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")
def _dump_run(self):
run_name = self._run_file()
if not os.path.exists(run_name):
raise Exception("Run must be run before attempting dump")
spats = Spats()
spats.load(run_name)
profiles = spats.compute_profiles()
mutations = spats.run.count_mutations
indels = spats.run.handle_indels
headers = [ "L", "site", "nt", "f+", "f-" ]
if indels:
headers += [ "ins+", "ins-", "del+", "del-" ]
if mutations:
headers += [ "mut+", "mut-", "beta", "mu", "r" ]
else:
headers += [ "beta", "theta", "rho" ]
headers += [ "c", "c alt" ]
data = []
if self.cotrans:
tgt = spats.targets.targets[0]
tseq = tgt.seq
for key in profiles.cotrans_keys():
end = int(key.split('_')[-1])
prof = profiles.profilesForTargetAndEnd(tgt.name, end)
for i in xrange(end + 1):
datapt = [ end, i, tseq[i - 1] if i else '*', prof.treated[i], prof.untreated[i] ]
if indels:
datapt += [ prof.treated_inserts[i], prof.untreated_inserts[i], prof.treated_deletes[i], prof.untreated_deletes[i] ]
if mutations:
datapt += [ prof.treated_muts[i], prof.untreated_muts[i], prof.beta[i], prof.mu[i], prof.r_mut[i] ]
else:
datapt += [ prof.beta[i], prof.theta[i], prof.rho[i] ]
datapt += [ prof.c, prof.c_alt ]
data.append(datapt)
output_path = os.path.join(self.path, '{}.csv'.format(tgt.name))
self._write_csv(output_path, headers, data)
empty_cell = ''
keys = [ 'treated', 'untreated' ]
if indels:
keys += [ 'treated_inserts', 'untreated_inserts', 'treated_deletes', 'untreated_deletes' ]
if mutations:
keys += [ 'treated_mut', 'untreated_mut', 'beta', 'mu', 'r' ]
else:
keys += [ 'beta', 'theta', 'rho' ]
cotrans_keys = profiles.cotrans_keys()
for key in keys:
ncols = 0
mat = []
for pkey in cotrans_keys:
end = int(pkey.split('_')[-1])
prof = profiles.profilesForTargetAndEnd(tgt.name, end)
vals = getattr(prof, key)
if not ncols:
ncols = len(cotrans_keys) + len(vals)
if len(vals) < ncols:
vals += ([empty_cell] * (ncols - len(vals)))
mat.append(vals)
self._write_csv('{}_{}_mat.csv'.format(tgt.name, key), None, mat)
else:
for tgt in spats.targets.targets:
tseq = tgt.seq
end = len(tgt.seq)
prof = profiles.profilesForTarget(tgt)
data = []
for i in xrange(end + 1):
datapt = [ end, i, tseq[i - 1] if i else '*', prof.treated[i], prof.untreated[i] ]
if indels:
datapt += [ prof.treated_inserts[i], prof.untreated_inserts[i], prof.treated_deletes[i], prof.untreated_deletes[i] ]
if mutations:
datapt += [ prof.treated_muts[i], prof.untreated_muts[i], prof.beta[i], prof.mu[i], prof.r_mut[i] ]
else:
datapt += [ prof.beta[i], prof.theta[i], prof.rho[i] ]
datapt += [ prof.c, prof.c_alt ]
data.append(datapt)
output_path = os.path.join(self.path, '{}.csv'.format(tgt.name))
self._write_csv(output_path, headers, data)