added tests for custom range brackets and sequence

bioforensics · Jun 21, 2024 · 8305c7d · 8305c7d
1 parent 59055d6
commit 8305c7d
Showing 1 changed file with 183 additions and 0 deletions.
diff --git a/lusSTR/tests/test_marker.py b/lusSTR/tests/test_marker.py
@@ -1467,3 +1467,186 @@ def test_new_power_config(locus, sequence, bracketed, conc, lus, sec, tert, flan
     assert marker.designation == (lus, sec, tert)
     assert marker.flank_5p == flank_5
     assert marker.flank_3p == flank_3
+
+
+@pytest.mark.parametrize(
+    "locus, sequence, cust_seq, bracketed",
+    [
+        (
+            "VWA",
+            "GGATAGATGGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGACAGACAGACAGACAGATAGATCAAT"
+            "CCAAGTCACATACTGATTATTCTTATCATCCACTAGGGCTTTCACATCTCAGCCAAGTCAACTTGGATCCTCTAGACCTGTTTCTTCT"
+            "TCTGGAA",
+            "TAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGACAGACAGACAGACAGATAGA",
+            "[TAGA]11 [CAGA]4 TAGA",
+        ),
+        (
+            "TPOX",
+            "CACTGGCCTGTGGGTCCCCCCATAGATCGTAAGCCCAGGAGGAAGGGCTGTGTTTCAGGGCTGTGATCACTAGCAC"
+            "CCAGAACCGTCGACTGGCACAGAACAGGCACTTAGGGAACCCTCACTGAATGAATGAATGAATGAATGAATGAATGAATGTTTG"
+            "GGCAAATAAACGCT",
+            "AATGAATGAATGAATGAATGAATGAATGAATG",
+            "[AATG]8",
+        ),
+        (
+            "TH01",
+            "CTCCATGGTGAATGAATGAATGAATGAATGAATGAATGAGGGAAATAAGGGAGGAACAGGCCAATGGGAATCACCC"
+            "CAGAGCCCAGATACCCTTTGAATTTTGCCCCCTATTTGCCCAGGACCCCCCACCATGAGCTGCTGCTAGAGCCTGGGAAGGGCC"
+            "TTGGGGCTGCCTCCCCAAGCAGGCAGGCTGGTTGGGGTGC",
+            "ATGGTGAATGAATGAATGAATGAATGAATGAATGAGGGA",
+            "ATGG TG [AATG]7 AGGG A",
+        ),
+        (
+            "PENTA E",
+            "TAATGATTACATAACATACATGTGTGTAAAGTGCTTAGTATCATGATTGATACATGGAAAGAATTCTCTTATT"
+            "TGGGTTATTAATTGAGAAAACTCCTTACAATTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTGAGAC",
+            "TCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTT",
+            "[TCTTT]7",
+        ),
+        (
+            "PENTA D",
+            "GAGCCATGATCACACCACTACACTCCAGCCTAGGTGACAGAGCAAGACACCATCTCAAGAAAGAAAAAAAAGA"
+            "AAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAAACGAAGGGGAAAAAAAGAGAATCATAAACATAAATG"
+            "TAAAATTTCTCAAAAAAATCGTTA",
+            "AAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAAGA",
+            "[AAAGA]9",
+        ),
+        (
+            "FGA",
+            "GTCTGAAATCGAAAATATGGTTATTGAAGTAGCTGCTGAGTGATTTGTCTGTAATTGCCAGCAAAAAAGAAAGGAAG"
+            "AAAGGAAGGAAGGAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAGAAAAAAGAAAGAAAGAAA",
+            "GGAAGGAAGGAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAGAAAAAAGAAAGAAAGAAA",
+            "[GGAA]2 GGAG [AAAG]12 AGAA AAAA [GAAA]3",
+        ),
+        (
+            "D8S1179",
+            "TTTCATGTGTACATTCGTATCTATCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATC"
+            "TATTCCCCACAGTGAAAATAATCTACAGGATAGGTAAATAAATTAAGGCATATTCACGCAATGGGATACGATACAGTGATGAAA"
+            "ATGAACTAATTATAGCTACGTGAAAC",
+            "TCTATCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATC" "TA",
+            "TCTA TCTG [TCTA]12",
+        ),
+        (
+            "D7S820",
+            "AGAATTGCACCAAATATTGGTAATTAAATGTTTACTATAGACTATTTAGTGAGATAAAAAAAAACTATCAATCT"
+            "GTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCGTTAGTTCGTTCTAAACTATGACAAGTGTTCTA"
+            "TCATACCCTTTATATATATTAACCTTAAAATAACTC",
+            "AGATAAAAAAAAACTATCAATCTGTCTATCTATCTATCTATCTA" "TCTATCTATCTATCTATCTATCTATCTATCGTTA",
+            "AGAT [AAAA]2 AC TATC AATC TGTC [TATC]12 GTTA",
+        ),
+        (
+            "D5S818",
+            "AACATTTGTATCTTTATCTGTATCCTTATTTATACCTCTATCTATCTATCTATCTATCTATCTATCTATCTATC"
+            "TATCTATCTTCAAAATATTACGTAAGGATACCAAAGAGGAAAATCACCCTTGTCACATACTTGCTATTAAAATATACTTTTATT"
+            "AGTACA",
+            "ATACCTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTTCAA",
+            "ATAC CTCT [ATCT]11 TCAA",
+        ),
+        (
+            "D3S1358",
+            "TGCCCACTTCTGCCCAGGGATCTATTTTTCTGTGGTGTGTATTCCCTGTGCCTTTGGGGGCATCTCTTATACT"
+            "CATGAAATCAACAGAGGCTTGCATGTATCTATCTGTCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTAT"
+            "CTATGAGACAGGGTCTTGCTCTGTC",
+            "CATGTATCTATCTGTCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTAT" "CTATCTATCTATGAGA",
+            "CATG TA TCTA [TCTG]2 [TCTA]12 TGAG A",
+        ),
+        (
+            "D2S441",
+            "TGCACCCAACATTCTAACAAAAGGCTGTAACAAGGGCTACAGGAATCATGAGCCAGGAACTGTGGCTCATCTAT"
+            "GAAAACTTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATTTATCTATCTATATCA",
+            "AACTTCTATCTA" "TCTATCTATCTATCTATCTATCTATCTATCTATCTATTTATCTATCTATATCA",
+            "AACT [TCTA]11 TTTA [TCTA]2 TATC A",
+        ),
+        (
+            "D2S1338",
+            "CTAGCATGGTACCTGCAGGTGGCCCATAATAATGAGTTATTCAGTAAGTTAAAGGATTGCAGGAGGGAAGGAA"
+            "GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGCAGGCAGGCAGGCAGGCAGGCAAGGCCAAGCCATTTCTGTTTCCAA"
+            "ATCCACTGGCTCCCTCCCACAGCT",
+            "GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGCAGGCAGGCA" "GGCAGGCAGGCA",
+            "[GGAA]11 [GGCA]6",
+        ),
+        (
+            "D22S1045",
+            "CCTTCTTATAGCTGCTATGGGGGCTAGATTTTCCCCGATGATAGTAGTCTCATTATTATTATTATTATTATT"
+            "ATTATTATTATTATTACTATTATTGTTATAAAAATATTG",
+            "TCTCATTATTATTATTATTATTATTATTATTATTATTATTA" "CTATTATTGTTA",
+            "TCT C [ATT]12 ACT [ATT]2 GTT A",
+        ),
+        (
+            "D21S11",
+            "TGAATTGCCTTCTATCTATCTATCTATCTATCTATCTGTCTGTCTGTCTGTCTGTCTATCTATCTATATCTATC"
+            "TATCTATCATCTATCTATCCATATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCGTCTATCTATCCAGT"
+            "CTATCTACCTCCTATTAGTCT",
+            "GCCTTCTATCTATCTATCTATCTATCTATCTGTCTGTCTGTCTGTCTGTCTATCTATCT"
+            "ATATCTATCTATCTATCATCTATCTATCCATATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCGTCT",
+            "GCCT [TCTA]6 [TCTG]5 [TCTA]3 TA [TCTA]3 TCA [TCTA]2 TCCA TA [TCTA]11 TCGT CT",
+        ),
+        (
+            "D1S1656",
