def test_all_orphan():
'All reads end up in orphan'
seqs = [SeqRecord(Seq('ACT'), id='seq1'),
SeqRecord(Seq('ACT'), id='seq2')]
seqs = list(assing_kind_to_seqs(SEQRECORD, seqs, None))
out_fhand = StringIO()
orphan_out_fhand = StringIO()
match_pairs(seqs, out_fhand, orphan_out_fhand, out_format='fasta')
assert orphan_out_fhand.getvalue() == '>seq1\nACT\n>seq2\nACT\n'
out_fhand = StringIO()
orphan_out_fhand = StringIO()
match_pairs(seqs, out_fhand, orphan_out_fhand, ordered=False,
out_format='fasta')
assert '>seq1\nACT\n' in orphan_out_fhand.getvalue()
assert '>seq2\nACT\n' in orphan_out_fhand.getvalue()
def test_all_orphan():
'All reads end up in orphan'
seqs = [
SeqRecord(Seq('ACT'), id='seq1'),
SeqRecord(Seq('ACT'), id='seq2')
]
seqs = list(assing_kind_to_seqs(SEQRECORD, seqs, None))
out_fhand = StringIO()
orphan_out_fhand = StringIO()
match_pairs(seqs, out_fhand, orphan_out_fhand, out_format='fasta')
assert orphan_out_fhand.getvalue() == '>seq1\nACT\n>seq2\nACT\n'
out_fhand = StringIO()
orphan_out_fhand = StringIO()
match_pairs(seqs,
out_fhand,
orphan_out_fhand,
ordered=False,
out_format='fasta')
assert '>seq1\nACT\n' in orphan_out_fhand.getvalue()
assert '>seq2\nACT\n' in orphan_out_fhand.getvalue()
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_mate_pair_unorderer_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')
fhand = NamedTemporaryFile()
fhand.write(open(file1).read())
fhand.write(open(file2).read())
fhand.flush()
seqs = read_seqs([fhand])
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = 'fastq'
match_pairs(seqs, out_fhand, orphan_out_fhand, out_format,
ordered=False)
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')
fhand = NamedTemporaryFile()
fhand.write(open(file1).read())
fhand.write(open(file2).read())
fhand.flush()
seqs = read_seqs([fhand])
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = 'fastq'
match_pairs(seqs, out_fhand, orphan_out_fhand, out_format,
ordered=False)
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')
fhand = NamedTemporaryFile()
fhand.write(open(file1).read())
fhand.write(open(file2).read())
fhand.flush()
seqs = read_seqs([fhand])
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = 'fastq'
match_pairs(seqs, out_fhand, orphan_out_fhand, out_format,
ordered=False)
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
# unordered file
file1 = os.path.join(TEST_DATA_DIR, 'pairend1.sfastq')
file2 = os.path.join(TEST_DATA_DIR, 'pairend2_unordered.sfastq')
fhand = NamedTemporaryFile()
fhand.write(open(file1).read())
fhand.write(open(file2).read())
fhand.flush()
seqs = read_seqs([fhand])
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = 'fastq'
match_pairs(seqs, out_fhand, orphan_out_fhand, out_format,
ordered=False)
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 reads with no direcction
file1 = os.path.join(TEST_DATA_DIR, 'pairend7.sfastq')
file2 = os.path.join(TEST_DATA_DIR, 'pairend2.sfastq')
fhand = NamedTemporaryFile()
fhand.write(open(file1).read())
fhand.write(open(file2).read())
fhand.flush()
seqs = read_seqs([fhand])
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = 'fastq'
match_pairs(seqs, out_fhand, orphan_out_fhand, out_format,
ordered=False)
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
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_mate_pair_unorderer_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')
fhand = NamedTemporaryFile()
fhand.write(open(file1).read())
fhand.write(open(file2).read())
fhand.flush()
seqs = read_seqs([fhand])
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = 'fastq'
match_pairs(seqs,
out_fhand,
orphan_out_fhand,
out_format,
ordered=False)
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')
fhand = NamedTemporaryFile()
fhand.write(open(file1).read())
fhand.write(open(file2).read())
fhand.flush()
seqs = read_seqs([fhand])
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = 'fastq'
match_pairs(seqs,
out_fhand,
orphan_out_fhand,
out_format,
ordered=False)
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')
fhand = NamedTemporaryFile()
fhand.write(open(file1).read())
fhand.write(open(file2).read())
fhand.flush()
seqs = read_seqs([fhand])
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = 'fastq'
match_pairs(seqs,
out_fhand,
orphan_out_fhand,
out_format,
ordered=False)
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
# unordered file
file1 = os.path.join(TEST_DATA_DIR, 'pairend1.sfastq')
file2 = os.path.join(TEST_DATA_DIR, 'pairend2_unordered.sfastq')
fhand = NamedTemporaryFile()
fhand.write(open(file1).read())
fhand.write(open(file2).read())
fhand.flush()
seqs = read_seqs([fhand])
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = 'fastq'
match_pairs(seqs,
out_fhand,
orphan_out_fhand,
out_format,
ordered=False)
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 reads with no direcction
file1 = os.path.join(TEST_DATA_DIR, 'pairend7.sfastq')
file2 = os.path.join(TEST_DATA_DIR, 'pairend2.sfastq')
fhand = NamedTemporaryFile()
fhand.write(open(file1).read())
fhand.write(open(file2).read())
fhand.flush()
seqs = read_seqs([fhand])
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = 'fastq'
match_pairs(seqs,
out_fhand,
orphan_out_fhand,
out_format,
ordered=False)
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