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FA_TOOL/fatool/tests/test_fa.py
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import unittest
import sys
from fatool import *
import os
class TestFa(unittest.TestCase):
def setUp(self):
with open('test.fa', 'w') as f:
f.write('>name3\nCTNACtacgatNNNNNNN\n>name4\nCTNAC\n>name5\nNNNNNACTGNNNN\n>name\nACTGactg\n>name7\nNNNACTGN\n>name8\nCTNACtacgatNNNNNNN\n>name2\nNNNNNNNNNACTGNNNN\n>name6\nCTNACtatNNN\n')
with open('f2.fa', 'w') as f:
f.write('')
pass
def test_setUpFa(self):
cl = []
cl.append(Sequence('>name', 'ACTGactg'))
cl.append(Sequence('>name2', 'CCCTAGACTG'))
cl.append(Sequence('>name3', 'CTNNNNNNACtacgat'))
f = Fa(cl, 'test-fa')
self.assertEqual(cl, f.contigs)
self.assertEqual('test-fa', f.name)
self.assertEqual({'>name':0, '>name2':1, '>name3':2}, f.contigs_idx)
cl.append('something')
with self.assertRaises(TypeError):
Fa(cl, 'name4')
def test_str(self):
cl = []
cl.append(Sequence('>name', 'ACTGactg'))
cl.append(Sequence('>name2', 'CCCTAGACTG'))
cl.append(Sequence('>name3', 'CTNNNNNNACtacgat'))
f = Fa(cl, 'test-fa')
self.assertEqual('>name\nACTGactg\n>name2\nCCCTAGACTG\n>name3\nCTNNNNNNACtacgat\n', str(f))
def test_add_contig(self):
cl = []
cl.append(Sequence('>name', 'ACTGactg'))
f = Fa(cl, 'test-fa')
self.assertEqual(cl, f.contigs)
f.add_contig(Sequence('>name2', 'CCCTAGACTG'))
cl.append(Sequence('>name2', 'CCCTAGACTG'))
self.assertEqual(cl, f.contigs)
f.add_contig(Sequence('>name2', 'ACTGaaaaaaa') )
self.assertEqual(cl, f.contigs)
cl = [Sequence('>name', 'ACTGactg'), Sequence('>name2', 'ACTGaaaaaaa')]
f.add_contig(Sequence('>name2', 'ACTGaaaaaaa'), 1)
self.assertEqual(cl, f.contigs)
def test_add_contigs(self):
cl = [Sequence('>name', 'ACTGactg')]
f = Fa(cl, 'test-fa')
self.assertEqual(cl, f.contigs)
cl.append(Sequence('>name2', 'CCCTAGACTG'))
cl.append(Sequence('>name3', 'CTNNNNNNACtacgat'))
f.add_contigs([Sequence('>name2', 'CCCTAGACTG'), Sequence('>name3', 'CTNNNNNNACtacgat')])
self.assertEqual(cl, f.contigs)
f.add_contigs([Sequence('>name2', 'NNNNNNNNNACTGNNNN'), Sequence('>name3', 'CTNACtacgatNNNNNNN')])
self.assertEqual(cl, f.contigs)
f.add_contigs([Sequence('>name2', 'NNNNNNNNNACTGNNNN'), Sequence('>name3', 'CTNACtacgatNNNNNNN')], 1)
cl = [Sequence('>name', 'ACTGactg'), Sequence('>name2', 'NNNNNNNNNACTGNNNN'), Sequence('>name3', 'CTNACtacgatNNNNNNN')]
self.assertEqual(cl, f.contigs)
#self.assertEqual(cl, f.contigs)
def test_show_names(self):
cl = [Sequence('>name', 'ACTGactg'), Sequence('>name2', 'NNNNNNNNNACTGNNNN'), Sequence('>name3', 'CTNACtacgatNNNNNNN')]
f = Fa(cl, 'test-fa')
self.assertEqual(['>name','>name2','>name3'], f.show_names())
f.add_contig(Sequence('>name2', 'ACTGaaaaaaa'), 1)
self.assertEqual(['>name','>name3','>name2'], f.show_names())
f.add_contig(Sequence('>name7', 'ACTGaaaaaaa'), 1)
self.assertEqual(['>name','>name3','>name2','>name7'], f.show_names())
def test_extract(self):
cl = [Sequence('>name', 'ACTGactg'), Sequence('>name2', 'NNNNNNNNNACTGNNNN'), Sequence('>name3', 'CTNACtacgatNNNNNNN')]
f = Fa(cl, 'test-fa')
self.assertEqual(cl, f.contigs)
cl2 = [Sequence('>name2', 'NNNNNNNNNACTGNNNN'), Sequence('>name3', 'CTNACtacgatNNNNNNN')]
self.assertEqual(cl2, f.extract(['>name2', '>name3']).contigs)
