def test_strobj_DYS390(sequence, bracketed, conc, lus, sec, tert, flank_5p,
kit):
marker = STRMarkerObject('DYS390', sequence, uas=False, kit=kit)
assert marker.annotation == bracketed
assert str(marker.canonical) == conc
assert marker.designation == (lus, sec, tert)
assert marker.flank_5p == flank_5p
def test_strobj_D18S51(sequence, bracketed, lus, sec, tert, flank_5, flank_3,
kit):
marker = STRMarkerObject('D18S51', sequence, uas=False, kit=kit)
assert marker.annotation == bracketed
assert marker.designation == (lus, sec, tert)
assert marker.flank_5p == flank_5
assert marker.flank_3p == flank_3
def test_annotation_and_lus(locus, sequence, forward_bracket, lus, sec, tert):
marker = STRMarkerObject(locus, sequence, uas=True)
assert marker.annotation == forward_bracket
lus_out, sec_out, tert_out = marker.designation
assert str(lus_out) == lus
assert str(sec_out) == sec
assert str(tert_out) == tert
def test_strobj_DXS10074(sequence, bracketed, conc, lus, sec, tert, flank_5p,
flank_3p):
marker = STRMarkerObject('DXS10074', sequence, uas=False, kit='forenseq')
assert marker.annotation == bracketed
assert str(marker.canonical) == conc
assert marker.designation == (lus, sec, tert)
assert marker.flank_5p == flank_5p
assert marker.flank_3p == flank_3p
def test_new_power_config(locus, sequence, bracketed, conc, lus, sec, tert,
flank_5, flank_3):
marker = STRMarkerObject(locus, sequence, uas=False, kit='powerseq')
assert marker.annotation == bracketed
assert str(marker.canonical) == conc
assert marker.designation == (lus, sec, tert)
assert marker.flank_5p == flank_5
assert marker.flank_3p == flank_3
def test_strobj_D19S433_newformat():
marker = STRMarkerObject(
'D19S433',
'AATAAAAATCTTCTCTCTTTCTTCCTCTCTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTACCT'
'TCCTTCCTTCAACAGAATCTTATTCTGTTGCCCAGGCTGGAGTCCAGTGTTACAATTATAGCT',
uas=False,
kit='forenseq')
assert marker.annotation == 'CT CTCT TTCT TCCT CTCT [CCTT]12 CCTA [CCTT]3'
def test_D21_lus_sec():
sequence = (
'TCTATCTATCTATCTATCTGTCTGTCTGTCTGTCTGTCTGTCTATCTATCTATATCTATCTATCTATCATCTATCTATCCATATCTATC'
'TATCTATCTATCTATCTATCTATCTATCTATCTA')
marker = STRMarkerObject('D21S11', sequence, uas=True)
lus, sec, tert = marker.designation
assert str(lus) == '10'
assert str(sec) == '4'
assert str(tert) == '6'
def test_strobj_D21S11_newformat():
marker = STRMarkerObject(
'D21S11',
'AAATATGTGAGTCAATTCCCCAAGTGAATTGCCTTCTATCTATCTATCTATCTATCTGTCTGTCTGTCTGTCTGTCTGTCTATCT'
'ATCTATATCTATCTATCTATCATCTATCTATCCATATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATATCT'
'ACTATCTAT',
uas=False,
kit='forenseq')
assert marker.annotation == (
'[TCTA]5 [TCTG]6 [TCTA]3 TA [TCTA]3 TCA [TCTA]2 TCCATA [TCTA]11 TA')
def test_FGA_anno():
uas_sequence = (
'TTTCTTTCTTTCTTTCTTTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTGTCTGTCTGTCTTTCTTTCTTTCTTTCTT'
'TCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTCCTTCCTTCCTTTCTTTCTTTCTCCTTCCTTCCTTCCTTCC'
)
annotation = '[GGAA]4 GGAG [AAAG]3 [GAAG]3 [AAAG]15 [ACAG]3 [AAAG]9 AA AAAA [GAAA]4'
marker = STRMarkerObject('FGA', uas_sequence, uas=True)
print(annotation)
print(marker.annotation)
assert marker.annotation == annotation
def test_strobj_DYS533():
marker = STRMarkerObject(
'DYS533',
'TAACTATATAACTATGTATTATCTATCAATCTTCTACCTATCATCTTTCTAGCTAGCTATCATCTATCTATCTATCTA'
'TCTATCTATCTATCTATCTATCTATCTATCTATCTATCATCTATCATCTTCTATTGTTT',
uas=False,
kit='forenseq')
assert marker.annotation == '[TATC]13'
assert str(marker.canonical) == '13'
assert marker.designation == ('13', None, None)
assert marker.flank_3p == 'ATCT ATCA TCTT CTAT TGTT T'
def test_strobj_DYS576_foren():
marker = STRMarkerObject(
'DYS576',
'AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAAGCCAA'
'GACAAATACGCTTATTACTCCCATCTCCT',
uas=False,
kit='forenseq')
assert marker.annotation == '[AAAG]17'
assert str(marker.canonical) == '17'
assert marker.designation == ('17', None, None)
assert marker.flank_3p == 'AAAA AGCC AAGA CAAA TACG CTTA TTAC TCCC ATCT CCT'
def test_strobj_DYS612():
marker = STRMarkerObject(
'DYS612',
'TTTCACACAGGTTCAGAGGTTTGCCTCCTCCTCCTCCTCTTTCTTCTTCTTCTCCTTCTTCTTCTTCTTCTTCTTCTT'
'CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTGTCACTTTTCCAAATTATTTTCTTTT',
uas=False,
kit='forenseq')
assert marker.annotation == '[CCT]5 CTT [TCT]4 CCT [TCT]24'
assert marker.canonical == 29
assert marker.designation == (24, 4, None)
assert marker.flank_3p == 'G TCA CTT TTC CAA [ATT]2 TTC TTT T'
def test_strobj_DYS635_foren():
marker = STRMarkerObject(
'DYS635',
'ATCAATCAATGAATGGATAAAGAAAATGTGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAG'
'ATACATACATAGATAGATACATACATAGATAGATAGATAGAGATTCTATGCAAAGTGAGAAGCCA',
uas=False,
kit='forenseq')
assert marker.annotation == '[TAGA]12 [TACA]2 [TAGA]2 [TACA]2 [TAGA]4'
assert str(marker.canonical) == '22'
assert marker.designation == ('12', None, None)
assert marker.flank_5p == 'A [TCAA]2 TGAA TGGA TAAA GAAA ATGT GA'
def test_strobj_DYS643_foren():
marker = STRMarkerObject(
'DYS643',
'TGATTTTTGCAGGTGTTCACTGCAAGCCATGCCTGGTTAAACTACTGTGCCTTTTCTTTTCTTTTCTTTTCTTTTCTT'
'TTCTTTTCTTTTCTTTTCTTTTCTTTCTTTTTAAAACTT',
uas=False,
kit='forenseq')
assert marker.annotation == '[CTTTT]10 CTTTC TTTT'
assert str(marker.canonical) == '10'
assert marker.designation == ('10', None, None)
assert marker.flank_3p == 'TAAAA CTT'
def test_strobj_DYS391_foren():
marker = STRMarkerObject(
'DYS391',
'ATATCTGTCTGTCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTGCCTATCT'
'GCCTGCCTACCTATCCCTCTAT',
uas=False,
kit='forenseq')
assert marker.annotation == '[TCTG]3 [TCTA]13 TCTG'
assert str(marker.canonical) == '13'
assert marker.designation == ('13', None, None)
assert marker.flank_3p == 'CCTA TCT [GCCT]2 ACCT ATCC CTCT AT'
def test_strobj_DYS522():
marker = STRMarkerObject(
'DYS522',
'AGTTAGAGAGAGAGATGATGGATAGATAAATAGATAGATGATAGATGAATAGATAGGCGGGTAATAGATTTTATATAG'
'ATAGATGATAGCTAGATAATGGATAGACATAGGTGACAGATGATAAATACATAGATAAATAGATGATAGATAGATAGATAGATAGATA'
'GATAGATAGATAGATAGATAGATAGACAGATGTCCACCATGAGGTTC',
uas=False,
kit='forenseq')
assert marker.annotation == 'ATA GATG [ATAG]12'
assert marker.canonical == 12
assert marker.designation == ('12', None, None)
def test_strobj_D7S820():
marker = STRMarkerObject(
'D7S820',
'TATTTAGTGAGATAAAAAAAAAACTATCAATCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCGTT'
'AGTTCGTTCTAAACTAT',
uas=False,
kit='forenseq')
assert marker.uas_sequence == 'GATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGACAGATTGATAGTTTT'
assert marker.forward_sequence == 'AAAACTATCAATCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATC'
assert marker.flank_5p == 'T ATTT AGTG AGAT AAAAAA'
assert marker.flank_3p == 'GTTA [GTTC]2 TAAA CTAT'
assert marker.annotation == 'A AAAC TATC AATC TGTC [TATC]10'
def test_strobj_D5S818():
marker = STRMarkerObject(
'D5S818',
'TATTTATACCTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTTCAAAAT',
uas=False,
kit='forenseq')
assert marker.uas_sequence == 'AGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGAG'
assert marker.forward_sequence == 'CTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCT'
assert marker.annotation == 'CTCT [ATCT]12'
assert marker.annotation_uas == '[AGAT]12 AGAG'
assert marker.canonical == 12, ' '
assert marker.designation == ('12', None, None)
def test_strobj_D16S539():
marker = STRMarkerObject(
'D16S539',
'TCCTCTTCCCTAGATCAATACAGACAGACAGACAGGTGGATAGATAGATAGATTGATTGATAGATAGATAGATAGATA'
'TCATTGAAAGACAAAACAGAGATGGATGATAGATAC',
uas=False,
kit='forenseq')
assert marker.uas_sequence == 'GATAGATAGATAGATTGATTGATAGATAGATAGATAGATA'
assert marker.forward_sequence == 'GATAGATAGATAGATTGATTGATAGATAGATAGATAGATA'
assert marker.flank_5p == 'TC CTCT T CCCT AGAT CAAT [ACAG]4 GTG'
assert marker.flank_3p == 'TCAT TGAA AGAC AAA A CAGA [GATG]2 ATA GA T AC'
assert marker.annotation == '[GATA]3 [GATT]2 [GATA]5'
def test_strobj_Y_GATA_H4():
marker = STRMarkerObject(
'Y-GATA-H4',
'CTATCTATCTATCTATTCATCCATCTAATCTATCCATTCTATCTATCTATCTATCTATCTATCTATCTATCTATC'
'TATCTACCTACCTACCTATCTATCTATAGATCTATCTATCTATCT',
uas=False,
kit='forenseq')
assert marker.annotation == (
'C [TATC]3 TATT [CATC]2 TAAT CTAT CCAT [TCTA]11 [CCTA]3 [TCTA]2 TAGA [TCTA]3 TCT'
)
assert str(marker.canonical) == '11'
assert marker.designation == ('11', None, None)
def test_strobj_DYS19_foren():
marker = STRMarkerObject(
'DYS19',
'TGGTCAATCTCTGCACCTGGAAATAGTGGCTGGGGCACCAGGAGTAATACTTCGGGCCATGGCCATGTAGTGAGGACAA'
'GGAGTCCATCTGGGTTAAGGAGAGTGTCACTATATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTACCTATCTATC'
'TATCTA',
uas=False,
kit='forenseq')
assert marker.annotation == '[TCTA]11 CCTA [TCTA]3'
assert str(marker.canonical) == '14'
assert marker.designation == ('11', None, None)
assert marker.flank_3p == ''
def test_strobj_D10S1248():
marker = STRMarkerObject(
'D10S1248',
'TTGAACAAATGAGTGAGTGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAATGAAGA'
'CAATACAACCAGAGTT',
uas=False,
kit='forenseq')
assert marker.uas_sequence == 'GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA'
assert marker.forward_sequence == 'GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA'
assert marker.annotation == '[GGAA]13'
assert marker.annotation_uas == '[GGAA]13'
assert marker.canonical == 13, ' '
assert marker.designation == ('13', None, None)
def test_strobj_D1S1656():
marker = STRMarkerObject(
'D1S1656',
'TTCAGAGAAATAGAATCACTAGGGAACCAAATATATATACATACAATTAAACACACACACACCTATCTATCTATCTAT'
'CTATCTATCTATCTATCTATCTATCTATCTA',
uas=False,
kit='forenseq')
assert marker.uas_sequence == 'TAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGGTGTGTGTGTG'
assert marker.forward_sequence == 'CACACACACACCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA'
assert marker.annotation == 'CA [CACA]2 CCTA [TCTA]11'
assert marker.annotation_uas == '[TAGA]11 TAGG [TGTG]2 TG'
assert marker.canonical == 12, ' '
assert marker.designation == ('11', '1', '0')
def test_strobj_DYS549_foren():
marker = STRMarkerObject(
'DYS549',
'TAATAAGGTAGACATAGCAATTAGGTAGGTAAAGAGGAAGATGATAGATGATTAGAAAGATGATAGATAGATAGATAG'
'ATAGATAGATAGATAGATAGATAGATAGATAGATAGAAAAAATCTACATAAACAAAATCACAAATGGAAAAGGGGACATTACCA',
uas=False,
kit='forenseq')
assert marker.annotation == '[GATA]13'
assert str(marker.canonical) == '13'
assert marker.designation == ('13', None, None)
assert marker.flank_5p == (
'TA ATAA GGTA GACA TAGC AATT [AGGT]2 AAAG AGGA AGAT GATA GATG ATTA GAAA GAT'
)
def test_strobj_DXS7132():
marker = STRMarkerObject(
'DXS7132',
'TCCAGAGAAACAGAACCAATAGGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGACAGTCAGATAGA'
'TGAGAGGGGATTTATTATGAAAATGGGCTCACACTATTAAGGAGGCTAAGAAGTTCCACAGTAT',
uas=False,
kit='forenseq')
assert marker.annotation == '[TAGA]13'
assert marker.canonical == 13
assert marker.designation == ('13', None, None)
assert marker.flank_3p == (
'CAGT C [AGAT]2 GAGA GGGG ATTT ATTA TGAA AAT G GGCT CACA CTAT TAAG GAGG CTAA GAAG TTCC '
'ACAG TAT')
def test_strobj_HPRTB():
marker = STRMarkerObject(
'HPRTB',
'CTAGAACTTATCTTCTGTAAATCTGTCTCTATTTCCATCTCTGTCTCCATCTTTGTCTCTATCTCTATCTGTCTATCTCTATCTATCT'
'ATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTAAAGCAAATTCATGCCCTTCTCCTATTT',
uas=False,
kit='forenseq')
assert marker.annotation == '[ATCT]12'
assert marker.canonical == 12
assert marker.designation == ('12', None, None)
assert marker.flank_5p == (
'CTAG AACT TATC TTCT GTAA ATCT GTCT CTAT TTCC ATCT CTGT CTCC ATCT TTGT CTCT ATCT CTAT '
'CTGT CTAT C TCT')
def test_strobj_CSF1PO():
marker = STRMarkerObject(
'CSF1PO',
'CTTCCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTAATCTATCTATCTT',
uas=False,
kit='forenseq')
assert marker.uas_sequence == 'AGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGAT'
assert marker.forward_sequence == 'ATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCT'
assert marker.annotation == '[ATCT]12'
assert marker.annotation_uas == '[AGAT]12'
assert marker.canonical == 12, ' '
assert marker.designation == ('12', '0', None)
assert marker.flank_5p == 'CT TCCT'
def test_strobj_DYS392_foren():
marker = STRMarkerObject(
'DYS392',
'TTAAACCTACCAATCCCATTCCTTAGTAAATAATAATAATAATAATAATAATAATAATAATAATAATAAATAAATGGT'
'GATACAAGAAAAAAATTTGTTTTCCTTCTTGGCTTTTAAATAACAAACACTTGAAATCAAATTAGTTGTTTTTAAAAGCTAGATTAAT'
'GAAGAA',
uas=False,
kit='forenseq')
assert marker.annotation == '[ATA]13'
assert str(marker.canonical) == '13'
assert marker.designation == ('13', None, None)
assert marker.flank_3p == (
'AAT AAA TGG TGA TAC AAG [AAA]2 ATT TGT TTT CCT TCT TGG CTT TTA AAT AAC AAA CAC TTG AAA '
'TCA AAT TAG TTG TTT TTA AAA GCT AGA TTA ATG AAG AA')
def test_strobj_DYS437_foren():
marker = STRMarkerObject(
'DYS437',
'ATGCCCATCCGGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTGTCTGTCTGTCTATCTATCTATCTATC'
'ATCTATCATCTGTGAATGATGTCTATCTACTTATCTATGAATGATATTTATCTGTGGTTATCTATCTATCTATATCATCTGTGAATGA'
'CAGGGTCTTCCTCTG',
uas=False,
kit='forenseq')
assert marker.annotation == '[TCTA]9 [TCTG]3 [TCTA]4'
assert str(marker.canonical) == '16'
assert marker.designation == ('9', None, None)
assert marker.flank_3p == (
'TCA TCTA TCAT CTGT GAAT GATG [TCTA]2 CTTA TCTA TGAA TGAT ATTT ATCT GTGG TTAT [CTAT]3 '
'ATCA TCTG TGAA TGAC AGGG TCTT CCTC TG')
def test_strobj_DXS8378():
marker = STRMarkerObject(
'DXS8378',
'AGTGAGCTGAGATGGTGCCACTGAACTCCAGCCTGGGCGACAAGAGCGAAACTCCAACTCAAAAAATAAATAAATAAAATATAGATAG'
'ATAGATAGATAGATAGATAGATAGATAGATAGATAGTGACCTGCCAGGAGCAGGGGACCACCGGGTTGCCTAAGGAGGGGTGAACTGT'
'CCCAGGATGGAAATGAAACA',
uas=False,
kit='forenseq')
assert marker.annotation == '[ATAG]11'
assert marker.canonical == 11
assert marker.designation == ('11', None, None)
assert marker.flank_5p == (
'AGTG AGCT GAGA TGGT GCCA C TGAA CTCC AGCC TGGG CGAC AAGA GC G AAA CTCC AACT CAAA [AAAT]3'
' AAAA T')
assert marker.flank_3p == (
'TGAC CTGC CAGG AGCA GGGG ACCA CC G GGTT GCCT AAGG AGGG GTGA ACTG TCCC AGGA TGGA AATG '
'AAAC A')
