class TestPrefixPairs(unittest.TestCase):
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 tearDown(self):
self.spats = None
def pair_for_case(self, case):
pair = Pair()
pair.set_from_data(case[0], case[1], case[2])
return pair
def run_case(self, case):
pair = self.pair_for_case(case)
self.spats.counters.reset()
self.spats.process_pair(pair)
self.assertEqual(
case[3], pair.site,
"res={} != {} ({}, {})".format(pair.site, case[3],
self.__class__.__name__, case[0]))
if case[4]:
self.assertEqual(
1, getattr(self.spats.counters, 'prefix_RRRY_' + case[4]),
"prefix {} not counted ({})".format(case[4], case[0]))
return pair
def test_pairs(self):
for case in prefix_cases:
self.run_case(case)
print("Ran {} prefix test cases.".format(len(cases)))
class TestShortAdapterB(unittest.TestCase):
def tearDown(self):
self.spats = None
def pair_for_case(self, case):
pair = Pair()
pair.set_from_data(case[0], case[1], case[2])
return pair
def run_case(self, case):
pair = self.pair_for_case(case)
print('running: {} / {}'.format(case[0], self.spats.run.algorithm))
self.spats.process_pair(pair)
self.assertEqual(case[3], pair.site, "site res={} != {} ({}, {}, {}, {})".format(pair.site, case[3], self.__class__.__name__, case[0], self.spats.run.algorithm, pair.failure))
def test_pairs(self):
for alg in algorithms:
if alg == 'native':
continue
self.run_algorithm(alg)
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()
def run_pairs(self):
for case in short_adapter_b_cases:
self.run_case(case)
print("Ran {} adapter_b test cases.".format(len(short_adapter_b_cases)))
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")
class TestOnlyPrefixes(unittest.TestCase):
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.run.collapse_only_prefixes = "T,ACGT,CCA"
self.spats.addTargets("test/cotrans/cotrans_single.fa")
def tearDown(self):
self.spats = None
def pair_for_case(self, case):
pair = Pair()
pair.set_from_data(case[0], case[1], case[2])
return pair
def run_case(self, case):
pair = self.pair_for_case(case)
self.spats.counters.reset()
self.spats.process_pair(pair)
if case[5]:
expect = case[4] if case[5] in self.spats.run.collapse_only_prefixes.split(',') else None
self.assertEqual(expect, pair.site, "PREF res={} != {} ({}, {})".format(pair.site, case[4], self.__class__.__name__, case[0]))
return pair
def test_pairs(self):
for case in prefix_cases:
self.run_case(case)
print("Ran {} prefix test cases.".format(len(cases)))
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 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()
class TestPrefixPairs(unittest.TestCase):
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 tearDown(self):
self.spats = None
def pair_for_case(self, case):
pair = Pair()
pair.set_from_data(case[0], case[1], case[2])
return pair
def run_case(self, case):
pair = self.pair_for_case(case)
self.spats.counters.reset()
self.spats.process_pair(pair)
self.assertEqual(case[3], pair.site, "res={} != {} ({}, {})".format(pair.site, case[3], self.__class__.__name__, case[0]))
if case[4]:
self.assertEqual(1, getattr(self.spats.counters, 'prefix_RRRY_' + case[4]), "prefix {} not counted ({})".format(case[4], case[0]))
return pair
def test_pairs(self):
for case in prefix_cases:
self.run_case(case)
print("Ran {} prefix test cases.".format(len(cases)))
def compare(self):
from spats_shape_seq import Spats
from spats_shape_seq.pair import Pair
json_base = { 'target' : self.config['target'], 'config' : { 'algorithm' : 'find_partial', 'debug' : True }, 'expect' : {}}
spats_fp = Spats(cotrans = self.cotrans)
spats_lookup = Spats(cotrans = self.cotrans)
self._update_run_config(spats_fp.run)
self._update_run_config(spats_lookup.run, json_base['config'])
spats_fp.run.algorithm = 'find_partial'
spats_lookup.run.algorithm = 'lookup'
spats_fp.addTargets(self.config['target'])
spats_lookup.addTargets(self.config['target'])
count = 0
match = 0
with FastFastqParser(self.r1, self.r2) as parser:
total = parser.appx_number_of_pairs()
for batch in parser.iterator(5000):
for item in batch:
pair_fp = Pair()
pair_lookup = Pair()
pair_fp.set_from_data(str(item[0]), item[1], item[2])
pair_lookup.set_from_data(str(item[0]), item[1], item[2])
try:
spats_fp.process_pair(pair_fp)
spats_lookup.process_pair(pair_lookup)
except:
print('Error after {}/{}'.format(match, count))
raise
if (pair_fp.has_site == pair_lookup.has_site):
if not pair_fp.has_site:
count += 1
continue
elif (pair_fp.target.name == pair_lookup.target.name and
pair_fp.end == pair_lookup.end and
pair_fp.site == pair_lookup.site and
pair_fp.mutations == pair_lookup.mutations):
count += 1
match += 1
continue
json_base["id"] = str(item[0])
json_base["R1"] = str(item[1])
json_base["R2"] = str(item[2])
print('After {}/{} matches; mismatched pair: {} != {}\n{}'.format(match, count, pair_fp, pair_lookup,
json.dumps(json_base, sort_keys = True,indent = 4, separators = (',', ': '))))
return
print('{}/{}-{}...'.format(match, count, total))
spats_fp.counters.total_pairs = count
spats_lookup.counters.total_pairs = count
print('All match {}/{}.'.format(match, count))
print(spats_fp._report_counts())
print(spats_lookup._report_counts())
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 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 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 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 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 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 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 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 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 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 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 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 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)
class TestMutPairs(unittest.TestCase):
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 setup_processor(self):
self.spats.run.algorithm = "find_partial"
self.spats.addTargets("test/mut/mut_single.fa")
def tearDown(self):
self.spats = None
def pair_for_case(self, case):
pair = Pair()
pair.set_from_data(case[0], case[1], case[2])
if len(case) > 6:
pair.r1.quality = case[6]
pair.r2.quality = case[7]
else:
pair.r1.quality = 'K' * len(case[1])
pair.r2.quality = 'K' * len(case[2])
return pair
def run_case(self, case):
pair = self.pair_for_case(case)
self.spats.process_pair(pair)
self.assertEqual(case[4], pair.site, "res={} != {} ({}, {}, {})".format(pair.site, case[4], self.__class__.__name__, case[0], pair.failure))
if pair.site is not None:
self.assertEqual(case[3], pair.end, "end={} != {} ({}, {}, {})".format(pair.end, case[3], self.__class__.__name__, case[0], pair.failure))
self.assertEqual(case[5], sorted(pair.mutations) if pair.mutations else pair.mutations, "muts={} != {} ({}, {}, {})".format(pair.mutations, case[5], self.__class__.__name__, case[0], pair.failure))
return pair
def cases(self):
return cotrans_cases if self.spats.run.cotrans else cases
def test_pairs(self):
self.spats.run.pair_length = len(cases[0][1])
for case in self.cases():
self.run_case(case)
print("Ran {} pair->site cases.".format(len(cases)))
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)
class TestPanelPairs(unittest.TestCase):
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 tearDown(self):
self.spats = None
def test_single_R1_match_with_adapter_multiple_without(self):
pair = Pair()
pair.set_from_data('M02465:8:000000000-A5D', 'CCCGCCGTCCTTGGTGCCCGAGTGAGATCGGAAGA','CACTCGGGCACCAAGGACGGCGGGAGATCGGAAGA')
self.spats.run.debug = True
self.spats.run.algorithm = "find_partial"
self.spats.process_pair(pair)
self.assertEqual(None, pair.target)
self.assertEqual(1, self.spats.counters.multiple_R1_match)
class TestOverlap(unittest.TestCase):
def tearDown(self):
self.spats = None
def pair_for_case(self, case):
pair = Pair()
pair.set_from_data(case[0], case[1], case[2])
return pair
def run_case(self, case):
pair = self.pair_for_case(case)
print('running: {} / {}'.format(case[0], self.spats.run.algorithm))
self.spats.process_pair(pair)
self.assertEqual(
case[3], pair.site, "site res={} != {} ({}, {}, {}, {})".format(
pair.site, case[3], self.__class__.__name__, case[0],
self.spats.run.algorithm, pair.failure))
self.assertEqual(
case[4], pair.failure, "failure res={} != {} ({}, {}, {})".format(
pair.failure, case[4], self.__class__.__name__, case[0],
self.spats.run.algorithm))
def test_pairs(self):
for alg in algorithms:
if alg == 'native':
continue
self.run_algorithm(alg)
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 run_pairs(self):
for case in overlap_cases:
self.run_case(case)
print("Ran {} overlap test cases.".format(len(overlap_cases)))
class TestPanelPairs(unittest.TestCase):
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 tearDown(self):
self.spats = None
def test_single_R1_match_with_adapter_multiple_without(self):
pair = Pair()
pair.set_from_data('M02465:8:000000000-A5D',
'CCCGCCGTCCTTGGTGCCCGAGTGAGATCGGAAGA',
'CACTCGGGCACCAAGGACGGCGGGAGATCGGAAGA')
self.spats.run.debug = True
self.spats.run.algorithm = "find_partial"
self.spats.process_pair(pair)
self.assertEqual(None, pair.target)
self.assertEqual(1, self.spats.counters.multiple_R1_match)
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 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)
class TestOverlap(unittest.TestCase):
def tearDown(self):
self.spats = None
def pair_for_case(self, case):
pair = Pair()
pair.set_from_data(case[0], case[1], case[2])
return pair
def run_case(self, case):
pair = self.pair_for_case(case)
print('running: {} / {}'.format(case[0], self.spats.run.algorithm))
self.spats.process_pair(pair)
self.assertEqual(case[3], pair.site, "site res={} != {} ({}, {}, {}, {})".format(pair.site, case[3], self.__class__.__name__, case[0], self.spats.run.algorithm, pair.failure))
self.assertEqual(case[4], pair.failure, "failure res={} != {} ({}, {}, {})".format(pair.failure, case[4], self.__class__.__name__, case[0], self.spats.run.algorithm))
def test_pairs(self):
for alg in algorithms:
if alg == 'native':
continue
self.run_algorithm(alg)
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 run_pairs(self):
for case in overlap_cases:
self.run_case(case)
print("Ran {} overlap test cases.".format(len(overlap_cases)))
class TestPairsPartial(unittest.TestCase):
def setUp(self):
self.spats = Spats()
self.spats.run.cotrans = True
self.spats.run.cotrans_linker = 'CTGACTCGGGCACCAAGGAC'
self.setup_processor()
self.spats.addTargets("test/cotrans/cotrans_single.fa")
def setup_processor(self):
self.spats.run.algorithm = "find_partial"
def tearDown(self):
self.spats = None
def pair_for_case(self, case):
pair = Pair()
pair.set_from_data(case[0], case[1], case[2])
return pair
def run_case(self, case):
pair = self.pair_for_case(case)
self.spats.process_pair(pair)
self.assertEqual(case[4], pair.site, "res={} != {} ({}, {})".format(pair.site, case[4], self.__class__.__name__, case[0]))
if pair.site is not None:
self.assertEqual(case[3], pair.end)
return pair
def test_pairs(self):
self.spats.run.pair_length = len(cases[0][1])
if not self.spats._processor.exists():
# just ignore the native test if it's not available
self.assertEqual("native", self.spats.run.algorithm)
return
for case in cases:
self.run_case(case)
print("Ran {} pair->site cases.".format(len(cases)))
class TestMutPairs(unittest.TestCase):
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 setup_processor(self):
self.spats.run.algorithm = "find_partial"
self.spats.addTargets("test/mut/mut_single.fa")
def tearDown(self):
self.spats = None
def pair_for_case(self, case):
pair = Pair()
pair.set_from_data(case[0], case[1], case[2])
if len(case) > 6:
pair.r1.quality = case[6]
pair.r2.quality = case[7]
else:
class TestShortAdapterB(unittest.TestCase):
def tearDown(self):
self.spats = None
def pair_for_case(self, case):
pair = Pair()
pair.set_from_data(case[0], case[1], case[2])
return pair
def run_case(self, case):
pair = self.pair_for_case(case)
print('running: {} / {}'.format(case[0], self.spats.run.algorithm))
self.spats.process_pair(pair)
self.assertEqual(
case[3], pair.site, "site res={} != {} ({}, {}, {}, {})".format(
pair.site, case[3], self.__class__.__name__, case[0],
self.spats.run.algorithm, pair.failure))
def test_pairs(self):
for alg in algorithms:
if alg == 'native':
continue
self.run_algorithm(alg)
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()
def run_pairs(self):
for case in short_adapter_b_cases:
self.run_case(case)
print("Ran {} adapter_b test cases.".format(
len(short_adapter_b_cases)))
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 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")
class TestPairs(unittest.TestCase):
def setUp(self):
from spats_shape_seq import Spats
self.spats = Spats()
self.spats.addTargets("test/5s/5s.fa")
def tearDown(self):
self.spats = None
def pair_for_case(self, case):
pair = Pair()
pair.set_from_data(case[0], case[1], case[2])
return pair
def run_case(self, case):
pair = self.pair_for_case(case)
self.spats.process_pair(pair)
self.assertEqual(
case[3], pair.site,
"res={} != {} ({}, {})".format(pair.site, case[3],
self.__class__.__name__, case[0]))
return pair
def test_pairs(self):
for case in cases:
self.run_case(case)
print("Ran {} pair->site cases.".format(len(cases)))
def test_find_partial_weird_case(self):
pair = Pair()
pair.set_from_data("x", 'CTCAGTCCTTGGTGCCCGAGTCAGGATCGGAAGAG',
'TGACTCGGGCACCAAAGACTGAGAGATCGGAAGAG')
self.spats.process_pair(pair)
print("{} / {}".format(pair.site, pair.failure))
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)
class TestPairs(unittest.TestCase):
def setUp(self):
from spats_shape_seq import Spats
self.spats = Spats()
self.spats.addTargets("test/5s/5s.fa")
def tearDown(self):
self.spats = None
def pair_for_case(self, case):
pair = Pair()
pair.set_from_data(case[0], case[1], case[2])
return pair
def run_case(self, case):
pair = self.pair_for_case(case)
self.spats.process_pair(pair)
self.assertEqual(case[3], pair.site, "res={} != {} ({}, {})".format(pair.site, case[3], self.__class__.__name__, case[0]))
return pair
def test_pairs(self):
for case in cases:
self.run_case(case)
print("Ran {} pair->site cases.".format(len(cases)))
def test_find_partial_weird_case(self):
pair = Pair()
pair.set_from_data("x", 'CTCAGTCCTTGGTGCCCGAGTCAGGATCGGAAGAG', 'TGACTCGGGCACCAAAGACTGAGAGATCGGAAGAG')
self.spats.process_pair(pair)
print("{} / {}".format(pair.site, pair.failure))
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.addTargets("test/5s/5s.fa")
case[3] = 135
self.run_case(case)
class TestPairsWithU(TestPairs):
def setUp(self):
from spats_shape_seq import Spats
self.spats = Spats()
self.spats.addTargets("test/5s/5su.fa")
class TestPairsWithU(TestPairs):
def setUp(self):
from spats_shape_seq import Spats
self.spats = Spats()
self.spats.addTargets("test/5s/5su.fa")