def test_bwa_parse():
'''
Test BWA parser
'''
print('#%s: Test parse BWA' % __name__)
options = {'-t': 'BWA', '--bed': 'back_spliced_junction.bed',
'<fusion>': 'RNA_seq_bwa.sam', '--pe': False}
parse(options, command='CIRCexplorer2 parse (BWA)', name='parse')
check_fusion('back_spliced_junction.bed', 'parse_BWA/fusion_junction.bed')
def test_star_parse():
'''
Test STAR parser
'''
print('#%s: Test parse STAR' % __name__)
options = {'-t': 'STAR', '--bed': 'back_spliced_junction.bed',
'<fusion>': 'Chimeric.out.junction', '--pe': False}
parse(options, command='CIRCexplorer2 parse (STAR)', name='parse')
check_fusion('back_spliced_junction.bed', 'parse_STAR/fusion_junction.bed')
def test_segemehl_parse():
'''
Test segemehl parser
'''
print('#%s: Test parse segemehl' % __name__)
options = {'-t': 'segemehl', '--bed': 'back_spliced_junction.bed',
'<fusion>': 'splicesites.bed', '--pe': False}
parse(options, command='CIRCexplorer2 parse (segemehl)', name='parse')
check_fusion('back_spliced_junction.bed',
'parse_segemehl/fusion_junction.bed')
def test_mapsplice_parse():
'''
Test MapSplice parser
'''
print('#%s: Test parse MapSplice' % __name__)
options = {'-t': 'MapSplice', '--bed': 'back_spliced_junction.bed',
'<fusion>': 'fusions_raw.txt', '--pe': False}
parse(options, command='CIRCexplorer2 parse (Mapsplice)', name='parse')
check_fusion('back_spliced_junction.bed',
'parse_MapSplice/fusion_junction.bed')
def test_segemehl_parse():
'''
Test segemehl parser
'''
print('#%s: Test parse segemehl' % __name__)
options = {'-t': 'segemehl', '--output': 'circ_out',
'<fusion>': 'splicesites.bed', '--pe': False}
parse(options, command='CIRCexplorer2 parse (segemehl)', name='parse')
assert os.path.isdir('circ_out'), 'No circ_out directory'
check_file('fusion_junction.bed', 'circ_out', 'segemehl_out')
def test_tophat_fusion_parse():
'''
Test TopHat-Fusion parser
'''
print('#%s: Test parse TopHat-Fusion' % __name__)
options = {'-t': 'TopHat-Fusion', '--bed': 'back_spliced_junction.bed',
'<fusion>': 'tophat_fusion.bam', '--pe': False, '-f': False}
parse(options, command='CIRCexplorer2 parse (TopHat-Fusion)', name='parse')
check_fusion('back_spliced_junction.bed',
'parse_TopHat_Fusion/fusion_junction.bed')
def test_mapsplice_parse():
'''
Test MapSplice parser
'''
print('#%s: Test parse MapSplice' % __name__)
options = {'-t': 'MapSplice', '--output': 'circ_out',
'<fusion>': 'fusions_raw.txt', '--pe': False}
parse(options, command='CIRCexplorer2 parse (Mapsplice)', name='parse')
assert os.path.isdir('circ_out'), 'No circ_out directory'
check_file('fusion_junction.bed', 'circ_out', 'MapSplice_out')
def test_bwa_parse():
'''
Test BWA parser
'''
print('#%s: Test parse BWA' % __name__)
options = {'-t': 'BWA', '--output': 'circ_out',
'<fusion>': 'RNA_seq_bwa.sam', '--pe': False}
parse(options, command='CIRCexplorer2 parse (BWA)', name='parse')
assert os.path.isdir('circ_out'), 'No circ_out directory'
check_file('fusion_junction.bed', 'circ_out', 'BWA_out')
def test_tophat_fusion_parse():
'''
Test TopHat-Fusion parser
'''
print('#%s: Test parse TopHat-Fusion' % __name__)
options = {'-t': 'TopHat-Fusion', '--output': 'circ_out',
'<fusion>': 'tophat_fusion.bam', '--pe': False}
parse(options, command='CIRCexplorer2 parse (TopHat-Fusion)', name='parse')
assert os.path.isdir('circ_out'), 'No circ_out directory'
check_file('fusion_junction.bed', 'circ_out', 'TopHat_Fusion_out')
def test_star_parse():
'''
Test STAR parser
'''
print('#%s: Test parse STAR' % __name__)
options = {'-t': 'STAR', '--output': 'circ_out',
'<fusion>': 'Chimeric.out.junction', '--pe': False}
parse(options, command='CIRCexplorer2 parse (STAR)', name='parse')
assert os.path.isdir('circ_out'), 'No circ_out directory'
check_file('fusion_junction.bed', 'circ_out', 'STAR_out')
def test_bwa_parse():
'''
Test BWA parser
'''
print('#%s: Test parse BWA' % __name__)
options = {
'-t': 'BWA',
'--bed': 'back_spliced_junction.bed',
'<fusion>': 'RNA_seq_bwa.sam',
'--pe': False
}
parse(options, command='CIRCexplorer2 parse (BWA)', name='parse')
check_fusion('back_spliced_junction.bed', 'parse_BWA/fusion_junction.bed')
def test_star_parse():
'''
Test STAR parser
'''
print('#%s: Test parse STAR' % __name__)
options = {
'-t': 'STAR',
'--bed': 'back_spliced_junction.bed',
'<fusion>': 'Chimeric.out.junction',
'--pe': False
}
parse(options, command='CIRCexplorer2 parse (STAR)', name='parse')
check_fusion('back_spliced_junction.bed', 'parse_STAR/fusion_junction.bed')
def test_mapsplice_parse():
'''
Test MapSplice parser
'''
print('#%s: Test parse MapSplice' % __name__)
options = {
'-t': 'MapSplice',
'--bed': 'back_spliced_junction.bed',
'<fusion>': 'fusions_raw.txt',
'--pe': False
}
parse(options, command='CIRCexplorer2 parse (Mapsplice)', name='parse')
check_fusion('back_spliced_junction.bed',
'parse_MapSplice/fusion_junction.bed')
def test_tophat_fusion_parse():
'''
Test TopHat-Fusion parser
'''
print('#%s: Test parse TopHat-Fusion' % __name__)
options = {
'-t': 'TopHat-Fusion',
'--bed': 'back_spliced_junction.bed',
'<fusion>': 'tophat_fusion.bam',
'--pe': False
}
parse(options, command='CIRCexplorer2 parse (TopHat-Fusion)', name='parse')
check_fusion('back_spliced_junction.bed',
'parse_TopHat_Fusion/fusion_junction.bed')
def test_segemehl_parse():
'''
Test segemehl parser
'''
print('#%s: Test parse segemehl' % __name__)
options = {
'-t': 'segemehl',
'--bed': 'back_spliced_junction.bed',
'<fusion>': 'splicesites.bed',
'--pe': False
}
parse(options, command='CIRCexplorer2 parse (segemehl)', name='parse')
check_fusion('back_spliced_junction.bed',
'parse_segemehl/fusion_junction.bed')