def test_mate_pair_checker():
'It test the mate pair function'
# with equal seqs but the last ones
file1 = os.path.join(TEST_DATA_DIR, 'pairend1.sfastq')
file2 = os.path.join(TEST_DATA_DIR, 'pairend2.sfastq')
fwd_seqs = read_seqrecords([open(file1)], 'fastq')
rev_seqs = read_seqrecords([open(file2)], 'fastq')
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = 'fastq'
seqs = flat_zip_longest(fwd_seqs, rev_seqs)
match_pairs(seqs, out_fhand, orphan_out_fhand, out_format)
output = out_fhand.getvalue()
assert '@seq1:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG' in output
assert '@seq2:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in output
orp = orphan_out_fhand.getvalue()
assert '@seq8:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in orp
# with the firsts seqs different
file1 = os.path.join(TEST_DATA_DIR, 'pairend1.sfastq')
file2 = os.path.join(TEST_DATA_DIR, 'pairend3.sfastq')
fwd_seqs = read_seqrecords([open(file1)], 'fastq')
rev_seqs = read_seqrecords([open(file2)], 'fastq')
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = 'fastq'
seqs = flat_zip_longest(fwd_seqs, rev_seqs)
match_pairs(seqs, out_fhand, orphan_out_fhand, out_format)
output = out_fhand.getvalue()
assert '@seq4:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG' in output
assert '@seq5:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in output
orp = orphan_out_fhand.getvalue()
assert '@seq1:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG' in orp
assert '@seq3:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in orp
assert '@seq6:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in orp
file1 = os.path.join(TEST_DATA_DIR, 'pairend4.sfastq')
file2 = os.path.join(TEST_DATA_DIR, 'pairend2.sfastq')
fwd_seqs = read_seqrecords([open(file1)], 'fastq')
rev_seqs = read_seqrecords([open(file2)], 'fastq')
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = 'fastq'
seqs = flat_zip_longest(fwd_seqs, rev_seqs)
match_pairs(seqs, out_fhand, orphan_out_fhand, out_format)
output = out_fhand.getvalue()
assert '@seq8:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG' in output
assert '@seq8:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in output
orp = orphan_out_fhand.getvalue()
assert '@seq1:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in orp
assert '@seq2:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in orp
def test_pair_matcher(self):
'It test the pair matcher function'
# with equal seqs but the last ones
file1 = os.path.join(TEST_DATA_DIR, 'pairend1.sfastq')
file2 = os.path.join(TEST_DATA_DIR, 'pairend2.sfastq')
fwd_seqs = read_seqs([open(file1)], file_format='fastq')
rev_seqs = read_seqs([open(file2)], file_format='fastq')
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = 'fastq'
seqs = flat_zip_longest(fwd_seqs, rev_seqs)
match_pairs(seqs, out_fhand, orphan_out_fhand, out_format)
output = out_fhand.getvalue()
assert '@seq1:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG' in output
assert '@seq2:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in output
orp = orphan_out_fhand.getvalue()
assert '@seq8:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in orp
# with the firsts seqs different
file1 = os.path.join(TEST_DATA_DIR, 'pairend1.sfastq')
file2 = os.path.join(TEST_DATA_DIR, 'pairend3.sfastq')
fwd_seqs = read_seqs([open(file1)], 'fastq')
rev_seqs = read_seqs([open(file2)], 'fastq')
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = 'fastq'
seqs = flat_zip_longest(fwd_seqs, rev_seqs)
match_pairs(seqs, out_fhand, orphan_out_fhand, out_format)
output = out_fhand.getvalue()
assert '@seq4:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG' in output
assert '@seq5:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in output
orp = orphan_out_fhand.getvalue()
assert '@seq1:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG' in orp
assert '@seq3:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in orp
assert '@seq6:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in orp
file1 = os.path.join(TEST_DATA_DIR, 'pairend4.sfastq')
file2 = os.path.join(TEST_DATA_DIR, 'pairend2.sfastq')
fwd_seqs = read_seqs([open(file1)], 'fastq')
rev_seqs = read_seqs([open(file2)], 'fastq')
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = 'fastq'
seqs = flat_zip_longest(fwd_seqs, rev_seqs)
match_pairs(seqs, out_fhand, orphan_out_fhand, out_format)
output = out_fhand.getvalue()
assert '@seq8:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG' in output
assert '@seq8:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in output
