allpy
changeset 1094:61b61f911a1a
Reorganized tests to make them more readable
| author | Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru> |
|---|---|
| date | Sat, 02 Jun 2012 22:15:27 +0400 |
| parents | 0aa68678861c |
| children | f05b08e13072 |
| files | test/test_base.py test/test_io_biopython.py test/test_io_emboss.py test/test_realign.py |
| diffstat | 4 files changed, 138 insertions(+), 143 deletions(-) [+] |
line diff
1.1 --- a/test/test_base.py Sat Jun 02 21:56:13 2012 +0400 1.2 +++ b/test/test_base.py Sat Jun 02 22:15:27 2012 +0400 1.3 @@ -1,22 +1,8 @@ 1.4 -import re 1.5 -from StringIO import StringIO 1.6 - 1.7 -import allpy.base 1.8 -import allpy.protein as p 1.9 -from allpy import processors 1.10 - 1.11 -# XXX Totally missed: 1.12 -# XXX - monomer representation (should we test it at all?) 1.13 -# XXX - sequence comparison 1.14 -# XXX - sequence representation 1.15 -# XXX - Alignment.columns_as_lists 1.16 -# XXX - Alignment.flush (which is a backwards-compatibility wrapper) 1.17 -# XXX - Alignment.process (which is a backwards-compatibility alias) 1.18 -# XXX - Block.from_alignment with None in either of arguments 1.19 +from allpy import protein, base 1.20 1.21 def test_new_monomers(): 1.22 """Test creation of monomer objects""" 1.23 - s = allpy.base.Sequence() 1.24 + s = base.Sequence() 1.25 1.26 try: 1.27 m = s.append_monomer(code1='A') 1.28 @@ -25,7 +11,7 @@ 1.29 else: 1.30 assert False, "base.Seqeuence must not be constructible from code1" 1.31 1.32 - m = p.Sequence().append_monomer(code3='ALA') 1.33 + m = protein.Sequence().append_monomer(code3='ALA') 1.34 assert m.__class__.__name__ == "Alanine" 1.35 assert m.code1 == "A" 1.36 assert m.code3 == "ALA" 1.37 @@ -48,123 +34,4 @@ 1.38 m = s.append_monomer(code3='SEC') 1.39 assert m.name == "Selenocysteine" 1.40 1.41 -def assert_alignment(alignment, *body): 1.42 - """Helper: check if alignment representation matches strings of body""" 1.43 - s = StringIO() 1.44 - alignment.to_file(s) 1.45 - body = "".join([">\n%s\n" % string for string in body]) 1.46 - assert s.getvalue() == body, "Expected:\n%s\nGot:\n%s" % (body, s.getvalue()) 1.47 - 1.48 -def test_alignment_changes(): 1.49 - """Test operations that modify alignment""" 1.50 - 1.51 - a = (p.Alignment(). 1.52 - append_row_from_string("a-------cdef"). 1.53 - append_row_from_string("ghiklmpq--"). 1.54 - append_row_from_string("-------------rst")) 1.55 - 1.56 - assert_alignment(a, 1.57 - "A-------CDEF----", 1.58 - "GHIKLMPQ--------", 1.59 - "-------------RST", 1.60 - ) 1.61 - 1.62 - a.realign(processors.Left()) 1.63 - assert_alignment(a, 1.64 - "ACDEF-----------", 1.65 - "GHIKLMPQ--------", 1.66 - "RST-------------", 1.67 - ) 1.68 - 1.69 - a.realign(processors.Center()) 1.70 - assert_alignment(a, 1.71 - "-----ACDEF------", 1.72 - "----GHIKLMPQ----", 1.73 - "------RST-------", 1.74 - ) 1.75 - 1.76 - a.realign(processors.Right()) 1.77 - assert_alignment(a, 1.78 - "-----------ACDEF", 1.79 - "--------GHIKLMPQ", 1.80 - "-------------RST", 1.81 - ) 1.82 - 1.83 -def test_stringio_conversions(): 1.84 - a = (p.Alignment(). 