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
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)))
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 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 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 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)
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)
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 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 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)
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)
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)
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 test_tags():
bp = "/Users/jbrink/mos/tasks/1RwIBa/tmp/5sq_dev/"
from spats_shape_seq import Spats
s = Spats()
from spats_shape_seq.tag import TagProcessor
s.run._processor_class = TagProcessor
#from spats_shape_seq.target import Targets
#s.addTargets(bp + "5S.fa")
s.addTarget("5s", "GGATGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCTGACTCGGGCACCAAGGAC")
#s.addTarget("rc(5s)", "GTCCTTGGTGCCCGAGTCAGATGCCTGGCAGTTCCCTACTCTCGCATGGGGAGACCCCACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGACCACCGCGCTACGGCCGCCAGGCATCC")
#s.addTarget("adapter_t", s.run.adapter_t)
#s.addTarget("adapter_b", s.run.adapter_b)
#s._targets._index_word_length = 8
#s._targets._minimum_length = 8
#s.addTarget("adapter_t_rc", reverse_complement(s.run.adapter_t))
#s.addTarget("adapter_b_rc", reverse_complement(s.run.adapter_b))
p = s._processor
p.addTagTarget("5s", "GGATGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCTGACTCGGGCACCAAGGAC")
p.addTagTarget("5s_rc", "GTCCTTGGTGCCCGAGTCAGATGCCTGGCAGTTCCCTACTCTCGCATGGGGAGACCCCACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGACCACCGCGCTACGGCCGCCAGGCATCC")
from spats_shape_seq.util import reverse_complement
p.addTagTarget("adapter_t_rc", reverse_complement(s.run.adapter_t))
p.addTagTarget("adapter_b", s.run.adapter_b)
from spats_shape_seq.pair import Pair
cases = [
[ "1101:20069:1063", "TTTAGTCCTTGGTGCCCGAGTCAGATGCCTGGCAG", "TCCCACCTGACCCCATGCCGAACTCAGAAGTGAAA" ],
[ "1101:11562:1050", "AAACGTCCTTGGTGCCCGAGTCAGATGCCTGGCAG", "CCACCTGACCCCATGCCGAACTCAGAAGTGAAACG" ],
[ "21189", "TTTGGTCCTTGGTGCCCGAGTCAGAGATCGGAAGA", "CTGACTCGGGCACCAAGGACCAAAAGATCGGAAGA" ],
[ "1101:12888:8140", "GGATGTCCTTGGTGCCCGAGTCAGATGCCAGATCG", "GGCATCTGACTCGGGCACCAAGGACATACAGATCG" ],
[ "18333", "GAGTGTCCTTGGTGCCCGAGTCAGTGGTAGATCGG", "ACCACTGACTCGGGCACCAAGGACACTCAGATCGG" ],
]
pair = Pair()
for case in cases:
pair.set_from_data(case[0], case[1], case[2])
s.process_pair(pair)
print pair.r1.original_seq
print pair.r1.tags
print pair.r2.original_seq
print pair.r2.tags
print "-----------------------------"
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 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 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)))
def _show_case(self, test_case):
from spats_shape_seq import Spats
from spats_shape_seq.diagram import diagram
alg = test_case.run_opts.get('algorithm')
algs = [ alg ] if alg else test_case.run_opts.get('algorithms', [ 'find_partial', 'lookup' ])
for algorithm in algs:
spats = Spats()
spats.run.algorithm = algorithm
for key, value in test_case.run_opts.items():
if str(key) == 'algorithms':
continue
if isinstance(value, unicode):
value = str(value)
if not hasattr(spats.run, key):
raise Exception('Invalid run_opt: {}'.format(key))
setattr(spats.run, key, value)
for name, seq in test_case.targets.iteritems():
spats.addTarget(name, seq)
pair = test_case.pair()
if len(algs) > 1:
print('\n[[ ALGORITHM: {} ]]'.format(algorithm))
spats.process_pair(pair)
if test_case.comment:
print('Comment: {}'.format(test_case.comment))
print(diagram(pair, spats.run))
if test_case.expect:
# should mirror `_check_expect` in test_harness.py...
expects = test_case.expect
fail = False
try:
if expects['site'] is None:
if pair.site is not None:
raise Exception("pair.site={} when expecting none.".format(pair.site))
else:
if pair.site is None:
raise Exception("pair.site is none when expecting {}.".format(expects['site']))
if pair.site != expects['site']:
raise Exception("pair.site={} != expect.site={}".format(pair.site, expects['site']))
if 'end' in expects and pair.end != expects['end']:
raise Exception("pair.end={} != expect.end={}".format(pair.end, expects['end']))
if 'muts' in expects:
if expects['muts'] is not None and len(expects['muts']) > 0:
if not sorted(expects['muts']) == (sorted(pair.mutations) if pair.mutations else pair.mutations):
raise Exception("mismatching mutations: expected={}, pair.mutations={}".format(expects['muts'], pair.mutations))
else:
if not (pair.mutations is None or len(pair.mutations) == 0):
raise Exception("unexpected mutations: {}".format(pair.mutations))
if 'r1_indels' in expects:
r1inds = objdict_to_dict(pair.r1.indels)
if expects['r1_indels']:
if expects['r1_indels'] != r1inds:
raise Exception("mismatching R1 indels: expected={}, pair.r1.indels={}".format(expects['r1_indels'], r1inds))
elif pair.r1.indels:
raise Exception("unexpected R1 indels: pair.r1.indels={}".format(pair.r1.indels))
if 'r2_indels' in expects:
r2inds = objdict_to_dict(pair.r2.indels)
if expects['r2_indels']:
if expects['r2_indels'] != r2inds:
raise Exception("mismatching R2 indels: expected={}, pair.r2.indels={}".format(expects['r2_indels'], r2inds))
elif pair.r2.indels:
raise Exception("unexpected R2 indels: pair.r2.indels={}".format(r2inds))
if 'counters' in expects:
for counter, value in expects['counters'].iteritems():
if getattr(spats.counters, str(counter)) != value:
raise Exception("counter '{}' value off: expected={} != got={}".format(counter, value, getattr(spats.counters, counter)))
if 'pair.target' in expects:
tname = pair.target.name if pair.target else None
if tname != expects['pair.target']:
raise Exception("pair.target={} != expect.pair.target={}".format(tname, expects['pair.target']))
except Exception as e:
print('FAIL: {}'.format(e))
sys.exit(1)
print('PASS')
class SpatsTestCase(unittest.TestCase):
def __init__(self, test_set, case):
super(TestHarness.SpatsTestCase, self).__init__()
self.test_set = test_set
self.case = case
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 tearDown(self):
self.spats = None
def runTest(self):
for algorithm in self.test_set.algorithms:
self.spats.reset_processor(
) # Necessary to change algorithm (which determines the processor)
self.spats.run.algorithm = algorithm
self._run_case(self.case)
def _run_case(self, case):
pair = case.pair()
self.spats.counters.reset()
self.spats.process_pair(pair)
self._check_expects(case, pair)
def _check_expects(self, case, pair):
expects = case.expect
msg = "testset='{}', test id='{}', algorithm='{}' failed: ".format(
self.test_set.name, case.id, self.spats.run.algorithm)
if expects['site'] is None:
self.assertIs(
pair.site, None, msg +
"pair.site={} when expecting none.".format(pair.site))
else:
self.assertIsNot(
pair.site, None,
msg + "pair.site is none when expecting {}.".format(
expects['site']))
self.assertEqual(
expects['site'], pair.site,
msg + "pair.site={} != expect.site={}".format(
pair.site, expects['site']))
if 'end' in expects:
self.assertEqual(
expects['end'], pair.end,
msg + "pair.end={} != expect.end={}".format(
pair.end, expects['end']))
if 'muts' in expects:
if expects['muts'] is not None and len(
expects['muts']) > 0:
self.assertEqual(
sorted(expects['muts']),
sorted(pair.mutations)
if pair.mutations else pair.mutations, msg +
"mismatching mutations: expected={}, pair.mutations={}"
.format(expects['muts'], pair.mutations))
else:
self.assertTrue(
pair.mutations is None or len(pair.mutations) == 0,
msg +
"unexpected mutations: {}".format(pair.mutations))
if 'r1_indels' in expects:
r1inds = dict(
zip(map(str, pair.r1.indels.keys()),
map(vars, pair.r1.indels.values())))
if expects['r1_indels']:
self.assertEqual(expects['r1_indels'], r1inds)
else:
self.assertTrue(
not pair.r1.indels,
msg + "unexpected R1 indels: {}".format(r1inds))
if 'r2_indels' in expects:
r2inds = dict(
zip(map(str, pair.r2.indels.keys()),
map(vars, pair.r2.indels.values())))
if expects['r2_indels']:
self.assertEqual(expects['r2_indels'], r2inds)
else:
self.assertTrue(
not pair.r2.indels,
msg + "unexpected R2 indels: {}".format(r2inds))
if 'counters' in expects:
for counter, value in expects['counters'].iteritems():
self.assertEqual(
getattr(self.spats.counters,
str(counter)), value, msg +
"counter '{}' value off: expected={} != got={}".format(
counter, value,
getattr(self.spats.counters, counter)))
if 'pair.target' in expects:
tname = pair.target.name if pair.target else None
self.assertEqual(
tname, expects['pair.target'],
msg + "pair.target={} != expect.pair.target={}".format(
tname, expects['pair.target']))
def test_tags():
bp = "/Users/jbrink/mos/tasks/1RwIBa/tmp/5sq_dev/"
from spats_shape_seq import Spats
s = Spats()
from spats_shape_seq.tag import TagProcessor
s.run._processor_class = TagProcessor
#from spats_shape_seq.target import Targets
#s.addTargets(bp + "5S.fa")
s.addTarget(
"5s",
"GGATGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCTGACTCGGGCACCAAGGAC"
)
#s.addTarget("rc(5s)", "GTCCTTGGTGCCCGAGTCAGATGCCTGGCAGTTCCCTACTCTCGCATGGGGAGACCCCACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGACCACCGCGCTACGGCCGCCAGGCATCC")
#s.addTarget("adapter_t", s.run.adapter_t)
#s.addTarget("adapter_b", s.run.adapter_b)
#s._targets._index_word_length = 8
#s._targets._minimum_length = 8
#s.addTarget("adapter_t_rc", reverse_complement(s.run.adapter_t))
#s.addTarget("adapter_b_rc", reverse_complement(s.run.adapter_b))
p = s._processor
p.addTagTarget(
"5s",
"GGATGCCTGGCGGCCGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCTGACTCGGGCACCAAGGAC"
)
p.addTagTarget(
"5s_rc",
"GTCCTTGGTGCCCGAGTCAGATGCCTGGCAGTTCCCTACTCTCGCATGGGGAGACCCCACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGACCACCGCGCTACGGCCGCCAGGCATCC"
)
from spats_shape_seq.util import reverse_complement
p.addTagTarget("adapter_t_rc", reverse_complement(s.run.adapter_t))
p.addTagTarget("adapter_b", s.run.adapter_b)
from spats_shape_seq.pair import Pair
cases = [
[
"1101:20069:1063", "TTTAGTCCTTGGTGCCCGAGTCAGATGCCTGGCAG",
"TCCCACCTGACCCCATGCCGAACTCAGAAGTGAAA"
],
[
"1101:11562:1050", "AAACGTCCTTGGTGCCCGAGTCAGATGCCTGGCAG",
"CCACCTGACCCCATGCCGAACTCAGAAGTGAAACG"
],
[
"21189", "TTTGGTCCTTGGTGCCCGAGTCAGAGATCGGAAGA",
"CTGACTCGGGCACCAAGGACCAAAAGATCGGAAGA"
],
[
"1101:12888:8140", "GGATGTCCTTGGTGCCCGAGTCAGATGCCAGATCG",
"GGCATCTGACTCGGGCACCAAGGACATACAGATCG"
],
[
"18333", "GAGTGTCCTTGGTGCCCGAGTCAGTGGTAGATCGG",
"ACCACTGACTCGGGCACCAAGGACACTCAGATCGG"
],
]
pair = Pair()
for case in cases:
pair.set_from_data(case[0], case[1], case[2])
s.process_pair(pair)
print pair.r1.original_seq
print pair.r1.tags
print pair.r2.original_seq
print pair.r2.tags
print "-----------------------------"