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from Bio import CAPS
import unittest
from Bio.Restriction import *
from Bio.Fasta import FastaAlign
from StringIO import StringIO
import sys
if sys.platform=="win32":
from tempfile import mktemp
import os
else :
from tempfile import NamedTemporaryFile
def createAlignment(alignment):
"""Create a FastaAlignment from an alignment string"""
alignment = alignment[alignment.find(">"):]
if sys.platform=="win32":
# On windows we cannot (re)open the tempfile to read it
# while it is still open for writing. And once closed,
# it gets automatically deleted.
#
# This is a crude and potentially "unsafe" work around
# (as in theory another program could use the same
# filename in the instant before we open it)
tmp_name = mktemp()
tmp = open(tmp_name, "w")
tmp.write(alignment)
tmp.close()
else :
tmp = NamedTemporaryFile(bufsize=0)
tmp_name = tmp.name
tmp.write(alignment)
#Don't close the file yet...
tmp.flush()
#import os
#assert os.path.isfile(tmp_name), 'Missing temp file "%s"' % tmp_name
align = FastaAlign.parse_file(tmp.name)
if sys.platform=="win32":
#We must remove the temp file ourselves.
os.remove(tmp.name)
else :
#This will delete the temp file
tmp.close()
return align
class UnevenAlignment(unittest.TestCase):
alignment = """
>foo1
aaaaaaaaaaaaaa
>foo2
aaaaaaaa
>foo3
aaaaaaaaaaaaaa
"""
def setUp(self):
self.align = createAlignment(self.alignment)
def test(self):
self.assertRaises(CAPS.AlignmentHasDifferentLengthsError, CAPS.CAPSMap, self.align)
class FastaAlignmentTest(unittest.TestCase):
alignment = """"""
enzymes = []
def setUp(self):
align = createAlignment(self.alignment)
self.map = CAPS.CAPSMap(align, self.enzymes)
class NonExample(FastaAlignmentTest):
alignment = """
>Sequence1
aaaaaaaaaaaaaaaaaaaa
>Sequence2
aaaaaaaaaaaaaaaaaaaa
"""
def testNoCAPS(self):
self.assertEqual(self.map.dcuts, [])
class ResultChecker(FastaAlignmentTest):
"""This class builds an alignment and then checks the results
subclass it and expose fields:
alignment - Text representation of the alignment to analyze
enzymes - The enzymes to analyze this with
"""
def check(self):
self.assertEqual(len(self.map.dcuts), len(self.results))
for i in range(0,len(self.results)):
self.assertEqual(self.results[i][0], self.map.dcuts[i].enzyme)
self.assertEqual(self.results[i][1], self.map.dcuts[i].start)
self.assertEqual(self.results[i][2], self.map.dcuts[i].cuts_in)
self.assertEqual(self.results[i][3], self.map.dcuts[i].blocked_in)
class Example1(ResultChecker):
alignment = """
>0
AAAagaattcTAGATATACCAAACCAGAGAAAACAAATACATAATCGGAGAAATACAGAT
AGAGAGCGAGAGAGATCGACGGCGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGT
TTAGTGAAAATGGAGGATCAAGTagAtTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTT
GGTCACTATCTCCGTAACAAAATCGAAGGAAACACTAGCCGCGACGTTGAAGTAGCCATC
AGCGAGGTCAACATCTGTAGCTACGATCCTTGGAACTTGCGCTGTAAGTTCCGAATTTTC
>1
AAAagaTttcTAGATATACCAAACCAGAGAAAACAAATACATAATCGGAGAAATACAGAT
AGAGAGCGAGAGAGATCGACGGCGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGT
TTAGTGAAAATGGAGGATCAAGTagctTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTT
GGTCACTATCTCCGTAACAAAATCGAAGGAAACACTAGCCGCGACGTTGAAGTAGCCATC
AGCGAGGTCAACATCTGTAGCTACGATCCTTGGAACTTGCGCTGTAAGTTCCGAATTTTC
>2
AAAagaTttcTAGATATACCAAACCAGAGAAAACAAATACATAATCGGAGAAATACAGAT
AGAGAGCGAGAGAGATCGACGGCGAAGCTCTTTACCCGGAAACCATTGAAATCGGACGGT
TTAGTGAAAATGGAGGATCAAGTagctTTTGGGTTCCGTCCGAACGACGAGGAGCTCGTT
GGTCACTATCTCCGTAACAAAATCGAAGGAAACACTAGCCGCGACGTTGAAGTAGCCATC
AGCGAGGTCAACATCTGTAGCTACGATCCTTGGAACTTGCGCTGTAAGTTCCGAATTTTC
"""
enzymes = [EcoRI, AluI]
results = []
results.append([EcoRI, 5, [0], [1,2]])
results.append([AluI, 144, [1,2], [0]])
def test(self):
self.check()
class TrivialExample(FastaAlignmentTest):
alignment = """
>1
gaattc
>2
gaactc
"""
enzymes = [EcoRI]
def testCAPS(self):
self.assertEqual(len(self.map.dcuts), 1)
self.assertEqual(self.map.dcuts[0].enzyme, EcoRI)
self.assertEqual(self.map.dcuts[0].start, 1)
self.assertEqual(self.map.dcuts[0].cuts_in, [0])
self.assertEqual(self.map.dcuts[0].blocked_in, [1])
def test_suite():
suite = unittest.TestSuite()
suite.addTest(UnevenAlignment("test"))
suite.addTest(TrivialExample("testCAPS"))
suite.addTest(Example1("test"))
return suite
if __name__ == "__main__":
runner = unittest.TextTestRunner()
runner.run(test_suite())
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