def show_failure_types():
from spats_clean import Spats, Pair, FastqRecord
spats = Spats("test/5s/5s.fa", "test/5s")
spats.setup()
bp = "/Users/jbrink/mos/tasks/1RwIBa/tmp/"
with open(bp + "t11/x/filtered_R1.fq", 'rb') as r1_in:
with open(bp + "t11/x/filtered_R2.fq", 'rb') as r2_in:
r1_record = FastqRecord()
r2_record = FastqRecord()
pair = Pair()
while True:
r1_record.read(r1_in)
if not r1_record.identifier:
break
r2_record.read(r2_in)
pair.set_from_records(r1_record, r2_record)
spats.process_pair(pair)
summary = "{} :: {}".format(pair.identifier, pair.site if pair.has_site else pair.failure)
if pair.r1.match_errors:
summary += " R1!: {}".format(pair.r1.match_errors)
if pair.r1.adapter_errors:
summary += " R1A!: {}, adapter_len={}".format(pair.r1.adapter_errors, pair.r1._rtrim)
if pair.r2.match_errors:
summary += " R2!: {}".format(pair.r2.match_errors)
if pair.r2.adapter_errors:
summary += " R2A!: {}, adapter_len={}".format(pair.r2.adapter_errors, pair.r2._rtrim - 4)
print summary
def show_failure_types():
from spats_clean import Spats, Pair, FastqRecord
spats = Spats("test/5s/5s.fa", "test/5s")
spats.setup()
bp = "/Users/jbrink/mos/tasks/1RwIBa/tmp/"
with open(bp + "t11/x/filtered_R1.fq", 'rb') as r1_in:
with open(bp + "t11/x/filtered_R2.fq", 'rb') as r2_in:
r1_record = FastqRecord()
r2_record = FastqRecord()
pair = Pair()
while True:
r1_record.read(r1_in)
if not r1_record.identifier:
break
r2_record.read(r2_in)
pair.set_from_records(r1_record, r2_record)
spats.process_pair(pair)
summary = "{} :: {}".format(
pair.identifier,
pair.site if pair.has_site else pair.failure)
if pair.r1.match_errors:
summary += " R1!: {}".format(pair.r1.match_errors)
if pair.r1.adapter_errors:
summary += " R1A!: {}, adapter_len={}".format(
pair.r1.adapter_errors, pair.r1._rtrim)
if pair.r2.match_errors:
summary += " R2!: {}".format(pair.r2.match_errors)
if pair.r2.adapter_errors:
summary += " R2A!: {}, adapter_len={}".format(
pair.r2.adapter_errors, pair.r2._rtrim - 4)
print summary
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 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"