def test_describe_derived_fields(self):
desc = describe_fields(('dist_closest',
'dist_TSS','dist_TES',
'direction',
'overlap_feature',
'overlap_promoter',
'in_the_feature',
'order','number_of_results'))
expected_fields = dict()
for x in ('dist_closest',
'dist_TSS','dist_TES',
'direction',
'overlap_feature',
'overlap_promoter',
'in_the_feature',
'order','number_of_results'):
expected_fields[x] = output.FIELDS[x].\
replace("<FEATURE>","feature").\
replace("<SOURCE>","source").\
replace("<TARGET>","target")
self.assertEqual(desc[0],('dist_closest',
expected_fields['dist_closest']))
self.assertEqual(desc[1],('dist_TSS',expected_fields['dist_TSS']))
self.assertEqual(desc[2],('dist_TES',expected_fields['dist_TES']))
self.assertEqual(desc[3],('direction',expected_fields['direction']))
self.assertEqual(desc[4],('overlap_feature',
expected_fields['overlap_feature']))
self.assertEqual(desc[5],('overlap_promoter',
expected_fields['overlap_promoter']))
self.assertEqual(desc[6],('in_the_feature',
expected_fields['in_the_feature']))
self.assertEqual(desc[7],('order',expected_fields['order']))
self.assertEqual(desc[8],('number_of_results',
expected_fields['number_of_results']))
def test_describe_derived_fields(self):
desc = describe_fields(('dist_closest',
'dist_TSS','dist_TES',
'direction',
'overlap_feature',
'overlap_promoter',
'in_the_feature',
'order','number_of_results'))
expected_fields = dict()
for x in ('dist_closest',
'dist_TSS','dist_TES',
'direction',
'overlap_feature',
'overlap_promoter',
'in_the_feature',
'order','number_of_results'):
expected_fields[x] = output.FIELDS[x].\
replace("<FEATURE>","feature").\
replace("<SOURCE>","source").\
replace("<TARGET>","target")
self.assertEqual(desc[0],('dist_closest',
expected_fields['dist_closest']))
self.assertEqual(desc[1],('dist_TSS',expected_fields['dist_TSS']))
self.assertEqual(desc[2],('dist_TES',expected_fields['dist_TES']))
self.assertEqual(desc[3],('direction',expected_fields['direction']))
self.assertEqual(desc[4],('overlap_feature',
expected_fields['overlap_feature']))
self.assertEqual(desc[5],('overlap_promoter',
expected_fields['overlap_promoter']))
self.assertEqual(desc[6],('in_the_feature',
expected_fields['in_the_feature']))
self.assertEqual(desc[7],('order',expected_fields['order']))
self.assertEqual(desc[8],('number_of_results',
expected_fields['number_of_results']))
def test_describe_listed_fields_for_features(self):
desc = describe_fields(('chr','start','list(id,TSS,strand)'))
self.assertEqual(desc[0],('chr',output.FIELDS['chr']))
self.assertEqual(desc[1],('start',output.FIELDS['start']))
self.assertEqual(desc[2],(('For each hit:',)))
self.assertEqual(desc[3],('id_#',output.FIELDS['id']))
self.assertEqual(desc[4],('TSS_#',output.FIELDS['TSS']))
self.assertEqual(desc[5],('strand_#',output.FIELDS['strand']))
def test_describe_peak_fields(self):
desc = describe_fields(('peak.id','peak.chr','peak.start','peak.end',
'peak.file'))
self.assertEqual(desc[0],('peak.id',output.FIELDS['peak.id']))
self.assertEqual(desc[1],('peak.chr',output.FIELDS['peak.chr']))
self.assertEqual(desc[2],('peak.start',output.FIELDS['peak.start']))
self.assertEqual(desc[3],('peak.end',output.FIELDS['peak.end']))
self.assertEqual(desc[4],('peak.file',output.FIELDS['peak.file']))
def test_describe_listed_fields_for_peaks(self):
desc = describe_fields(('id','list(chr,start,end,dist_TSS)'))
self.assertEqual(desc[0],('id',output.FIELDS['id']))
self.assertEqual(desc[1],(('For each hit:',)))
self.assertEqual(desc[2],('chr_#',output.FIELDS['chr']))
self.assertEqual(desc[3],('start_#',output.FIELDS['start']))
self.assertEqual(desc[4],('end_#',output.FIELDS['end']))
self.assertEqual(desc[5],('dist_TSS_#',output.FIELDS['dist_TSS']))
def test_describe_unqualified_fields(self):
desc = describe_fields(('chr','start','end','id',
'strand','TSS','TES',
'differentially_expressed'))
self.assertEqual(desc[0],('chr',output.FIELDS['chr']))
self.assertEqual(desc[1],('start',output.FIELDS['start']))
self.assertEqual(desc[2],('end',output.FIELDS['end']))
self.assertEqual(desc[3],('id',output.FIELDS['id']))
self.assertEqual(desc[4],('strand',output.FIELDS['strand']))
self.assertEqual(desc[5],('TSS',output.FIELDS['TSS']))
self.assertEqual(desc[6],('TES',output.FIELDS['TES']))
def test_describe_listed_fields_for_peaks(self):
desc = describe_fields(('id','list(chr,start,end,dist_TSS)'))
expected_fields = dict()
for x in ('id','chr','start','end','dist_TSS'):
expected_fields[x] = output.FIELDS[x].\
replace("<FEATURE>","feature")
self.assertEqual(desc[0],('id',expected_fields['id']))
self.assertEqual(desc[1],(('For each hit:',)))
self.assertEqual(desc[2],('chr_#',expected_fields['chr']))
self.assertEqual(desc[3],('start_#',expected_fields['start']))
self.assertEqual(desc[4],('end_#',expected_fields['end']))
self.assertEqual(desc[5],('dist_TSS_#',expected_fields['dist_TSS']))
def test_describe_listed_fields_for_features(self):
desc = describe_fields(('chr','start','list(id,TSS,strand)'))
expected_fields = dict()
for x in ('chr','start','id','TSS','strand'):
expected_fields[x] = output.FIELDS[x].\
replace("<FEATURE>","feature")
self.assertEqual(desc[0],('chr',expected_fields['chr']))
self.assertEqual(desc[1],('start',expected_fields['start']))
self.assertEqual(desc[2],(('For each hit:',)))
self.assertEqual(desc[3],('id_#',expected_fields['id']))
self.assertEqual(desc[4],('TSS_#',expected_fields['TSS']))
self.assertEqual(desc[5],('strand_#',expected_fields['strand']))
def test_describe_listed_fields_for_features(self):
desc = describe_fields(('chr','start','list(id,TSS,strand)'))
expected_fields = dict()
for x in ('chr','start','id','TSS','strand'):
expected_fields[x] = output.FIELDS[x].\
replace("<FEATURE>","feature")
self.assertEqual(desc[0],('chr',expected_fields['chr']))
self.assertEqual(desc[1],('start',expected_fields['start']))
self.assertEqual(desc[2],(('For each hit:',)))
self.assertEqual(desc[3],('id_#',expected_fields['id']))
self.assertEqual(desc[4],('TSS_#',expected_fields['TSS']))
self.assertEqual(desc[5],('strand_#',expected_fields['strand']))
def test_describe_listed_fields_for_peaks(self):
desc = describe_fields(('id','list(chr,start,end,dist_TSS)'))
expected_fields = dict()
for x in ('id','chr','start','end','dist_TSS'):
expected_fields[x] = output.FIELDS[x].\
replace("<FEATURE>","feature")
self.assertEqual(desc[0],('id',expected_fields['id']))
self.assertEqual(desc[1],(('For each hit:',)))
self.assertEqual(desc[2],('chr_#',expected_fields['chr']))
self.assertEqual(desc[3],('start_#',expected_fields['start']))
self.assertEqual(desc[4],('end_#',expected_fields['end']))
self.assertEqual(desc[5],('dist_TSS_#',expected_fields['dist_TSS']))
def test_describe_feature_fields(self):
desc = describe_fields(('feature.chr','feature.id',
'feature.start','feature.end',
'feature.strand',
'feature.TSS','feature.TES'))
self.assertEqual(desc[0],('feature.chr',output.FIELDS['feature.chr']))
self.assertEqual(desc[1],('feature.id',output.FIELDS['feature.id']))
self.assertEqual(desc[2],('feature.start',
output.FIELDS['feature.start']))
self.assertEqual(desc[3],('feature.end',output.FIELDS['feature.end']))
self.assertEqual(desc[4],('feature.strand',
output.FIELDS['feature.strand']))
self.assertEqual(desc[5],('feature.TSS',output.FIELDS['feature.TSS']))
self.assertEqual(desc[6],('feature.TES',output.FIELDS['feature.TES']))
def test_describe_unqualified_fields(self):
desc = describe_fields(('chr','start','end','id',
'strand','TSS','TES',
'differentially_expressed'))
expected_fields = dict()
for x in ('chr','start','end','id',
'strand','TSS','TES',
'differentially_expressed'):
expected_fields[x] = output.FIELDS[x].\
replace("<FEATURE>","feature")
self.assertEqual(desc[0],('chr',expected_fields['chr']))
self.assertEqual(desc[1],('start',expected_fields['start']))
self.assertEqual(desc[2],('end',expected_fields['end']))
self.assertEqual(desc[3],('id',expected_fields['id']))
self.assertEqual(desc[4],('strand',expected_fields['strand']))
self.assertEqual(desc[5],('TSS',expected_fields['TSS']))
self.assertEqual(desc[6],('TES',expected_fields['TES']))
def test_describe_unqualified_fields(self):
desc = describe_fields(('chr','start','end','id',
'strand','TSS','TES',
'differentially_expressed'))
expected_fields = dict()
for x in ('chr','start','end','id',
'strand','TSS','TES',
'differentially_expressed'):
expected_fields[x] = output.FIELDS[x].\
replace("<FEATURE>","feature")
self.assertEqual(desc[0],('chr',expected_fields['chr']))
self.assertEqual(desc[1],('start',expected_fields['start']))
self.assertEqual(desc[2],('end',expected_fields['end']))
self.assertEqual(desc[3],('id',expected_fields['id']))
self.assertEqual(desc[4],('strand',expected_fields['strand']))
self.assertEqual(desc[5],('TSS',expected_fields['TSS']))
self.assertEqual(desc[6],('TES',expected_fields['TES']))
def test_update_placeholders_in_fields(self):
desc = describe_fields(('chr','start','list(id,TSS,strand,direction)'),
feature="gene",
source="peak",
target="gene")
expected_fields = dict()
for x in ('chr','start','id','TSS','strand','direction'):
expected_fields[x] = output.FIELDS[x].\
replace("<FEATURE>","gene").\
replace("<SOURCE>","peak").\
replace("<TARGET>","gene")
self.assertEqual(desc[0],('chr',expected_fields['chr']))
self.assertEqual(desc[1],('start',expected_fields['start']))
self.assertEqual(desc[2],(('For each hit:',)))
self.assertEqual(desc[3],('id_#',expected_fields['id']))
self.assertEqual(desc[4],('TSS_#',expected_fields['TSS']))
self.assertEqual(desc[5],('strand_#',expected_fields['strand']))
self.assertEqual(desc[6],('direction_#',
expected_fields['direction']))
def test_update_placeholders_in_fields(self):
desc = describe_fields(('chr','start','list(id,TSS,strand,direction)'),
feature="gene",
source="peak",
target="gene")
expected_fields = dict()
for x in ('chr','start','id','TSS','strand','direction'):
expected_fields[x] = output.FIELDS[x].\
replace("<FEATURE>","gene").\
replace("<SOURCE>","peak").\
replace("<TARGET>","gene")
self.assertEqual(desc[0],('chr',expected_fields['chr']))
self.assertEqual(desc[1],('start',expected_fields['start']))
self.assertEqual(desc[2],(('For each hit:',)))
self.assertEqual(desc[3],('id_#',expected_fields['id']))
self.assertEqual(desc[4],('TSS_#',expected_fields['TSS']))
self.assertEqual(desc[5],('strand_#',expected_fields['strand']))
self.assertEqual(desc[6],('direction_#',
expected_fields['direction']))
def test_describe_feature_fields(self):
desc = describe_fields(('feature.chr','feature.id',
'feature.start','feature.end',
'feature.strand',
'feature.TSS','feature.TES'))
expected_fields = dict()
for x in ('feature.chr','feature.id',
'feature.start','feature.end',
'feature.strand',
'feature.TSS','feature.TES'):
expected_fields[x] = output.FIELDS[x].\
replace("<FEATURE>","feature")
self.assertEqual(desc[0],('feature.chr',expected_fields['feature.chr']))
self.assertEqual(desc[1],('feature.id',expected_fields['feature.id']))
self.assertEqual(desc[2],('feature.start',
expected_fields['feature.start']))
self.assertEqual(desc[3],('feature.end',expected_fields['feature.end']))
self.assertEqual(desc[4],('feature.strand',
expected_fields['feature.strand']))
self.assertEqual(desc[5],('feature.TSS',expected_fields['feature.TSS']))
self.assertEqual(desc[6],('feature.TES',expected_fields['feature.TES']))
def test_describe_derived_fields(self):
desc = describe_fields(('dist_closest',
'dist_TSS','dist_TES',
'direction',
'overlap_feature',
'overlap_promoter',
'in_the_feature',
'order','number_of_results'))
self.assertEqual(desc[0],('dist_closest',
output.FIELDS['dist_closest']))
self.assertEqual(desc[1],('dist_TSS',output.FIELDS['dist_TSS']))
self.assertEqual(desc[2],('dist_TES',output.FIELDS['dist_TES']))
self.assertEqual(desc[3],('direction',output.FIELDS['direction']))
self.assertEqual(desc[4],('overlap_feature',
output.FIELDS['overlap_feature']))
self.assertEqual(desc[5],('overlap_promoter',
output.FIELDS['overlap_promoter']))
self.assertEqual(desc[6],('in_the_feature',
output.FIELDS['in_the_feature']))
self.assertEqual(desc[7],('order',output.FIELDS['order']))
self.assertEqual(desc[8],('number_of_results',
output.FIELDS['number_of_results']))
def test_describe_feature_fields(self):
desc = describe_fields(('feature.chr','feature.id',
'feature.start','feature.end',
'feature.strand',
'feature.TSS','feature.TES',
'feature.file'))
expected_fields = dict()
for x in ('feature.chr','feature.id',
'feature.start','feature.end',
'feature.strand',
'feature.TSS','feature.TES',
'feature.file'):
expected_fields[x] = output.FIELDS[x].\
replace("<FEATURE>","feature")
self.assertEqual(desc[0],('feature.chr',expected_fields['feature.chr']))
self.assertEqual(desc[1],('feature.id',expected_fields['feature.id']))
self.assertEqual(desc[2],('feature.start',
expected_fields['feature.start']))
self.assertEqual(desc[3],('feature.end',expected_fields['feature.end']))
self.assertEqual(desc[4],('feature.strand',
expected_fields['feature.strand']))
self.assertEqual(desc[5],('feature.TSS',expected_fields['feature.TSS']))
self.assertEqual(desc[6],('feature.TES',expected_fields['feature.TES']))
self.assertEqual(desc[7],('feature.file',expected_fields['feature.file']))
def test_field_with_no_description(self):
desc = describe_fields(('missing_desc',))
self.assertEqual(desc[0],('missing_desc','missing_desc'))
def test_describe_peak_fields(self):
desc = describe_fields(('peak.chr','peak.start','peak.end'))
self.assertEqual(desc[0],('peak.chr',output.FIELDS['peak.chr']))
self.assertEqual(desc[1],('peak.start',output.FIELDS['peak.start']))
self.assertEqual(desc[2],('peak.end',output.FIELDS['peak.end']))