print 'printing contigs'
for c in f.extract(['name2', 'name3']).contigs:
print c
self.assertEqual('>extr_test-fa', f.extract(['>name2', '>name3']).name)
self.assertEqual(cl2, f.extract(['>name2', '>name3', '>name321']).contigs)
def test_remove(self):
cl = [Sequence('>name', 'ACTGactg'), Sequence('>name2', 'NNNNNNNNNACTGNNNN'), Sequence('>name3', 'CTNACtacgatNNNNNNN')]
f = Fa(cl, 'test-fa')
self.assertEqual([Sequence('>name2', 'NNNNNNNNNACTGNNNN'), Sequence('>name3', 'CTNACtacgatNNNNNNN')], f.remove(['>name']).contigs)
self.assertEqual([Sequence('>name', 'ACTGactg')], f.remove(['>name2','>name3']).contigs)
self.assertEqual([Sequence('>name', 'ACTGactg')], f.remove(['>name2','>name3','>name234']).contigs)
self.assertEqual([Sequence('>name2', 'NNNNNNNNNACTGNNNN'), Sequence('>name3', 'CTNACtacgatNNNNNNN')], f.remove(['>name']).contigs)
def test_statistics(self):
cl = [Sequence('>name', 'ACTGactg'), Sequence('>name2', 'NNNNNNNNNACTGNNNN'), Sequence('>name3', 'CTNACtacgatNNNNNNN'), Sequence('>name4', 'CTNAC')]
f = Fa(cl, 'test-fa')
stat = {
'A': 7, 'C': 8, 'T': 7, 'G': 4, 'N': 22, 'L': 48,
'nbp1000': 0, 'nbp5000': 0, 'nbp10000': 0, 'nbp25000': 0, 'nbp50000': 0,
'lbp1000': 0, 'lbp5000': 0, 'lbp10000': 0, 'lbp25000': 0, 'lbp50000': 0,
'totalc':4, 'N50':17, 'L50':2, 'N75':8, 'L75':3, 'N90':8, 'L90':3,
'longest':18
}
self.assertEqual(stat, f.statistics())
def test_sort(self):
cl = [Sequence('>name', 'ACTGactg'), Sequence('>name2', 'NNNNNNNNNACTGNNNN'), Sequence('>name3', 'CTNACtacgatNNNNNNN'), Sequence('>name4', 'CTNAC')]
f = Fa(cl, 'test-fa')
cl = [Sequence('>name3', 'CTNACtacgatNNNNNNN'), Sequence('>name2', 'NNNNNNNNNACTGNNNN'), Sequence('>name', 'ACTGactg'), Sequence('>name4', 'CTNAC')]
#for r in f.sort(1).contigs:
# print r
#for r in cl.reverse():
# print r
self.assertEqual(cl, f.sort(-1).contigs)
cl = [Sequence('>name4', 'CTNAC'), Sequence('>name', 'ACTGactg'), Sequence('>name2', 'NNNNNNNNNACTGNNNN'), Sequence('>name3', 'CTNACtacgatNNNNNNN')]
self.assertEqual(cl, f.sort(1).contigs)
def test_join(self):
cl = [Sequence('>name', 'ACTGactg'), Sequence('>name2', 'NNNNNNNNNACTGNNNN'), Sequence('>name3', 'CTNACtacgatNNNNNNN'), Sequence('>name4', 'CTNAC')]
f = Fa(cl, 'test-fa')
cl2 = [Sequence('>name', 'NNNNNNNN'), Sequence('>name5', 'NNNNNNNNNACTGNNNN'), Sequence('>name6', 'CTNACtacgatNNNNNNN')]
f2 = Fa(cl2, 'test2-fa')
f.join([f2])
cl.append(Sequence('>name5', 'NNNNNNNNNACTGNNNN'))
cl.append(Sequence('>name6', 'CTNACtacgatNNNNNNN'))
self.assertEqual(cl, f.contigs)
cl = [
Sequence('>name', 'ACTGactg'), Sequence('>name2', 'NNNNNNNNNACTGNNNN'), Sequence('>name3', 'CTNACtacgatNNNNNNN'), Sequence('>name4', 'CTNAC'),
Sequence('>name5', 'NNNNNACTGNNNN'), Sequence('>name6', 'CTNACtatNNN'), Sequence('>name7', 'NNNACTGN'), Sequence('>name8', 'CTNACtacgatNNNNNNN')
]
f = Fa([Sequence('>name', 'ACTGactg'), Sequence('>name2', 'NNNNNNNNNACTGNNNN')], 'fa1')
f2 = Fa([Sequence('>name3', 'CTNACtacgatNNNNNNN'), Sequence('>name4', 'CTNAC')], 'fa2')
f3 = Fa([Sequence('>name5', 'NNNNNACTGNNNN'), Sequence('>name6', 'CTNACtatNNN')], 'fa3')
f4 = Fa([Sequence('>name7', 'NNNACTGN'), Sequence('>name8', 'CTNACtacgatNNNNNNN')], 'fa4')
f.join([f2,f3,f4])
self.assertEqual(cl, f.contigs)
