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import sys
import os
import inspect
basedir = os.path.dirname(__file__)
sys.path.insert(0, basedir + '/../src/')
#sys.path.insert(0, '/home/travis/build/mad-lab/transit/src/')
import shutil
import unittest
from transit_test import *
from pytpp.tpp_tools import cleanargs
import pytpp.__main__
tppMain = pytpp.__main__.main
def get_bwa():
if (os.path.exists("/usr/bin/bwa")):
return "/usr/bin/bwa"
elif (os.path.exists("/usr/local/bin/bwa")):
return "/usr/local/bin/bwa"
return ""
bwa_path = get_bwa()
NOFLAG_PRIMER = [
"# TA_sites: 74605",
"# TAs_hit: 914",
"# mapped_reads (both R1 and R2 map into genome, and R2 has a proper barcode): 967",
"# density: 0.012",
"# NZ_mean (among templates): 1.0",
"# FR_corr (Fwd templates vs. Rev templates): 0.019",
"# transposon type: Himar1",
"# protocol type: Sassetti",
"# primer_matches: 8 reads (0.8%) contain CTAGAGGGCCCAATTCGCCCTATAGTGAGT (Himar1)"
]
MME1_PROTOCOL = [
"# TA_sites: 74605",
"# TAs_hit: 34",
"# mapped_reads (both R1 and R2 map into genome, and R2 has a proper barcode): 967",
"# density: 0.000",
"# NZ_mean (among templates): 1.0",
"# transposon type: Himar1",
"# protocol type: Mme1",
"# primer_matches: 8 reads (0.8%) contain CTAGAGGGCCCAATTCGCCCTATAGTGAGT (Himar1)"
]
FLAG_PRIMER = [
"# TA_sites: 74605",
"# TAs_hit: 914",
"# bwa flags: -k 1",
"# mapped_reads (both R1 and R2 map into genome, and R2 has a proper barcode): 967",
"# density: 0.012",
"# NZ_mean (among templates): 1.0",
"# FR_corr (Fwd templates vs. Rev templates): 0.019"
]
MULTICONTIG = [
"# TA_sites:",
"# a: 89994",
"# b: 646",
"# c: 664",
"# TAs_hit:",
"# a: 63",
"# b: 0",
"# c: 0",
"# density:",
"# a: 0.001",
"# b: 0.000",
"# c: 0.000",
"# max_count (among templates):",
"# a: 1",
"# b: 0",
"# c: 0",
"# max_site (coordinate):",
"# a: 4977050",
"# b: 57441",
"# c: 38111" ]
MULTICONTIG_AUTO_IDS = [
"# TA_sites:",
"# 1: 89994",
"# 2: 646",
"# 3: 664",
"# TAs_hit:",
"# 1: 63",
"# 2: 0",
"# 3: 0",
"# density:",
"# 1: 0.001",
"# 2: 0.000",
"# 3: 0.000",
"# max_count (among templates):",
"# 1: 1",
"# 2: 0",
"# 3: 0",
"# max_site (coordinate):",
"# 1: 4977050",
"# 2: 57441",
"# 3: 38111" ]
def get_stats(path):
for line in open(path):
if line.startswith("#"):
print(line[1:].split(":"))
continue
break
return [float(x) if (type(x) != list) else x for x in tmp[2:]]
def verify_stats(stats_file, expected):
with open(stats_file) as f:
lines = set([line.strip() for line in f])
diff = set(expected) - lines
if (len(diff) == 0):
return True
print("Diff: ", diff)
return False
class TestTPP(TransitTestCase):
# since I changed default BWA mode from 'mem' back to 'aln', specify mem to make the output shown above (TRI, 12/2/24)
@unittest.skipUnless(os.path.exists("../misc/test"), "requires local data file")
def test_tpp_noflag_primer(self):
(args, kwargs) = cleanargs(["-bwa", bwa_path, "-ref", h37fna, "-reads1", reads1, "-output", tpp_output_base, "-protocol", "sassetti" , "-bwa-alg", "mem"])
tppMain(*args, **kwargs)
self.assertTrue(verify_stats("{0}.tn_stats".format(tpp_output_base), NOFLAG_PRIMER))
@unittest.skipUnless(os.path.exists("../misc/test"), "requires local data file")
def test_tpp_flag_primer(self):
(args, kwargs) = cleanargs(["-bwa", bwa_path, "-ref", h37fna, "-reads1", reads1, "-output", tpp_output_base, "-himar1", "-flags", "-k 1" , "-bwa-alg", "mem"])
tppMain(*args, **kwargs)
self.assertTrue(verify_stats("{0}.tn_stats".format(tpp_output_base), FLAG_PRIMER))
@unittest.skipUnless(os.path.exists("../misc/test"), "requires local data file")
def test_tpp_protocol_mme1(self):
(args, kwargs) = cleanargs(["-bwa", bwa_path, "-ref", h37fna, "-reads1", reads1, "-output", tpp_output_base, "-protocol", "Mme1", "-bwa-alg", "mem"])
tppMain(*args, **kwargs)
self.assertTrue(verify_stats("{0}.tn_stats".format(tpp_output_base), MME1_PROTOCOL))
@unittest.skipUnless(len(bwa_path) > 0, "requires BWA")
def test_tpp_multicontig_empty_prefix(self):
(args, kwargs) = cleanargs(["-bwa", bwa_path, "-ref", test_multicontig, "-reads1", test_multicontig_reads1, "reads2", test_multicontig_reads2, "-output", tpp_output_base, "-replicon-ids", "a,b,c", "-maxreads", "10000", "-primer", "" , "-bwa-alg", "mem"])
tppMain(*args, **kwargs)
self.assertTrue(verify_stats("{0}.tn_stats".format(tpp_output_base), MULTICONTIG))
@unittest.skipUnless(len(bwa_path) > 0, "requires BWA")
def test_tpp_multicontig_auto_replicon_ids(self):
(args, kwargs) = cleanargs(["-bwa", bwa_path, "-ref", test_multicontig, "-reads1", test_multicontig_reads1, "reads2", test_multicontig_reads2, "-output", tpp_output_base, "-replicon-ids", "auto", "-maxreads", "10000", "-primer", "" , "-bwa-alg", "mem"])
tppMain(*args, **kwargs)
self.assertTrue(verify_stats("{0}.tn_stats".format(tpp_output_base), MULTICONTIG_AUTO_IDS))
if __name__ == '__main__':
unittest.main()
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