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"""
Unit tests for ConvertHeaders
"""
# Info
__author__ = 'Jason Anthony Vander Heiden'
# Imports
import os
import sys
import time
import unittest
# Paths
test_path = os.path.dirname(os.path.realpath(__file__))
# Import script
sys.path.append(os.path.join(test_path, os.pardir, 'bin'))
import ConvertHeaders
class TestConvertHeaders(unittest.TestCase):
def setUp(self):
print('-> %s()' % self._testMethodName)
# IMGT
self.desc_imgt = ['M99641|IGHV1-18*01|Homo sapiens|F|V-REGION|188..483|296 nt|1| | | | |296+24=320| | |',
'Z29978|IGHV1-69*07|Homo sapiens|F|V-REGION|1..233|233 nt|1| | | | |233+58=291|partial in 5\' and in 3\' | |',
'AB019439|IGHV(III)-22-2*01|Homo sapiens|P|L-PART1+V-EXON|168065..168119+168222..168262|96 nt|1| | | | |96+0=96| | |',
'AE000659|TRAV11*01|Homo sapiens|(P)|V-REGION|85121..85397|276 nt|1| | | | |276+42=318| | |']
# GenBank
self.desc_genbank = ['gi|568336023|gb|CM000663.2| Homo sapiens chromosome 1, GRCh38 reference primary assembly',
'CM000663.2 Homo sapiens chromosome 1, GRCh38 reference primary assembly']
# SRA, ENA
self.desc_sra = ['SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36',
'SRR735691.1 GXGJ56Z01AE06X length=222',
'SRR1383326.1 1 length=250',
'SRR1383326.1.2 1 length=250',
'ERR346596.6 BS-DSFCONTROL04:4:000000000-A3F0Y:1:1101:13220:1649/1']
# 454
self.desc_454 = ['000034_0199_0169 length=437 uaccno=GNDG01201ARRCR',
'GXGJ56Z01AE06X length=222']
# Illumina, Solexa
self.desc_illumina = ['MISEQ:132:000000000-A2F3U:1:1101:14340:1555 1:N:0:ATCACG',
'HWI-EAS209_0006_FC706VJ:5:58:5894:21141#ATCACG/1',
'MS6_33112:1:1101:18371:1066/1']
# Start clock
self.start = time.time()
def tearDown(self):
# End clock
t = time.time() - self.start
print('<- %s() %.3f' % (self._testMethodName, t))
#@unittest.skip('-> convertGenericHeader() skipped\n')
def test_convertGenericHeader(self):
results = [ConvertHeaders.convertGenericHeader(x) for x in self.desc_genbank]
for x in results:
print('%s' % x)
self.assertTrue(all([x is not None for x in results]))
results = [ConvertHeaders.convertGenericHeader(x) for x in self.desc_imgt]
for x in results:
print('%s' % x)
self.assertTrue(all([x is not None for x in results]))
#@unittest.skip('-> convertIMGTHeader() skipped\n')
def test_convertIMGTHeader(self):
results = [ConvertHeaders.convertIMGTHeader(x) for x in self.desc_imgt]
for x in results:
print('%s' % x)
self.assertTrue(all([x is not None for x in results]))
results = [ConvertHeaders.convertIMGTHeader(x, simple=True) for x in self.desc_imgt]
for x in results:
print('%s' % x)
self.assertTrue(all([x is not None for x in results]))
#@unittest.skip('-> convertIlluminaHeader() skipped\n')
def test_convertIlluminaHeader(self):
results = [ConvertHeaders.convertIlluminaHeader(x) for x in self.desc_illumina]
for x in results:
print('%s' % x)
self.assertTrue(all([x is not None for x in results]))
#@unittest.skip('-> convertGenbankHeader() skipped\n')
def test_convertGenbankHeader(self):
results = [ConvertHeaders.convertGenbankHeader(x) for x in self.desc_genbank]
for x in results:
print('%s' % x)
self.assertTrue(all([x is not None for x in results]))
#@unittest.skip('-> convertSRAHeader() skipped\n')
def test_convertSRAHeader(self):
results = [ConvertHeaders.convertSRAHeader(x) for x in self.desc_sra]
for x in results:
print('%s' % x)
self.assertTrue(all([x is not None for x in results]))
#@unittest.skip('-> convert454Header() skipped\n')
def test_convert454Header(self):
results = [ConvertHeaders.convert454Header(x) for x in self.desc_454]
for x in results:
print('%s' % x)
self.assertTrue(all([x is not None for x in results]))
if __name__ == '__main__':
unittest.main()
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