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"
seq_fhand = NamedTemporaryFile(suffix=".fasta")
write_seqs(seqs, seq_fhand, file_format="fasta")
seq_fhand.flush()
out_fhand = StringIO()
orphan_out_fhand = StringIO()
match_pairs_unordered(seq_fhand.name, out_fhand, orphan_out_fhand, 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'
seq_fhand = NamedTemporaryFile(suffix='.fasta')
write_seqs(seqs, seq_fhand, file_format='fasta')
seq_fhand.flush()
out_fhand = StringIO()
orphan_out_fhand = StringIO()
match_pairs_unordered(seq_fhand.name, out_fhand, orphan_out_fhand,
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'
seq_fhand = NamedTemporaryFile(suffix='.fasta')
write_seqs(seqs, seq_fhand, file_format='fasta')
seq_fhand.flush()
out_fhand = StringIO()
orphan_out_fhand = StringIO()
match_pairs_unordered(seq_fhand.name,
out_fhand,
orphan_out_fhand,
out_format='fasta')
assert '>seq1\nACT\n' in orphan_out_fhand.getvalue()
assert '>seq2\nACT\n' in orphan_out_fhand.getvalue()
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()
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = 'fastq'
match_pairs_unordered(fhand.name, 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')
fhand = NamedTemporaryFile()
fhand.write(open(file1).read())
fhand.write(open(file2).read())
fhand.flush()
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = 'fastq'
match_pairs_unordered(fhand.name, 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')
fhand = NamedTemporaryFile()
fhand.write(open(file1).read())
fhand.write(open(file2).read())
fhand.flush()
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = 'fastq'
match_pairs_unordered(fhand.name, 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
# 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()
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = 'fastq'
match_pairs_unordered(fhand.name, 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 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()
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = 'fastq'
match_pairs_unordered(fhand.name, 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
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()
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = "fastq"
match_pairs_unordered(fhand.name, 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")
fhand = NamedTemporaryFile()
fhand.write(open(file1).read())
fhand.write(open(file2).read())
fhand.flush()
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = "fastq"
match_pairs_unordered(fhand.name, 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")
fhand = NamedTemporaryFile()
fhand.write(open(file1).read())
fhand.write(open(file2).read())
fhand.flush()
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = "fastq"
match_pairs_unordered(fhand.name, 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
# 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()
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = "fastq"
match_pairs_unordered(fhand.name, 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 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()
out_fhand = StringIO()
orphan_out_fhand = StringIO()
out_format = "fastq"
match_pairs_unordered(fhand.name, 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