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 setUp(self):
from spats_shape_seq import Spats
self.spats = Spats()
self.spats.run.cotrans = True
self.spats.run.cotrans_linker = 'CTGACTCGGGCACCAAGGAC'
self.spats.run.collapse_left_prefixes = True
self.spats.addTargets("test/cotrans/cotrans_single.fa")
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 setUp(self):
try:
self.spats = Spats()
self.test_set.spats_setUp(self.spats)
except Exception as e:
print("exception caught on testset '{}' setup : {}".format(
self.test_set.name, e))
raise e
def setUp(self):
self.spats = Spats()
self.spats.run.count_mutations = True
self.spats.run.mutations_require_quality_score = ord('.') - ord('!')
self.spats.run.allowed_target_errors = 1
self.spats.run.ignore_stops_with_mismatched_overlap = True
self.spats.run.adapter_b = "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG"
self.setup_processor()
def run_algorithm(self, alg):
from spats_shape_seq import Spats
self.spats = Spats()
self.spats.run.algorithm = alg
self.spats.run.count_mutations = True
self.spats.run.allowed_target_errors = True
self.spats.run.ignore_stops_with_mismatched_overlap = True
self.spats.addTargets("test/SRP/SRP.fa")
self.run_pairs()
def cotrans_debug():
from spats_shape_seq import Spats
s = Spats()
s.run.cotrans = True
#s.run.cotrans_linker = 'CTGACTCGGGCACCAAGGAC'
#s.run.algorithm = "find_partial"
#s.run._p_v102_compat = True
s.run.minimum_target_match_length = 10
bp = "/Users/jbrink/mos/tasks/1RwIBa/tmp/datasets/cotrans/"
s.addTargets(bp + "cotrans_single.fa")
from spats_shape_seq.pair import Pair
pair = Pair()
import cjb.util
d = cjb.util.jsonAtPath("/tmp/spats_test.json")
pair.set_from_data(str(d['id']), str(d['r1']), str(d['r2']))
#c = ['683779', 'TCCGGTCCTTGGTGCCCGAGTCAGAAAAAAATAGAA', 'TCTATTTTTTTCTGACTCGGGCACCAAGGACCGGAA', 82, 71]
#c = [ "1116:19486:8968", "TCCGGTCCTTGGTGCCCGAGTCAGTCCTTCCTCCTA", "GAGTCTATTTTTTTAGGAGGAAGGACTGACTCGGGC", 93, 68 ]
#c = [ "301028", "AAGTGTCCTTGGTGCCCGAGTCAGAGATAGATCGGA", "ATCTCTGACTCGGGCACCAAGGACACTTAGATCGGA", 96, 92 ]
#c = [ "31631284", "TTCAGTCCTTGGTGCCCGAGTCAGAGATAGATCGGA", "ATCTCTGACTCGGGCACCAATGACCGGAAGATCGGA", 96, 92 ]
#c = [ "7232", "AGGTGTCCTTGGTGCCCGAGTCAGTAGCTAAGAAAT", "TTATAGGCGATGGAGTTCGCCATAAACGCTGCTTAG", -1, -1 ]
#c = [ "16845404", "AAATGTCCTTGGTGCCCGAGTCAGACTGGTAGGAGT", "TCTTATAGGCGATGGAGTTCGCCATAAACGCTGCTT", -1, -1 ]
#c = [ "24102328", "AAGCGTCCTTGGTGCCCGAGTCAGGAGTCATAGATC", "ATGACTCCTGACTCGGGCACCAAGGACGCTTAGATC", 46, 39 ]
#c = [ "51216106", "GGGTGTCCTTGGTGCCCGAGTCAGATTAGCTAAGCA", "AGCTAATCTGACTCGGGCACCAAGGACGCTGCTTAG", 41, 34 ]
c = [
"1116:19486:8968", "TCCGGTCCTTGGTGCCCGAGTCAGTCCTTCCTCCTA",
"GAGTCTATTTTTTTAGGAGGAAGGACTGACTCGGGC", 93, 68
]
#c = [ "41823514", "GAATGTCCTTGGTGCCCGAGTCAGAACTCCAAGATC", "TGGAGTTCTGACTCGGGCACCAAGGACATTCAGATC", -1, -1 ]
#c = [ "180", "AAGCTGTCCTTGGTGCCCGAGTCAGGAAAAGTTCTT", "TTTTTTTAGGAGGAAGGATCTATGAGCAAAGGAGAA", 120, 75 ]
#c = [ "67219", "GAGTGTCCTTGGTGCCCGAGTCAGTCGACAACTCCA", "TTATAGGCGATGGAGTTCGCCATAAACGCTGCTTAG", 134, 0 ]
#c = [ "58726", "GGATGTCCTTGGTGCCCGAGTCAGCCTTAGATCGGA", "AAGGCTGACTCGGGCACCAAGGACATCCAGATCGGA", None, None ]
#c = [ "188425", "GGACGTCCTTGGTGCCCGAGTCAGTATAGATCGGAA", "ATACTGACTCGGGCACCAAGGACTTCCAGATCGGAA", 24, 21 ]
#c = [ "jjb_L21", "GGACGTCCTTGGTGCCCGAGTCAGGGCGAACTAGAT", "AGTTCGCCCTGACTCGGGCACCAAGGACGTCCAGAT", 21, 13 ]
#c = [ "jjb_L20", "GGACGTCCTTGGTGCCCGAGTCAGGCGAACTCAGAT", "GAGTTCGCCTGACTCGGGCACCAAGGACGTCCAGAT", 20, 12 ]
#c = [ "jjb_L19", "GGACGTCCTTGGTGCCCGAGTCAGCGAACTCCAGAT", "GGAGTTCGCTGACTCGGGCACCAAGGACGTCCAGAT", None, None ]
#c = [ "406149", "AGGTGTCCTTGGTGCCCGAGTCAGGACAACTCCAGT", "TTATAGGCGATGGAGTTCGCCATAAACGCTGCTTAG", 132, 0 ]
#c = [ "89185", "TCCAGTCCTTGGTGCCCGAGTCAGCTAAGCAGCGTT", "AATGACTCCTACCAGTATCACTACTGGTAGGAGTCT", 36, 38 ]
#c = [ "3185000", "GAACGTCCTTGGTGCCCGAGTCAGGTTTATGGCGAA", "TCGCCATAAACCTGACTCGGGCACCAAGGACGTTCC", -1, -1 ]
#c = [ "jjb_3185000'", "GAACGTCCTTGGTGCCCGAGTCAGGTTTATGGCGAA", "TCGCCATAAACCTGACTCGGGCACCAAGGACGTTCA", None, None ]
#c = ['1', 'TCTGAGATCGGAAGAGCACACGTCTGAACTCCAGT', 'CAGAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGT', None, None]
#c = ['24941', 'TCCAGTCCTTGGTGCCCGAGTCAGAGACTCCTACCA', 'TATAGGCGATGGAGTTCGCCATAAACGCTGCTTAGC', -1, -1]
c = [
'jjbn', 'TTTGGTCCTTGGTGCCCGAGTCAGTAAAAAAATAGA',
'TCTATTTTTTTACTGACTCGGGCACCAAGGACCAAA', 83, 71
]
pair.set_from_data(c[0], c[1], c[2])
print "{}\n{} / {}".format(pair.identifier, pair.r1.original_seq,
pair.r2.original_seq)
s.process_pair(pair)
if pair.has_site:
print "{}: {} / {}".format(pair.target.name, pair.site, pair.end)
else:
print "FAIL: {}".format(pair.failure)
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 dbrun():
db_path = sys.argv[2]
