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 ligation_run():
bp = "/Users/jbrink/mos/tasks/1RwIBa/tmp/datasets/Shape_Seq_ligation/"
from spats_shape_seq import Spats
s = Spats()
#s.config.debug = True
#s.run.minimum_target_match_length = 10
#s.run.num_workers = 1
#from spats_shape_seq.partial import PartialFindProcessor
#s.run._processor_class = PartialFindProcessor
s.run.skip_database = True
s.addTargets(bp + "panel_RNAs_complete.fa")
s.process_pair_data(bp + "data/KEW1_S1_L001_R1_001.fastq",
bp + "data/KEW1_S1_L001_R2_001.fastq")
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 ligation_run():
bp = "/Users/jbrink/mos/tasks/1RwIBa/tmp/datasets/Shape_Seq_ligation/"
from spats_shape_seq import Spats
s = Spats()
#s.config.debug = True
#s.run.minimum_target_match_length = 10
#s.run.num_workers = 1
#from spats_shape_seq.partial import PartialFindProcessor
#s.run._processor_class = PartialFindProcessor
s.run.skip_database = True
s.addTargets(bp + "panel_RNAs_complete.fa")
s.process_pair_data(bp + "data/KEW1_S1_L001_R1_001.fastq",
bp + "data/KEW1_S1_L001_R2_001.fastq")
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 prof_run():
from spats_shape_seq import Spats
spats = Spats()
#spats.run.cotrans = True
#spats.run.cotrans_linker = 'CTGACTCGGGCACCAAGGAC'
#spats.run.writeback_results = False
spats.run._process_all_pairs = True
spats.run.skip_database = True
spats.run.algorithm = "lookup"
spats.run.count_mutations = True
spats.run.num_workers = 1
bp = "/Users/jbrink/mos/tasks/1RwIBa/tmp/datasets/pdc_muts/PDC_tweaked/PDC_09_001_6/"
spats.addTargets(bp + "target.fa")
spats.process_pair_data(bp + "2k_R1.fastq", bp + "2k_R2.fastq")
exit(0)
def indels_run():
from spats_shape_seq import Spats
s = Spats()
s.run.algorithm = True
s.run.count_indels = True
s.run.count_mutations = True
s.run.allowed_target_errors = 8
s.collapse_left_prefixes = True
s.run.ignore_stops_with_mismatched_overlap = True
s.run.allow_negative_values = True
s.mutations_require_quality_score = 30
bp = "/Users/steve/mos/tasks/oughxX/code"
s.addTargets(bp + "/test/hairpin/hairpinA_circ.fa")
rp = bp + "/TESTING/cmp_muts_favored/steve_test"
s.process_pair_data(rp + "/R1_match_failures.fastq",
rp + "/R2_match_failures.fastq")
exit(0)
def prof_run():
from spats_shape_seq import Spats
spats = Spats()
#spats.run.cotrans = True
#spats.run.cotrans_linker = 'CTGACTCGGGCACCAAGGAC'
#spats.run.writeback_results = False
spats.run._process_all_pairs = True
spats.run.skip_database = True
spats.run.algorithm = "lookup"
spats.run.count_mutations = True
spats.run.num_workers = 1
bp = "/Users/jbrink/mos/tasks/1RwIBa/tmp/datasets/pdc_muts/PDC_tweaked/PDC_09_001_6/"
spats.addTargets(bp + "target.fa")
spats.process_pair_data(bp + "2k_R1.fastq",
bp + "2k_R2.fastq")
exit(0)
def indels_run():
from spats_shape_seq import Spats
s = Spats()
s.run.algorithm = True
s.run.count_indels = True
s.run.count_mutations = True
s.run.allowed_target_errors = 8
s.collapse_left_prefixes = True
s.run.ignore_stops_with_mismatched_overlap = True
s.run.allow_negative_values = True
s.mutations_require_quality_score = 30
bp = "/Users/steve/mos/tasks/oughxX/code"
s.addTargets(bp + "/test/hairpin/hairpinA_circ.fa")
rp = bp + "/TESTING/cmp_muts_favored/steve_test"
s.process_pair_data(rp + "/R1_match_failures.fastq",
rp + "/R2_match_failures.fastq")
exit(0)
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 run(self):
"""Process the SPATS data for the configured target(s) and r1/r2 fragment pairs.
"""
run_name = self._run_file()
if os.path.exists(run_name):
self._add_note("** removing previous run file")
os.remove(run_name)
native_tool = self._native_tool('cotrans')
if native_tool and not self.cotrans:
self._add_note("skipping native tool due to non-cotrans run")
native_tool = None
spats = Spats(cotrans = self.cotrans)
if self._update_run_config(spats.run) and native_tool:
self._add_note("skipping native tool due to custom config")
native_tool = None
if native_tool:
self._add_note("using native cotrans processor")
subprocess.check_call([native_tool, self.config['target'], self.r1, self.r2, run_name], cwd = self.path)
else:
self._add_note("using python processor")
spats.addTargets(self.config['target'])
if self.using_separate_channel_files:
spats.process_pair_data(self.r1_plus, self.r2_plus, force_mask = spats.run.masks[0])
spats.process_pair_data(self.r1_minus, self.r2_minus, force_mask = spats.run.masks[1])
else:
spats.process_pair_data(self.r1, self.r2)
spats.store(run_name)
self._add_note("wrote output to {}".format(os.path.basename(run_name)))
nb = self._notebook()
if nb:
nb.add_spats_run(self.cotrans, spats.run.count_mutations).save()
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")