1.85 - append_row_from_string("a-c-d", name="Seq1"). 1.86 - append_row_from_string("tgcga", name="Seq2")) 1.87 - 1.88 - o = StringIO() 1.89 - a.to_file(o, "fasta") 1.90 - got = o.getvalue() 1.91 - expect = ">Seq1\nA-C-D\n>Seq2\nTGCGA\n" 1.92 - assert expect == got, "Expected:\n%r\nGot:\n%r" % (expect, got) 1.93 - 1.94 - o = StringIO() 1.95 - a.to_file(o, "msf") 1.96 - got = o.getvalue() 1.97 - got = re.sub('(stdout MSF: 5 Type: N) .*', r'\1', got) 1.98 - expect = ( 1.99 - "!!NA_MULTIPLE_ALIGNMENT 1.0\n" 1.100 - "\n" 1.101 - " stdout MSF: 5 Type: N 03/06/11 CompCheck: 1918 ..\n" 1.102 - "\n" 1.103 - " Name: Seq1 Len: 5 Check: 882 Weight: 1.00\n" 1.104 - " Name: Seq2 Len: 5 Check: 1036 Weight: 1.00\n" 1.105 - "\n" 1.106 - "//\n" 1.107 - "\n" 1.108 - " 1 5\n" 1.109 - "Seq1 A.C.D\n" 1.110 - "Seq2 TGCGA\n" 1.111 - "\n" 1.112 - ) 1.113 - expect = re.sub('(stdout MSF: 5 Type: N) .*', r'\1', expect) 1.114 - assert expect == got, "Expected:\n%r\nGot:\n%r" % (expect, got) 1.115 - 1.116 - o.name = 'whoopie.msf' 1.117 - o.seek(0) 1.118 - b = p.Alignment().append_file(o, format='msf') 1.119 - assert b.rows_as_strings() == ["A-C-D", "TGCGA"] 1.120 - assert b.sequences[0].source == o.name 1.121 - 1.122 -def test_bio_io(): 1.123 - """Test Bio python IO. 1.124 - 1.125 - BioPython does not support msf, so it is not covered in many other tests. 1.126 - """ 1.127 - file = ( 1.128 - "# STOCKHOLM 1.0\n" 1.129 - "#=GS seqA AC seqA123\n" 1.130 - "#=GS seqA DR PDB; 1abc ; 1-42;\n" 1.131 - "#=GS seqB AC seqB345\n" 1.132 - "SeqA SEQVENCEHELLO\n" 1.133 - "#=GR SeqA SS -HHHHH---CHHH\n" 1.134 - "SeqB SI-VENCE--LLO\n" 1.135 - "#=GR SeqB SS X-HHHHH--HHHH\n" 1.136 - "#=GC SS_cons X-HHHHH--HHHH\n" 1.137 - "#=GC seq_cons Si.VENCE.eLLo\n" 1.138 - "//\n" 1.139 - ) 1.140 - 1.141 - o = StringIO() 1.142 - o.write(file) 1.143 - o.seek(0) 1.144 - 1.145 - aln = p.Alignment().append_file(o, "stockholm") 1.146 - assert len(aln.sequences) == 2 1.147 - assert len(aln.columns) == 13 1.148 - assert aln.sequences[1] not in aln.columns[2] 1.149 - assert aln.sequences[0][2].code1 == 'Q' 1.150 - 1.151 - o = StringIO() 1.152 - aln.to_file(o, format='stockholm') 1.153 - o.seek(0) 1.154 - for line in o: 1.155 - hd = line.strip().split()[0] 1.156 - assert hd in ('#', '#=GS', '#=GF', '#=GC', 'SeqA', 'SeqB', '//') 1.157 - o.seek(0) 1.158 - assert iter(o).next() == "# STOCKHOLM 1.0\n" 1.159 - 1.160 # 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_biopython.py Sat Jun 02 22:15:27 2012 +0400 2.3 @@ -0,0 +1,42 @@ 2.4 +from StringIO import StringIO 2.5 +from allpy import protein 2.6 + 2.7 +def test_bio_io(): 2.8 + """Test Bio python IO. 2.9 + 2.10 + BioPython does not support msf, so it is not covered in many other tests. 