def pair(self):
pair = Pair()
pair.set_from_data(self.id, self.r1, self.r2)
if self.r1_quality:
pair.r1.quality = self.r1_quality
pair.r2.quality = self.r2_quality
return pair
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 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)
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 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 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 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 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 rdiff_func(db_path, rs1_name, rs2_name, diag_spats=None):
from spats_shape_seq.db import PairDB
from spats_shape_seq.diagram import diagram
from spats_shape_seq.pair import Pair
db = PairDB(db_path)
n1 = db.num_results(rs1_name)
n2 = db.num_results(rs2_name)
print "{}: {} results / {}: {} results".format(rs1_name, n1, rs2_name,
n2)
if not n1 or not n2:
print "** Abort."
exit(1)
print "Diffs:"
ours_only = []
theirs_only = []
differences = []
for r in db.differing_results(rs1_name, rs2_name):
if r[4] == -1:
assert (r[9] != -1)
theirs_only.append(r)
elif r[9] == -1:
ours_only.append(r)
else:
differences.append(r)
all_lists = [ours_only, theirs_only, differences]
for l in all_lists:
reasons = {}
for r in l:
key = r[7] or r[12] or "different values"
assert (key)
rlist = reasons.get(key)
if not rlist:
rlist = []
reasons[key] = rlist
rlist.append(r)
for reason, rlist in reasons.iteritems():
for r in rlist[:min(len(rlist), 10)]:
print " {}:{} s{}m{} ({}) -- {}:{} s{}m{} ({}) ([ '{}', '{}', '{}', {}, {}, [ {} ] ])".format(
r[3] or 'x', r[4], r[5], r[6], r[7] or "OK", r[8] or 'x',
r[9], r[10], r[11], r[12] or "OK", r[0], r[1], r[2], r[4],
r[5], "" if -1 == r[6] else r[6])
if len(rlist) > 0:
print "... {} total.".format(len(rlist))
if diag_spats:
pair = Pair()
pair.set_from_data(str(r[0]), str(r[1]), str(r[2]))
diag_spats.process_pair(pair)
print diagram(pair, diag_spats.run)
print "{} total diffs.".format(sum(map(len, all_lists)))
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 rdiff_func(db_path, rs1_name, rs2_name, diag_spats = None):
from spats_shape_seq.db import PairDB
from spats_shape_seq.diagram import diagram
from spats_shape_seq.pair import Pair
db = PairDB(db_path)
n1 = db.num_results(rs1_name)
n2 = db.num_results(rs2_name)
print "{}: {} results / {}: {} results".format(rs1_name, n1, rs2_name, n2)
if not n1 or not n2:
print "** Abort."
exit(1)
print "Diffs:"
ours_only = []
theirs_only = []
differences = []
for r in db.differing_results(rs1_name, rs2_name):
if r[4] == -1:
assert(r[9] != -1)
theirs_only.append(r)
elif r[9] == -1:
ours_only.append(r)
else:
differences.append(r)
all_lists = [ ours_only, theirs_only, differences ]
for l in all_lists:
reasons = {}
for r in l:
key = r[7] or r[12] or "different values"
assert(key)
rlist = reasons.get(key)
if not rlist:
rlist = []
reasons[key] = rlist
rlist.append(r)
for reason, rlist in reasons.iteritems():
for r in rlist[:min(len(rlist), 10)]:
print " {}:{} s{}m{} ({}) -- {}:{} s{}m{} ({}) ([ '{}', '{}', '{}', {}, {}, [ {} ] ])".format(r[3] or 'x', r[4], r[5], r[6], r[7] or "OK",
r[8] or 'x', r[9], r[10], r[11], r[12] or "OK",
r[0], r[1], r[2], r[4], r[5], "" if -1 == r[6] else r[6] )
if len(rlist) > 0:
print "... {} total.".format(len(rlist))
if diag_spats:
pair = Pair()
pair.set_from_data(str(r[0]), str(r[1]), str(r[2]))
diag_spats.process_pair(pair)
print diagram(pair, diag_spats.run)
print "{} total diffs.".format(sum(map(len, all_lists)))
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 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 "-----------------------------"
def align_pairs():
from spats_shape_seq.pair import Pair
from spats_shape_seq.target import Targets
from spats_shape_seq.util import reverse_complement, AlignmentParams
from spats_shape_seq.mask import Mask, match_mask_optimized, base_similarity_ind
target_seq = "GGACCCGATGCCGGACGAAAGTCCGCGCATCAACTATGCCTCTACCTGCTTCGGCCGATAAAGCCGACGATAATACTCCCAAAGCCC" # HairpinC_SS2
r1_seq = "GGGTGAGCGTGCTTTGGGAGTATTATCGTCGGCTTTATCGGCCGAAGCAGGTAGTGCATAGTTGATGCTCGGACTTTCG"
r2_seq = "GGACCCGATGCCGGACGAAAGTCCGAGCATCAACTATGCCCTACCTGCTTCGGCCGATAAAGCCAAAAGACGATAAT"
pair = Pair()
pair.set_from_data("TEST_PAIR", r1_seq, r2_seq)
targets = Targets()
targets.minimum_match_length = 10
targets.addTarget("TEST_TARGET", target_seq, 0)
targets.index()
mask = match_mask_optimized(pair.r1.original_seq)
assert (mask)
pair.set_mask(Mask(mask))
target = pair.r1.find_in_targets(targets)
pair.target = pair.r2.find_in_targets(targets, force_target=target)
assert (pair.matched)
masklen = pair.mask.length()
adapter_t = "AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT"
r2suffix = reverse_complement(
pair.r1.original_seq[:masklen]) + reverse_complement(adapter_t)
simfn = lambda nt1, nt2: base_similarity_ind(nt1, nt2, 3, 2, 1.5)
ap = AlignmentParams(simfn, 5, 1)
pair.r2.align_with_target(pair.target, ap, r2suffix)
r2_adapter_trim = max(
0, pair.r2.match_index + pair.r2.match_len - pair.target.n)
r1_adapter_trim = pair.r1.seq_len - (pair.target.n - pair.r2.match_index)
if r1_adapter_trim > 0:
pair.r1.rtrim += r1_adapter_trim
pair.r1.match_start -= r1_adapter_trim
pair.r1.align_with_target(pair.target, ap)
exit(0)
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)
def align_pairs():
from spats_shape_seq.pair import Pair
from spats_shape_seq.target import Targets
from spats_shape_seq.util import reverse_complement, AlignmentParams
from spats_shape_seq.mask import Mask, match_mask_optimized, base_similarity_ind
target_seq = "GGACCCGATGCCGGACGAAAGTCCGCGCATCAACTATGCCTCTACCTGCTTCGGCCGATAAAGCCGACGATAATACTCCCAAAGCCC" # HairpinC_SS2
r1_seq = "GGGTGAGCGTGCTTTGGGAGTATTATCGTCGGCTTTATCGGCCGAAGCAGGTAGTGCATAGTTGATGCTCGGACTTTCG"
r2_seq = "GGACCCGATGCCGGACGAAAGTCCGAGCATCAACTATGCCCTACCTGCTTCGGCCGATAAAGCCAAAAGACGATAAT"
pair = Pair()
pair.set_from_data("TEST_PAIR", r1_seq, r2_seq)
targets = Targets()
targets.minimum_match_length = 10
targets.addTarget("TEST_TARGET", target_seq, 0)
targets.index()
mask = match_mask_optimized(pair.r1.original_seq)
assert(mask)
pair.set_mask(Mask(mask))
target = pair.r1.find_in_targets(targets)
pair.target = pair.r2.find_in_targets(targets, force_target = target)
assert(pair.matched)
masklen = pair.mask.length()
adapter_t = "AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT"
r2suffix = reverse_complement(pair.r1.original_seq[:masklen]) + reverse_complement(adapter_t)
simfn = lambda nt1, nt2: base_similarity_ind(nt1, nt2, 3, 2, 1.5)
ap = AlignmentParams(simfn, 5, 1)
pair.r2.align_with_target(pair.target, ap, r2suffix)
r2_adapter_trim = max(0, pair.r2.match_index + pair.r2.match_len - pair.target.n)
r1_adapter_trim = pair.r1.seq_len - (pair.target.n - pair.r2.match_index)
if r1_adapter_trim > 0:
pair.r1.rtrim += r1_adapter_trim
pair.r1.match_start -= r1_adapter_trim
pair.r1.align_with_target(pair.target, ap)
exit(0)
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 processed_pair(self, matched_pair):
pair = Pair()
pair.set_from_data(matched_pair.identifier, matched_pair.r1, matched_pair.r2, matched_pair.multiplicity)
self.ui.processor.process_pair_detail(pair)
return pair
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 pair_for_case(self, case):
pair = Pair()
pair.set_from_data(case[0], case[1], case[2])
return pair