f = Fa([Sequence('>name', 'ACTGactg'), Sequence('>name2', 'NNNNNNNNNACTGNNNN'), Sequence('>name3', 'CTNACtacgatNNNNNNN')], 'fa1')
f2 = Fa([Sequence('>name3', 'CTNACtacgatNNNNNNN'), Sequence('>name4', 'CTNAC'), Sequence('>name', 'AnnnnnCTGactg')], 'fa2')
f3 = Fa([Sequence('>name5', 'NNNNNACTGNNNN'), Sequence('>name6', 'CTNACtatNNN'), Sequence('>name4', 'annaCTNAC'), Sequence('>name', 'AaaCTnnaGactg')], 'fa3')
f4 = Fa([Sequence('>name7', 'NNNACTGN'), Sequence('>name8', 'CTNACtacgatNNNNNNN'), Sequence('>name3', 'CTNaaaACtacgatNNNNNNN'), Sequence('>name', 'AnnnCTGactg')], 'fa4')
f.join([f2,f3,f4])
self.assertEqual(cl, f.contigs)
cl = [
Sequence('>name3', 'CTNACtacgatNNNNNNN'), Sequence('>name4', 'CTNAC'), Sequence('>name5', 'NNNNNACTGNNNN'), Sequence('>name', 'ACTGactg'),
Sequence('>name7', 'NNNACTGN'), Sequence('>name8', 'CTNACtacgatNNNNNNN'), Sequence('>name2', 'NNNNNNNNNACTGNNNN'), Sequence('>name6', 'CTNACtatNNN')
]
f = Fa([Sequence('>name', 'NNN'), Sequence('>name2', 'ACTGNNNN'), Sequence('>name3', 'NNNNNNN')], 'fa1')
f2 = Fa([Sequence('>name3', 'CTNACtacgatNNNNNNN'), Sequence('>name4', 'CTNAC')], 'fa2')
f3 = Fa([Sequence('>name5', 'NNNNNACTGNNNN'), Sequence('>name6', 'CTNNN'), Sequence('>name', 'ACTGactg')], 'fa3')
f4 = Fa([Sequence('>name7', 'NNNACTGN'), Sequence('>name8', 'CTNACtacgatNNNNNNN'),Sequence('>name2', 'NNNNNNNNNACTGNNNN'), Sequence('>name6', 'CTNACtatNNN') ], 'fa4')
f.join([f2,f3,f4], 1)
self.assertEqual(cl, f.contigs)
def test_load_from_file(self):
cl = [
Sequence('>name3', 'CTNACtacgatNNNNNNN'), Sequence('>name4', 'CTNAC'), Sequence('>name5', 'NNNNNACTGNNNN'), Sequence('>name', 'ACTGactg'),
Sequence('>name7', 'NNNACTGN'), Sequence('>name8', 'CTNACtacgatNNNNNNN'), Sequence('>name2', 'NNNNNNNNNACTGNNNN'), Sequence('>name6', 'CTNACtatNNN')
]
with open('test.fa') as f:
fob = Fa.load_from_file(f)
self.assertEqual('test.fa', fob.name)
self.assertEqual(cl, fob.contigs)
f2 = Fa.load_from_file('test.fa')
self.assertEqual('test.fa', f2.name)
self.assertEqual(cl, f2.contigs)
def test_write(self):
cl = [
Sequence('>name3', 'CTNACtacgatNNNNNNN'), Sequence('>name4', 'CTNAC'), Sequence('>name5', 'NNNNNACTGNNNN'), Sequence('>name', 'ACTGactg'),
Sequence('>name7', 'NNNACTGN'), Sequence('>name8', 'CTNACtacgatNNNNNNN'), Sequence('>name2', 'NNNNNNNNNACTGNNNN'), Sequence('>name6', 'CTNACtatNNN')
]
f = Fa(cl, 'fa1')
f.write('f2.fa')
with open('test.fa') as f1, open('f2.fa') as f2:
f1_content = f1.read()
f2_content = f2.read()
self.assertEqual(f1_content, f2_content)
def tearDown(self):
os.remove('f2.fa')
os.remove('test.fa')
pass
def test_conv_to_fq(self):
cl = []
test = 'ATGGAATCGGCTTTTAATACTGCAGGGGCGTTAAGTTGGCATGAACTCACAACCAATAATACCGAAGAGGCCATGCGCTTCTATGCTGAGATTTTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTATCACATTATTGAAAACGAGGGGATCAGCATTGGCGGAATTACCGACAGTTTAATCCCCACCCTTCCCTCACATTGGACTGGCTATATTACCGTTAACGATGTGGATCAAGTGGCTATCAGTGCTAAAAAACTCGGCGGTGACATTCTGTTTGGCCCTGAAGACATTCCAGAGGTGGGCCGTTTTTGTTGGATAAAAGACCCACAGGGCGCCATTATTGCGGCCATTAGCTATTTAAAACGTTGATGTAA'
cl.append(Sequence('>test', test))
cl.append(Sequence('>test2','ATGGAATCGGCTTTTAATACTGCAGGGGCGTTAAGTTGGCATGAACTCACAACCAATAATACCGAAGAGGCCATGCGCTTCTATGCTGAGATTTTTGGCTGGCACTTTAAAACCGTCAAAATGCCCCACGGTCACTNNNNNN'))
f = Fa(cl,'fa_test')
fq = f.convert_to_fq(40)
print fq
if __name__ == "__main__":
unittest.main()