2.11 + """ 2.12 + file = ( 2.13 + "# STOCKHOLM 1.0\n" 2.14 + "#=GS seqA AC seqA123\n" 2.15 + "#=GS seqA DR PDB; 1abc ; 1-42;\n" 2.16 + "#=GS seqB AC seqB345\n" 2.17 + "SeqA SEQVENCEHELLO\n" 2.18 + "#=GR SeqA SS -HHHHH---CHHH\n" 2.19 + "SeqB SI-VENCE--LLO\n" 2.20 + "#=GR SeqB SS X-HHHHH--HHHH\n" 2.21 + "#=GC SS_cons X-HHHHH--HHHH\n" 2.22 + "#=GC seq_cons Si.VENCE.eLLo\n" 2.23 + "//\n" 2.24 + ) 2.25 + 2.26 + o = StringIO() 2.27 + o.write(file) 2.28 + o.seek(0) 2.29 + 2.30 + aln = protein.Alignment().append_file(o, "stockholm") 2.31 + assert len(aln.sequences) == 2 2.32 + assert len(aln.columns) == 13 2.33 + assert aln.sequences[1] not in aln.columns[2] 2.34 + assert aln.sequences[0][2].code1 == 'Q' 2.35 + 2.36 + o = StringIO() 2.37 + aln.to_file(o, format='stockholm') 2.38 + o.seek(0) 2.39 + for line in o: 2.40 + hd = line.strip().split()[0] 2.41 + assert hd in ('#', '#=GS', '#=GF', '#=GC', 'SeqA', 'SeqB', '//') 2.42 + o.seek(0) 2.43 + assert iter(o).next() == "# STOCKHOLM 1.0\n" 2.44 + 2.45 +# vim: set et ts=4 sts=4 sw=4:
3.1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 3.2 +++ b/test/test_io_emboss.py Sat Jun 02 22:15:27 2012 +0400 3.3 @@ -0,0 +1,47 @@ 3.4 +import re 3.5 +from StringIO import StringIO 3.6 + 3.7 +from allpy import protein 3.8 + 3.9 +def test_stringio_conversions(): 3.10 + # MSF is not supported by any other handler, except EMBOSS, 3.11 + # so by testing MSF we essentially test EMBOSS 3.12 + a = (protein.Alignment(). 3.13 + append_row_from_string("a-c-d", name="Seq1"). 3.14 + append_row_from_string("tgcga", name="Seq2")) 3.15 + 3.16 + o = StringIO() 3.17 + a.to_file(o, "fasta") 3.18 + got = o.getvalue() 3.19 + expect = ">Seq1\nA-C-D\n>Seq2\nTGCGA\n" 3.20 + assert expect == got, "Expected:\n%r\nGot:\n%r" % (expect, got) 3.21 + 3.22 + o = StringIO() 3.23 + a.to_file(o, "msf") 3.24 + got = o.getvalue() 3.25 + got = re.sub('(stdout MSF: 5 Type: N) .*', r'\1', got) 3.26 + expect = ( 3.27 + "!!NA_MULTIPLE_ALIGNMENT 1.0\n" 3.28 + "\n" 3.29 + " stdout MSF: 5 Type: N 03/06/11 CompCheck: 1918 ..\n" 3.30 + "\n" 3.31 + " Name: Seq1 Len: 5 Check: 882 Weight: 1.00\n" 3.32 + " Name: Seq2 Len: 5 Check: 1036 Weight: 1.00\n" 3.33 + "\n" 3.34 + "//\n" 3.35 + "\n" 3.36 + " 1 5\n" 3.37 + "Seq1 A.C.D\n" 3.38 + "Seq2 TGCGA\n" 3.39 + "\n" 3.40 + ) 3.41 + expect = re.sub('(stdout MSF: 5 Type: N) .*', r'\1', expect) 3.42 + assert expect == got, "Expected:\n%r\nGot:\n%r" % (expect, got) 3.43 + 3.44 + o.name = 'whoopie.msf' 3.45 + o.seek(0) 3.46 + b = protein.Alignment().append_file(o, format='msf') 3.47 + assert b.rows_as_strings() == ["A-C-D", "TGCGA"] 3.48 + assert b.sequences[0].source == o.name 3.49 + 3.50 + # vim: set et ts=4 sts=4 sw=4: