAC' spats.run.count_mutations = True spats.run.algorithm = alg spats.run.allowed_target_errors = 1 spats.run.adapter_b = "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG" spats.run._process_all_pairs = True spats.run.writeback_results = True spats.run.num_workers = 1 spats.run.result_set_name = "mut_" + alg spats.process_pair_db(pair_db) pair_db.store_run(spats.run) pair_db.store_counters(spats.run.result_set_name, spats.counters) spatss.append(spats) rdiff_func(bp + "ds_cmp.spats", "mut_find_partial", "mut_lookup", diag_spats=spatss[0])