orp = orphan_out_fhand.getvalue()
assert '@seq1:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in orp
assert '@seq2:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in orp
# with reads with no direcction
file1 = os.path.join(TEST_DATA_DIR, 'pairend7.sfastq')
file2 = os.path.join(TEST_DATA_DIR, 'pairend2.sfastq')
fwd_seqs = read_seqs([open(file1)], 'fastq')
rev_seqs = read_seqs([open(file2)], 'fastq')
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = 'fastq'
seqs = flat_zip_longest(fwd_seqs, rev_seqs)
match_pairs(seqs, out_fhand, orphan_out_fhand, out_format)
output = out_fhand.getvalue()
assert '@seq8:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG' in output
assert '@seq8:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in output
assert '@seq1:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in output
assert '@seq1:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in output
orp = orphan_out_fhand.getvalue()
assert '@seq6:136:FC706VJ:2:2104:15343:197393.mpl_1' in orp
assert '@seq7:136:FC706VJ:2:2104:15343:197393.hhhh' in orp
assert '@seq2:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCAC' in orp
# File is not sorted
file1 = '''@s1.f
AACCAGTCAAC
+
CCCFFFFFGHH
@s2.f
AACCAGTCAAC
+
CCCFFFFFGHH
@s1.r
AACCAGTCAAC
+
CCCFFFFFGHH
'''
file1 = StringIO(file1)
seqs = read_seqs([file1], 'fastq')
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = 'fastq'
try:
match_pairs(seqs, out_fhand, orphan_out_fhand, out_format)
output = out_fhand.getvalue()
self.fail('MalformedFile error expected')
except MalformedFile:
pass
def test_pair_matcher(self):
'It test the pair matcher function'
# with equal seqs but the last ones
file1 = os.path.join(TEST_DATA_DIR, 'pairend1.sfastq')
file2 = os.path.join(TEST_DATA_DIR, 'pairend2.sfastq')
fwd_seqs = read_seqs([open(file1)])
rev_seqs = read_seqs([open(file2)])
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = 'fastq'
seqs = flat_zip_longest(fwd_seqs, rev_seqs)
match_pairs(seqs, out_fhand, orphan_out_fhand, out_format)
output = out_fhand.getvalue()
assert '@seq1:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG' in output
assert '@seq2:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in output
orp = orphan_out_fhand.getvalue()
assert '@seq8:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in orp
# with the firsts seqs different
file1 = os.path.join(TEST_DATA_DIR, 'pairend1.sfastq')
file2 = os.path.join(TEST_DATA_DIR, 'pairend3.sfastq')
fwd_seqs = read_seqs([open(file1)])
rev_seqs = read_seqs([open(file2)])
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = 'fastq'
seqs = flat_zip_longest(fwd_seqs, rev_seqs)
match_pairs(seqs, out_fhand, orphan_out_fhand, out_format)
output = out_fhand.getvalue()
assert '@seq4:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG' in output
assert '@seq5:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in output
orp = orphan_out_fhand.getvalue()
assert '@seq1:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG' in orp
assert '@seq3:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in orp
assert '@seq6:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in orp
file1 = os.path.join(TEST_DATA_DIR, 'pairend4.sfastq')
file2 = os.path.join(TEST_DATA_DIR, 'pairend2.sfastq')
fwd_seqs = read_seqs([open(file1)])
rev_seqs = read_seqs([open(file2)])
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = 'fastq'
seqs = flat_zip_longest(fwd_seqs, rev_seqs)
match_pairs(seqs, out_fhand, orphan_out_fhand, out_format)
output = out_fhand.getvalue()
assert '@seq8:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG' in output
assert '@seq8:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in output
orp = orphan_out_fhand.getvalue()
assert '@seq1:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in orp
assert '@seq2:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in orp
# with reads with no direcction
file1 = os.path.join(TEST_DATA_DIR, 'pairend7.sfastq')
file2 = os.path.join(TEST_DATA_DIR, 'pairend2.sfastq')
fwd_seqs = read_seqs([open(file1)])
rev_seqs = read_seqs([open(file2)])
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = 'fastq'
seqs = flat_zip_longest(fwd_seqs, rev_seqs)
match_pairs(seqs, out_fhand, orphan_out_fhand, out_format)
output = out_fhand.getvalue()
assert '@seq8:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG' in output
assert '@seq8:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in output
assert '@seq1:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in output
assert '@seq1:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in output
orp = orphan_out_fhand.getvalue()
assert '@seq6:136:FC706VJ:2:2104:15343:197393.mpl_1' in orp
assert '@seq7:136:FC706VJ:2:2104:15343:197393.hhhh' in orp
assert '@seq2:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCAC' in orp
# File is not sorted
file1 = '''@s1.f
AACCAGTCAAC
+
CCCFFFFFGHH
@s2.f
AACCAGTCAAC
+
CCCFFFFFGHH
@s1.r
AACCAGTCAAC
+
CCCFFFFFGHH
'''
file1 = StringIO(file1)
set_format(file1, 'fastq')
seqs = read_seqs([file1])
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = 'fastq'
try:
match_pairs(seqs, out_fhand, orphan_out_fhand, out_format,
check_order_buffer_size=10)
output = out_fhand.getvalue()
self.fail('ItemsNotSortedError error expected')
except ItemsNotSortedError:
pass
def test_pair_matcher(self):
"It test the pair matcher function"
# with equal seqs but the last ones
file1 = os.path.join(TEST_DATA_DIR, "pairend1.sfastq")
file2 = os.path.join(TEST_DATA_DIR, "pairend2.sfastq")
fwd_seqs = read_seqs([open(file1)], file_format="fastq")
rev_seqs = read_seqs([open(file2)], file_format="fastq")
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = "fastq"
seqs = flat_zip_longest(fwd_seqs, rev_seqs)
match_pairs(seqs, out_fhand, orphan_out_fhand, out_format)
output = out_fhand.getvalue()
assert "@seq1:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG" in output
assert "@seq2:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG" in output
orp = orphan_out_fhand.getvalue()
assert "@seq8:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG" in orp
# with the firsts seqs different
file1 = os.path.join(TEST_DATA_DIR, "pairend1.sfastq")
file2 = os.path.join(TEST_DATA_DIR, "pairend3.sfastq")
fwd_seqs = read_seqs([open(file1)], "fastq")
rev_seqs = read_seqs([open(file2)], "fastq")
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = "fastq"
seqs = flat_zip_longest(fwd_seqs, rev_seqs)
match_pairs(seqs, out_fhand, orphan_out_fhand, out_format)
output = out_fhand.getvalue()
assert "@seq4:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG" in output
assert "@seq5:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG" in output
orp = orphan_out_fhand.getvalue()
assert "@seq1:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG" in orp
assert "@seq3:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG" in orp
assert "@seq6:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG" in orp
file1 = os.path.join(TEST_DATA_DIR, "pairend4.sfastq")
file2 = os.path.join(TEST_DATA_DIR, "pairend2.sfastq")
fwd_seqs = read_seqs([open(file1)], "fastq")
rev_seqs = read_seqs([open(file2)], "fastq")
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = "fastq"
seqs = flat_zip_longest(fwd_seqs, rev_seqs)
match_pairs(seqs, out_fhand, orphan_out_fhand, out_format)
output = out_fhand.getvalue()
assert "@seq8:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG" in output
assert "@seq8:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG" in output
orp = orphan_out_fhand.getvalue()
assert "@seq1:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG" in orp
assert "@seq2:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG" in orp
# with reads with no direcction
file1 = os.path.join(TEST_DATA_DIR, "pairend7.sfastq")
file2 = os.path.join(TEST_DATA_DIR, "pairend2.sfastq")
fwd_seqs = read_seqs([open(file1)], "fastq")
rev_seqs = read_seqs([open(file2)], "fastq")
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = "fastq"
seqs = flat_zip_longest(fwd_seqs, rev_seqs)
match_pairs(seqs, out_fhand, orphan_out_fhand, out_format)
output = out_fhand.getvalue()
assert "@seq8:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG" in output
assert "@seq8:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG" in output
assert "@seq1:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG" in output
assert "@seq1:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG" in output
orp = orphan_out_fhand.getvalue()
assert "@seq6:136:FC706VJ:2:2104:15343:197393.mpl_1" in orp
assert "@seq7:136:FC706VJ:2:2104:15343:197393.hhhh" in orp
assert "@seq2:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCAC" in orp
# File is not sorted
file1 = """@s1.f
AACCAGTCAAC
+
CCCFFFFFGHH
@s2.f
AACCAGTCAAC
+
CCCFFFFFGHH
@s1.r
AACCAGTCAAC
+
CCCFFFFFGHH
"""
file1 = StringIO(file1)
seqs = read_seqs([file1], "fastq")
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = "fastq"
try:
match_pairs(seqs, out_fhand, orphan_out_fhand, out_format)
output = out_fhand.getvalue()
self.fail("MalformedFile error expected")
except MalformedFile:
pass