1.1 --- a/test/test_fastq.py	Sat Jun 02 19:33:42 2012 +0400
     1.2 +++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
     1.3 @@ -1,27 +0,0 @@
     1.4 -from StringIO import StringIO
     1.5 -from allpy import dna
     1.6 -
     1.7 -example = """
     1.8 -@HWI-ST992:108:D06T0ACXX:6:1107:13562:94150 1:N:0:
     1.9 -TCAATGGTGCTGTATAAAACACGTAGAATTACTATTATGGATTATATTCGTCTTCATTTGTTAAAATCAGTGGCTTAACTGGCTAAATTTTGTGGACTATA
    1.10 -+
    1.11 -#8::4AD,A+C<D>EDEIEDFIE:FF<A@B+1??999E?<DDE<9:DADBD;D=8BD?B@B=B)===)7=..)-66@CCD)?=A;@?@AAAB>;(>AAAA>
    1.12 -@HWI-ST992:108:D06T0ACXX:6:1107:13630:94150 1:N:0:
    1.13 -GGTGAAGCGCTTTGAGTCCCTCTCCAGCCAGCGCTTCCTGCAGGGCGTGATCGTGGCGCTCATCACGGGCATGTTCTGGTGGCAGCGCGGCCGCGGCGGCT
    1.14 -+
    1.15 -<@@DDFDBHHGFHIAHHIIIIIIIIIGHGIGAGHIHIIIIHIIII?G@BHHHHABDDDDDDDDDDDD?B@BCD@C@CDDACDDDDDDDDDBDBDBDD@B<>
    1.16 -""".strip()
    1.17 -
    1.18 -def test_fastq_io():
    1.19 -    file = StringIO(example)
    1.20 -    aln = dna.Alignment().append_file(file, format="fastq")
    1.21 -    assert len(aln.sequences) == 2
    1.22 -    a, b = aln.sequences
    1.23 -    assert str(a)[:10] == "TCAATGGTGC"
    1.24 -    assert str(b)[:10] == "GGTGAAGCGC"
    1.25 -    qa = list(a.markups['quality'].sorted_values())
    1.26 -    assert qa[:10] == [2, 23, 25, 25, 19, 32, 35, 11, 32, 10]
    1.27 -    qb = list(b.markups['quality'].sorted_values())
    1.28 -    assert qb[:10] == [27, 31, 31, 35, 35, 37, 35, 33, 39, 39]
    1.29 -
    1.30 -# vim: set et ts=4 sts=4 sw=4:

     2.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     2.2 +++ b/test/test_io_fastq.py	Sat Jun 02 19:52:06 2012 +0400
     2.3 @@ -0,0 +1,27 @@
     2.4 +from StringIO import StringIO
     2.5 +from allpy import dna
     2.6 +
     2.7 +example = """
     2.8 +@HWI-ST992:108:D06T0ACXX:6:1107:13562:94150 1:N:0:
     2.9 +TCAATGGTGCTGTATAAAACACGTAGAATTACTATTATGGATTATATTCGTCTTCATTTGTTAAAATCAGTGGCTTAACTGGCTAAATTTTGTGGACTATA
    2.10 ++
    2.11 +#8::4AD,A+C<D>EDEIEDFIE:FF<A@B+1??999E?<DDE<9:DADBD;D=8BD?B@B=B)===)7=..)-66@CCD)?=A;@?@AAAB>;(>AAAA>
    2.12 +@HWI-ST992:108:D06T0ACXX:6:1107:13630:94150 1:N:0:
    2.13 +GGTGAAGCGCTTTGAGTCCCTCTCCAGCCAGCGCTTCCTGCAGGGCGTGATCGTGGCGCTCATCACGGGCATGTTCTGGTGGCAGCGCGGCCGCGGCGGCT
    2.14 ++
    2.15 +<@@DDFDBHHGFHIAHHIIIIIIIIIGHGIGAGHIHIIIIHIIII?G@BHHHHABDDDDDDDDDDDD?B@BCD@C@CDDACDDDDDDDDDBDBDBDD@B<>
    2.16 +""".strip()
    2.17 +
    2.18 +def test_fastq_io():
    2.19 +    file = StringIO(example)
    2.20 +    aln = dna.Alignment().append_file(file, format="fastq")
    2.21 +    assert len(aln.sequences) == 2
    2.22 +    a, b = aln.sequences
    2.23 +    assert str(a)[:10] == "TCAATGGTGC"
    2.24 +    assert str(b)[:10] == "GGTGAAGCGC"
    2.25 +    qa = list(a.markups['quality'].sorted_values())
    2.26 +    assert qa[:10] == [2, 23, 25, 25, 19, 32, 35, 11, 32, 10]
    2.27 +    qb = list(b.markups['quality'].sorted_values())
    2.28 +    assert qb[:10] == [27, 31, 31, 35, 35, 37, 35, 33, 39, 39]
    2.29 +
    2.30 +# vim: set et ts=4 sts=4 sw=4: