allpy: b556c96c6719 test/test_io

allpy

blocks3d/www Makefile: never check certificates of github, they are too confusing for wget

author	Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru>
date	Mon, 26 May 2014 17:20:29 +0400
parents	b8ddd35fac65
children

line source

1 from StringIO import StringIO

2 from allpy import dna

4 example = """

5 @HWI-ST992:108:D06T0ACXX:6:1107:13562:94150 1:N:0:

6 TCAATGGTGCTGTATAAAACACGTAGAATTACTATTATGGATTATATTCGTCTTCATTTGTTAAAATCAGTGGCTTAACTGGCTAAATTTTGTGGACTATA

8 #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>

9 @HWI-ST992:108:D06T0ACXX:6:1107:13630:94150 1:N:0:

10 GGTGAAGCGCTTTGAGTCCCTCTCCAGCCAGCGCTTCCTGCAGGGCGTGATCGTGGCGCTCATCACGGGCATGTTCTGGTGGCAGCGCGGCCGCGGCGGCT

12 <@@DDFDBHHGFHIAHHIIIIIIIIIGHGIGAGHIHIIIIHIIII?G@BHHHHABDDDDDDDDDDDD?B@BCD@C@CDDACDDDDDDDDDBDBDBDD@B<>

13 """.strip()

15 def test_fastq_io():

16 file = StringIO(example)

17 aln = dna.Alignment().append_file(file, format="fastq")

18 assert len(aln.sequences) == 2

19 a, b = aln.sequences

20 assert str(a)[:10] == "TCAATGGTGC"

21 assert str(b)[:10] == "GGTGAAGCGC"

22 qa = list(a.markups['quality'].sorted_values())

23 assert qa[:10] == [2, 23, 25, 25, 19, 32, 35, 11, 32, 10]

24 qb = list(b.markups['quality'].sorted_values())

25 assert qb[:10] == [27, 31, 31, 35, 35, 37, 35, 33, 39, 39]

27 # vim: set et ts=4 sts=4 sw=4: