allpy: b556c96c6719 test/test_io

allpy

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

2 from StringIO import StringIO

4 from allpy import protein

6 def test_stringio_conversions():

7 # MSF is not supported by any other handler, except EMBOSS,

8 # so by testing MSF we essentially test EMBOSS

9 a = (protein.Alignment().

10 append_row_from_string("a-c-d", name="Seq1").

11 append_row_from_string("tgcga", name="Seq2"))

13 o = StringIO()

14 a.to_file(o, "fasta")

15 got = o.getvalue()

16 expect = ">Seq1\nA-C-D\n>Seq2\nTGCGA\n"

17 assert expect == got, "Expected:\n%r\nGot:\n%r" % (expect, got)

19 o = StringIO()

20 a.to_file(o, "msf")

21 got = o.getvalue()

22 got = re.sub('(stdout MSF: 5 Type: N) .*', r'\1', got)

23 expect = (

24 "!!NA_MULTIPLE_ALIGNMENT 1.0\n"

25 "\n"

26 " stdout MSF: 5 Type: N 03/06/11 CompCheck: 1918 ..\n"

27 "\n"

28 " Name: Seq1 Len: 5 Check: 882 Weight: 1.00\n"

29 " Name: Seq2 Len: 5 Check: 1036 Weight: 1.00\n"

30 "\n"

31 "//\n"

32 "\n"

33 " 1 5\n"

34 "Seq1 A.C.D\n"

35 "Seq2 TGCGA\n"

36 "\n"

38 expect = re.sub('(stdout MSF: 5 Type: N) .*', r'\1', expect)

39 assert expect == got, "Expected:\n%r\nGot:\n%r" % (expect, got)

41 o.name = 'whoopie.msf'

42 o.seek(0)

43 b = protein.Alignment().append_file(o, format='msf')

44 assert b.rows_as_strings() == ["A-C-D", "TGCGA"]

45 assert b.sequences[0].source == o.name

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