run_name = sys.argv[3]
from spats_shape_seq import Spats
from spats_shape_seq.db import PairDB
db = PairDB(db_path)
s = Spats()
s.run.writeback_results = True
s.run.result_set_name = run_name
#s.run.resume_processing = True
s.process_pair_db(db)
def test_minimum_length(self):
from spats_shape_seq import Spats
self.spats = Spats()
self.spats.run.algorithm = "find_partial"
self.spats.run.minimum_target_match_length = 11
self.spats.addTargets("test/5s/5s.fa")
self.assertEqual(11, self.spats._targets.minimum_match_length)
case = [
'1109:22737:14675', 'TCCAGTCCTTGGAGATCGGAAGAGCACACGTCTGA',
'CCAAGGACTGGAAGATCGGAAGAGCGTCGTGTAGG', None
]
self.run_case(case)
# this case only matches if the minimum length is set to 8
self.spats.run.minimum_target_match_length = 8
self.spats = Spats()
self.spats.run.algorithm = "lookup"
self.spats.addTargets("test/5s/5s.fa")
case[3] = 135
self.run_case(case)
def tmut_case():
from spats_shape_seq import Spats
from spats_shape_seq.db import PairDB
from spats_shape_seq.diagram import diagram
bp = "/Users/jbrink/mos/tasks/1RwIBa/tmp/mutsl/"
spats = Spats(cotrans=False)
spats.run.cotrans_linker = 'CTGACTCGGGCACCAAGGAC'
spats.run.count_mutations = True
spats.run.algorithm = "find_partial"
spats.run.allowed_target_errors = 1
spats.run.adapter_b = "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG"
spats.run._process_all_pairs = True
spats.run.writeback_results = True
spats.run.num_workers = 1
spats.run.result_set_name = "mut"
spats.addTargets(bp + "mut_single.fa")
from spats_shape_seq.pair import Pair
pair = Pair()
#c = [ 'GAATGTCCTTGGTGCCCGAGTCAGTCCTTGGTGCCCGAGTCAGTCCTTGGTTCCCGAGTCACTCCTTTGTTCCCC', 'AGGACTGACTCGGGCACCAAGGACTTTCTCGTTCACCTATTTCTTTCTCTTCCCCCTTTTTCTTTCTCTTTCTCC' ]
#c = [ 'GAGCGTCCTTGGTGCCCGAGTCAGATGCCGACCCGGGTGGGGGCCCTGCCAGCTACATCCCGGCACACGCGTCAT', 'TAGGTCAGGTCCGGAAGGAAGCAGCCAAGGCAGATGACGCGTGTGCCGGGATGTAGCTGGCAGGGCCCCCACCCG' ]
#c = [ 'GAATGTCCTTGGTGCCCGAGTCAGGACACGCGTCATCTGCCTTGGCTGCTTCCTTCCGGACCTGACCTGGTAAAC', 'ATCGGGGGCTCTGTTGGTTCCCCCGCAACGCTACTCTGTTTACCAGGTCAGGTCCGGAAGGAAGCAGCCAAGTCA' ]
#c = [ 'AGGCGTCCTTGGTGCCCGAGTCAGCCTTGGCTGCTTCCTTCCGGACCTGACCTGGTAAACAGAGTAGCGTTGCGG', 'ATCGGGGGCTCTGTTGGTTCCCCCGCAACGCTACTCTGTTTACCAGGTCAGGTCCGGAAGGAAGCAGCCAAGTCT' ]
#c = [ 'TTCAGTCCTTGGTGCCCGAGTCAGCCAGCTACATCCCGGCACACGCGTCATCTGCCTTGGCTGCTTCCTTCCGGA', 'AGGTCAGATCCGGAAGGAAGCAGCCAAGGCAGATGACGCGTGTGCCGGGATGTAGCTGGCTGACTCGGGCACCAA' ]
#c = [ 'AAATGTCCTTGGTGCCCGAGTCAGATCTGCCTTAAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGA', 'TAAGGCAGATCTGACTCGGGCACCAAGGACATTTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCG' ]
#c = [ 'CTCAGTCCTTGGTGCCCGAGTCAGTGAGCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTC', 'AGCTCACTGACTCGGGCACCAAGGACTGAGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGG' ]
#c = [ 'AAGCGTCCTTGGTGCCCGAGTCAGTGGAGGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCT', 'ACCTCCACTGACTCGGGCACCAAGGACGCTTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTG' ]
#c = [ 'TCCGGTCCTTGGTGCCCGAGTCAGATGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGT', 'ACATCTGACTCGGGCACCAAGGACCGGAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTC' ]
#c = [ 'TTTAAGTCCTTGGTGCCCGAGTCAGGTCATCTGCCTTGGCTGCTTCCTTCCGGACCTGACCTGGTAAACAGAGTA', 'TACTCTGTTTACCAGGTCAGGTCCGGAAGGAAGCAGCCAAGGCAGATGACCTGACTCGGGCACCAAGGACTTAAA' ]
#c = [ 'TTCACAACAAGAATTGGGACAACTCCAGTGAAAAGTTCTTCTCCTTTGCTCATCATTAACCTCCTGAATCACTAT', 'GGACAAGCAATGCTTACCTTGATGTTGAACTTTTGAATAGTGATTCAGGAGGTTAATGATGAGCAAAGGAGAAGA' ]
#c = [ 'AGATCAACAAGAATTAGGACAACTCCAGTGAAAAGTTCTTCTCCTTTGCTCATCATTAACCTCCTGAATCACTAT', 'ACAAGCAATGCTTGCCTTGATGTTGAACTTTTGAATAGTGATTCAGGAGGTTAATGATGAGCAAAGGAGAAGAAC' ]
#c = [ 'AAATCAACAAGAATTGGGACAACTCCAGTGAAAAGTTCTTCTCCTTTGCTCATCATTAACCTCCTGAATCACTAT', 'AATAGTGATTCAGGAGGTTAATGATGAGCAAAGGAGAAGAACTTTTCACTGGAGTTGTCCCAATTCTTGTTGATT' ]
#c = [ 'TCCGCAACAAGAATTGGGACAACTCCAGTGAAAAGTTCTTCTCCTTTGCTCATCATTAACCTCCTGAATCACTAT', 'ATAGTGATTCAGGAGGTTAATGATGAGCAAAGGAGAAGAACTTTTCACTGGAGTTGTCCCAATTCTTGTTGCGGA' ]
#c = [ 'TCCACAACAAGAATTGGGACAACTCCAGTGAAAAGTTCTTCTCATTTGCTCATCATTAACCTCCTGAATCACTAT', 'GGACAAGCAATGCTTGCCTTGATGTTGAACTTTTGAATAGTGATTCAGGAGGTTAATGATGAGCAAAGGAGAAGA' ]
#c = [ 'GGGTCAACAAGAATTGGGACAACTCCAGTGAAAAGTTCTTCTCCTTTGCTCATCATTTAGATCGGAAGAGCACAC', 'AAATGATGAGCAAAGGAGAAGAACTTTTCACTGGAGTTGTCCCAATTCTTGTTGACCCAGATCGGAAGAGCGTCG' ]
c = [
'GAACCAACAAGAATTGGGACAACTCCAGTGAAAGGTTCTTCTCCTTTGCTCATCATTAACCTCCTGAAGATCGGA',
'TCAGGAGGTTAATGATGAGCAAAGGAGAAGAACCTTTCACTGGAGTTGTCCCAATTCTTGTTGGTTCAGATCGGA'
]
#c = [ 'CCTACAACAAGAATTGGGACAACTCCAGTGAGAAGTTCTTCTCCTTTGCTCATCATTAAGATCGGAAGAGCACAC', 'TAATGATGAGCAAAGGAGAAGAACTTCTCACTGGAGTTGTCCCAATTCTTGTTGTAGGAGATCGGAAGAGCGTCG' ]
