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")