def d5s_run(): bp = "/Users/jbrink/mos/tasks/1RwIBa/tmp/" #from spats_shape_seq.db import PairDB #pair_db = PairDB(bp + "dev_out/pairs.db") #if False: # pair_db.add_targets_table(bp + "5s/5S.fa") # pair_db.parse(bp + "5s/data/17571-AD1AW-KEW11-5S-2p1-18x-23FEB15-GGCTAC_S10_L001_R1_001.fastq", # bp + "5s/data/17571-AD1AW-KEW11-5S-2p1-18x-23FEB15-GGCTAC_S10_L001_R2_001.fastq") from spats_shape_seq import Spats from spats_shape_seq.partial import PartialFindProcessor s = Spats() #s.run._processor_class = PartialFindProcessor s.run.skip_database = True #s.run.writeback_results = True #s.run.resume_processing = True #s.run.result_set_name = "lookup" s.addTargets(bp + "5s/5S.fa") #s.process_pair_db(pair_db) s.process_pair_data( bp + "5s/data/17571-AD1AW-KEW11-5S-2p1-18x-23FEB15-GGCTAC_S10_L001_R1_001.fastq", bp + "5s/data/17571-AD1AW-KEW11-5S-2p1-18x-23FEB15-GGCTAC_S10_L001_R2_001.fastq" ) s.compute_profiles() s.write_reactivities(bp + "dev_out/rx2.out")
def spats(target, r1, r2, out, show_sites = True): from spats_shape_seq import Spats, spats_config s = Spats() s.addTargets(target) s.addMasks("RRRY", "YYYR") if show_sites: spats_config.show_id_to_site = True s.process_pair_data(r1, r2) if not show_sites: s.compute_profiles() s.write_reactivities(out + "/rx.out")
def spats(target, r1, r2, out, show_sites=True): from spats_shape_seq import Spats, spats_config s = Spats() s.addTargets(target) s.addMasks("RRRY", "YYYR") if show_sites: spats_config.show_id_to_site = True s.process_pair_data(r1, r2) if not show_sites: s.compute_profiles() s.write_reactivities(out + "/rx.out")
def test_refactor(): from spats_clean import Spats bp = "/Users/jbrink/mos/tasks/1RwIBa/tmp/5sq_dev/" out = bp + "t3/" s = Spats(bp + "5S.fa", out) s.setup() s.process_pair_data(bp + "data/17571-AD1AW-KEW11-5S-2p1-18x-23FEB15-GGCTAC_S10_L001_R1_001.fastq", bp + "data/17571-AD1AW-KEW11-5S-2p1-18x-23FEB15-GGCTAC_S10_L001_R2_001.fastq") s.compute_profiles() s.write_reactivities() import subprocess subprocess.check_call(["diff", bp + "t2/rx.out", out + "/rx.out"]) print "Diff OK"
def cotrans_run(): bp = "/Users/jbrink/mos/tasks/1RwIBa/tmp/datasets/cotrans/" from spats_shape_seq import Spats s = Spats() #from spats_shape_seq.partial import PartialFindProcessor #s.run._processor_class = PartialFindProcessor s.run.skip_database = True #s.run.writeback_results = True #s.run.resume_processing = True #s.run.result_set_name = "lookup" s.addTargets(bp + "F_wt.fa") s.process_pair_data(bp + "data/EJS_6_F_10mM_NaF_Rep1_GCCAAT_R1.fastq", bp + "data/EJS_6_F_10mM_NaF_Rep1_GCCAAT_R2.fastq") s.compute_profiles() s.write_reactivities(bp + "dev_out/rx.out")
def cotrans_run(): bp = "/Users/jbrink/mos/tasks/1RwIBa/tmp/datasets/cotrans/" from spats_shape_seq import Spats s = Spats() #from spats_shape_seq.partial import PartialFindProcessor #s.run._processor_class = PartialFindProcessor s.run.skip_database = True #s.run.writeback_results = True #s.run.resume_processing = True #s.run.result_set_name = "lookup" s.addTargets(bp + "F_wt.fa") s.process_pair_data(bp + "data/EJS_6_F_10mM_NaF_Rep1_GCCAAT_R1.fastq", bp + "data/EJS_6_F_10mM_NaF_Rep1_GCCAAT_R2.fastq") s.compute_profiles() s.write_reactivities(bp + "dev_out/rx.out")
def test_refactor(): from spats_clean import Spats bp = "/Users/jbrink/mos/tasks/1RwIBa/tmp/5sq_dev/" out = bp + "t3/" s = Spats(bp + "5S.fa", out) s.setup() s.process_pair_data( bp + "data/17571-AD1AW-KEW11-5S-2p1-18x-23FEB15-GGCTAC_S10_L001_R1_001.fastq", bp + "data/17571-AD1AW-KEW11-5S-2p1-18x-23FEB15-GGCTAC_S10_L001_R2_001.fastq" ) s.compute_profiles() s.write_reactivities() import subprocess subprocess.check_call(["diff", bp + "t2/rx.out", out + "/rx.out"]) print "Diff OK"
def d5s_run(): bp = "/Users/jbrink/mos/tasks/1RwIBa/tmp/" #from spats_shape_seq.db import PairDB #pair_db = PairDB(bp + "dev_out/pairs.db") #if False: # pair_db.add_targets_table(bp + "5s/5S.fa") # pair_db.parse(bp + "5s/data/17571-AD1AW-KEW11-5S-2p1-18x-23FEB15-GGCTAC_S10_L001_R1_001.fastq", # bp + "5s/data/17571-AD1AW-KEW11-5S-2p1-18x-23FEB15-GGCTAC_S10_L001_R2_001.fastq") from spats_shape_seq import Spats from spats_shape_seq.partial import PartialFindProcessor s = Spats() #s.run._processor_class = PartialFindProcessor s.run.skip_database = True #s.run.writeback_results = True #s.run.resume_processing = True #s.run.result_set_name = "lookup" s.addTargets(bp + "5s/5S.fa") #s.process_pair_db(pair_db) s.process_pair_data(bp + "5s/data/17571-AD1AW-KEW11-5S-2p1-18x-23FEB15-GGCTAC_S10_L001_R1_001.fastq", bp + "5s/data/17571-AD1AW-KEW11-5S-2p1-18x-23FEB15-GGCTAC_S10_L001_R2_001.fastq") s.compute_profiles() s.write_reactivities(bp + "dev_out/rx2.out")