#c = [ 'CTTGCAACAAGAATTGGGACAACTCCAGTGAAAAGTTCTTCTCCTTTGCTCATCTTTAACCTCCTGAATCACTAA', 'TAGTGATTCAGGAGGTTAATGATGAGCAAAGGAGAAGAACTTTTCACTGGAGTTGTCCCAATTCTTGTTGCAAGA' ]
pair.set_from_data('x', c[0], c[1])
spats.process_pair(pair)
print diagram(pair, spats.run)
if pair.has_site:
print "{}: {} / {} {}".format(pair.target.name, pair.site, pair.end,
pair.mutations)
else:
print "FAIL: {}".format(pair.failure)
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_test():
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.addTargets(bp + "F_wt.fa")
from spats_shape_seq.pair import Pair
pair = Pair()
pair.set_from_data('x', 'GAGCGTCCTTGGTGCCCGAGTCAGAAATAGACTCCT',
'TATCACTACTGGTAGGAGTCTATTTCTGACTCGGGC')
s.process_pair(pair)
print "{}: {}".format(pair.target.name, pair.site)
def d5s_writeback_run():
bp = "/Users/jbrink/mos/tasks/1RwIBa/tmp/"
from spats_shape_seq.db import PairDB
pair_db = PairDB(bp + "dev_out/pairs.db")
pair_db.add_targets_table(bp + "5s/5S.fa")
from spats_shape_seq import Spats
s = Spats()
s.addTargets(bp + "5s/5S.fa")
s.writeback_results = True
s.result_set_name = "pure_python"
s.process_pair_db(pair_db)
def __init__(self, reads_data, cotrans = False):
self._reads_data = reads_data
self._pair_db = reads_data.pair_db
s = Spats()
s.run._p_use_tag_processor = True
s.run.cotrans = cotrans
s.run.writeback_results = True
s.run.result_set_name = "tags"
s.run.allow_indeterminate = True
s.run.allowed_target_errors = 2
s.run.allowed_adapter_errors = 2
s.run.num_workers = 8
self._spats = s
self._extra_tag_targets = []
self._plugins = {}
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 make_test_dataset():
bp = "/Users/jbrink/mos/tasks/1RwIBa/tmp/datasets/cotrans/data/"
from spats_shape_seq import Spats
from spats_shape_seq.db import PairDB
pair_db = PairDB(bp + "ds.spats")
pair_db.add_targets_table(bp + "../cotrans_single.fa")
pair_db.parse(bp + "med_R1.fq", bp + "med_R2.fq")
s = Spats(cotrans=True)
s.run.num_workers = 1
s.run.writeback_results = True
s.run._process_all_pairs = True
s.run.algorithm = "find_partial"
s.run.result_set_name = "test_validation"
s.process_pair_db(pair_db)
pair_db.store_run(s.run)
pair_db.store_counters('spats', s.counters)
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 tags():
bp = "/Users/jbrink/mos/tasks/1RwIBa/tmp/datasets/cotrans/"
from spats_shape_seq.db import PairDB
pair_db = PairDB(bp + "db/pairs.db")
if True:
print "Parsing to db..."
pair_db.wipe()
pair_db.add_targets_table(bp + "cotrans_single.fa")
pair_db.parse(bp + "data/EJS_6_F_10mM_NaF_Rep1_GCCAAT_R1.fastq",
bp + "data/EJS_6_F_10mM_NaF_Rep1_GCCAAT_R2.fastq",
sample_size=100000)
from spats_shape_seq import Spats
from spats_shape_seq.tag import TagProcessor
from spats_shape_seq.util import reverse_complement
s = Spats()
s.run._processor_class = TagProcessor
s.run.writeback_results = True
s.run.result_set_name = "tags"
s.run.num_workers = 1
s.run.cotrans = True
s.run.cotrans_linker = 'CTGACTCGGGCACCAAGGAC'
s.loadTargets(pair_db)
s.run.allow_indeterminate = True
s.run.allowed_target_errors = 2
s.run.allowed_adapter_errors = 2
p = s._processor
for target in pair_db.targets():
p.addTagTarget(target[0], target[1])
p.addTagTarget(target[0] + "_rc", reverse_complement(target[1]))
p.addTagTarget("adapter_t_rc", reverse_complement(s.run.adapter_t))
p.addTagTarget("adapter_b", s.run.adapter_b)
if s.run.cotrans:
p.addTagTarget("linker_cotrans", s.run.cotrans_linker)
p.addTagTarget("linker_cotrans_rc",
reverse_complement(s.run.cotrans_linker))
s.process_pair_db(pair_db)
rsid = pair_db.result_set_id_for_name(s.run.result_set_name)
pair_db.count_tags(rsid)
print pair_db.tag_counts(rsid)
class TestDatasets(unittest.TestCase):
def test_datasets(self):
for case in cases:
for alg in algorithms:
if os.environ.get('SKIP_SLOW_TESTS') and alg == 'native':
raise nose.SkipTest('skipping slow tests')
self.run_dataset(case, alg)
print("Ran {} datasets.".format(len(cases)))
def run_dataset(self, case, algorithm):
bp = "test/{}/".format(case)
test_file = bp + "test.spats.tmp"
try:
shutil.copyfile(bp + "ds.spats", test_file)
db = PairDB(test_file)
s = Spats()
db.load_run(s.run)
if not s.run.cotrans and algorithm == "native":
return
s.run.writeback_results = True
s.run.result_set_name = "test"
s.run.algorithm = algorithm
s.run.quiet = True
s.loadTargets(db)
if not s._processor.exists():
# just ignore the native test if it's not available
self.assertEqual("native", algorithm)
return
s.process_pair_db(
db, batch_size=1024
) # small batch_size just to exercise multiprocessing code
msg = None
count = 0
for res in db.differing_results("test", "test_validation"):
msg = str([str(x) for x in res])
count += 1
self.assertEqual(
0, count, "{} differing results: {} / {} \n{}".format(
count, case, algorithm, msg))
finally:
if os.path.exists(test_file):
os.remove(test_file)
def tag_test():
from spats_shape_seq import Spats
s = Spats()
s.run.cotrans = True
s.run.cotrans_linker = 'CTGACTCGGGCACCAAGGAC'
s.run.algorithm = "find_partial"
bp = "/Users/jbrink/mos/tasks/1RwIBa/tmp/datasets/cotrans/"
s.addTargets(bp + "cotrans_single.fa")
from spats_shape_seq.pair import Pair
pair = Pair()
import cjb.util
d = cjb.util.jsonAtPath("/tmp/spats_test.json")
pair.set_from_data(str(d['id']), str(d['r1']), str(d['r2']))
print "{}\n{} / {}".format(pair.identifier, pair.r1.original_seq,
pair.r2.original_seq)
s.process_pair(pair)
if pair.has_site:
print "{}: {} / {}".format(pair.target.name, pair.site, pair.right)
else:
print "FAIL: {}".format(pair.failure)
def _loadDBAndModel(self):
rsnames = self._db.result_sets()
if rsnames:
self.result_set_id = self._db.result_set_id_for_name(rsnames[0])
self._db.index_results()
self.has_tags = bool(self.result_set_id)
else:
self.result_set_id = -1
self.has_tags = False
self.has_counters = self._db.has_counters()
s = Spats()
self._db.load_run(s.run)
s.run._p_use_tag_processor = True
s.loadTargets(self._db)
if self.has_counters:
self._db.load_counters("spats", s.counters)
if self.has_tags:
p = s._processor
for t in s._targets.targets:
p.addTagTarget(t.name, t.seq)
p.addTagTarget(t.name + "_rc", reverse_complement(t.seq))
self.colors._colors[t.name.lower()] = self.colors.color("target")
p.addTagTarget("adapter_t_rc", reverse_complement(s.run.adapter_t))
p.addTagTarget("adapter_b", s.run.adapter_b)
if s.run.cotrans:
p.addTagTarget("linker_cotrans", s.run.cotrans_linker)
p.addTagTarget("linker_cotrans_rc", reverse_complement(s.run.cotrans_linker))
if s.run._p_extra_tags:
for tag, seq in s.run._p_extra_tags.iteritems():
p.addTagTarget(tag, seq)
if not self.has_counters:
p.counters.load_from_db_data(self._db.counter_data_for_results(self.result_set_id))
self._spats = s
def tmut():
from spats_shape_seq import Spats
from spats_shape_seq.db import PairDB
from spats_shape_seq.diagram import diagram
bp = "/Users/jbrink/mos/tasks/1RwIBa/tmp/mutsl/"
pair_db = PairDB(bp + "ds_cmp.spats")
if True:
print "Parsing to db..."
pair_db.wipe()
pair_db.add_targets_table(bp + "mut_single.fa")
fq_name = "mut2"
pair_db.parse(bp + fq_name + "_R1.fastq", bp + fq_name + "_R2.fastq")
spatss = []
for alg in ["find_partial", "lookup"]:
spats = Spats(cotrans=False)
spats.run.cotrans_linker = 'CTGACTCGGGCACCAAGGAC'
spats.run.count_mutations = True
spats.run.algorithm = alg
spats.run.allowed_target_errors = 1
spats.run.adapter_b = "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG"
spats.run._process_all_pairs = True
spats.run.writeback_results = True
spats.run.num_workers = 1
spats.run.result_set_name = "mut_" + alg
spats.process_pair_db(pair_db)
pair_db.store_run(spats.run)
pair_db.store_counters(spats.run.result_set_name, spats.counters)
spatss.append(spats)
rdiff_func(bp + "ds_cmp.spats",
"mut_find_partial",
"mut_lookup",
diag_spats=spatss[0])
def diag_case():
from spats_shape_seq import Spats
from spats_shape_seq.pair import Pair
from spats_shape_seq.tests.test_mut import cases
#from spats_shape_seq.tests.test_pairs import prefix_cases as cases
from spats_shape_seq.diagram import diagram
#spats_config.minimum_target_match_length = 8
spats = Spats()
#spats.addTargets("test/5s/5s.fa")
spats.addTargets("test/mut/mut_single.fa")
spats.run.debug = True
spats.run.algorithm = "find_partial"
spats.run.count_mutations = True
#spats.run.mutations_require_quality_score = ord('.') - ord('!')
spats.run.allowed_target_errors = 1
spats.run.ignore_stops_with_mismatched_overlap = True
spats.run.adapter_b = "AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG"
#spats.run.collapse_left_prefixes = True
spats._case_errors = False
def run_case(case):
pair = Pair()
pair.set_from_data(case[0], case[1], case[2])
spats.process_pair(pair)
print diagram(pair, spats.run)
if case[3] != pair.site:
spats._case_errors = True
print "******* mismatch: {} != {}".format(case[3], pair.site)
for case in cases:
if case[0].startswith("*"):
run_case(case)
spats.run.debug = False
if spats._case_errors:
raise Exception("Case failed")
def setUp(self):
from spats_shape_seq import Spats
self.spats = Spats()
self.spats.run.collapse_left_prefixes = True
self.spats.addTargets("test/5s/5s.fa")
def setUp(self):
from spats_shape_seq import Spats
self.spats = Spats()
self.spats.run.minimum_target_match_length = 10
self.spats.addTargets("test/panel_RNAs/panel_RNAs_complete.fa")
def setUp(self):
from spats_shape_seq import Spats
self.spats = Spats()
self.spats.addTargets("test/5s/5su.fa")
def run_algorithm(self, alg):
from spats_shape_seq import Spats
self.spats = Spats()
self.spats.run.algorithm = alg
self.spats.addTargets("test/5SrRNA/5SrRNA.fa")
self.run_pairs()