+            "GAAATAGAATCACTAGGGAACCAAATATATATACATACAATTAAACACACACACACCTATCTATCTATCTATC"
+            "TATCTATCTATCTATCTATCTATCTATCTATCATCTATCTATCTATCTACATCATACAGTTGACCCTTGA",
+            "CCTATCTATC" "TATCTATCTATCTATCTATCTATCTATCTATCTATCTATCATCTATCTATCTATCTA",
+            "CCTA [TCTA]11 TCA [TCTA]4",
+        ),
+        (
+            "D19S433",
+            "AAGTTCTTTAGCAGTGATTTCTGATATTTTGGTGCACCCATTACCCGAATAAAAATCTTCTCTCTTTCTTCCT"
+            "CTCTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTACCTTCTTTCCTTCAACAGAATCTTATTC"
+            "TGTTGCCCAGGCTGGAGTGCA",
+            "ATCTTCTCTCTTTCTTCCTCTCTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTT"
+            "CCTTCCTTCCTTCCTACCTTCTTTCCTTCAACA",
+            "ATC TTCT CTCT TTCT TCCT CTCT [CCTT]12 CCTA CCTT CTTT CCTT CAAC A",
+        ),
+        (
+            "D18S51",
+            "AGGCTGCAGTGAGCCATGTTCATGCCACTGCACTTCACTCTGAGTGACAAATTGAGACCTTGTCTCAGAAAGAA"
+            "AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAAGAGAGAGGAAAGAAAGAGAAAAAGAAAAGAAATAGTAGCAA"
+            "CTGTTATTGTA",
+            "TCTCAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAAGAGAGAGGAAAGAAA",
+            "TCTC [AGAA]12 AAAG AGAG AGGA A AGAA A",
+        ),
+        (
+            "D16S539",
+            "GTGCACAAATCTAAATGCAGAAAAGCACTGAAAGAAGAATCCAGAAAACCACAGTTCCCATTTTTATATGGGA"
+            "GCAAACAAAGGCAGATCCCAAGCTCTTCCTCTTCCCTAGATCAATACAGACAGACAGACAGGTGGATAGATAGATAGATAGATA"
+            "GATAGATAGATAGATATCAT",
+            "GATAGATAGATAGATAGATAGATAGATAGATAGATA",
+            "[GATA]9",
+        ),
+        (
+            "D13S317",
+            "TTCTTTAGTGGGCATCCGTGACTCTCTGGACTCTGACCCATCTAACGCCTATCTGTATTTACAAATACATTAT"
+            "CTATCTATCTATCTATCTATCTATCTATCTATCAATCAATCATCTATCTATCTTTCTGTCTGTCTTTTTGGGCTGCCTATGGCT"
+            "CAACCCAAGTTGAAGGAGGAGATTT",
+            "ACATTATCTATCTATCTATCTATCTATCTATCTATCTATCAATCAATCATCTATC" "TATCTTTCTGTCTGTCTTTTT",
+            "ACAT [TATC]9 [AATC]2 ATC [TATC]2 TTTC [TGTC]2 TTTT T",
+        ),
+        (
+            "D12S391",
+            "CAATGGATGCATAGGTAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGACAGACA"
+            "GACAGACAGACAGACAGATGAGAGGG",
+            "TGCATAGGTAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATA"
+            "GATAGACAGACAGACAGACAGACAGACAGATGAGA",
+            "TGCA TAGG T [AGAT]12 [AGAC]6 AGAT GAGA",
+        ),
+        (
+            "D10S1248",
+            "CCCCAGGACCAATCTGGTCACAAACATATTAATGAATTGAACAAATGAGTGAGTGGAAGGAAGGAAGGAAGG"
+            "AAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAA",
+            "GGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGG" "AAGGAAGGAAGGAA",
+            "[GGAA]14",
+        ),
+        (
+            "CSF1PO",
+            "CTAAGTACTTCCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTAATCTATCTATCTTCTATCTA"
+            "TGAAGGCAGTTACTGTTAATATCTTCATTTTACAGGTAGGAAAACTGAGACACAGGGTGGTTAGCAACCTGCTAGTCCTTGGCA"
+            "GACTCAG",
+            "CTTCCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTAATCT",
+            "CTTC CT [ATCT]10 A ATCT",
+        ),
+    ],
+)
+def test_custom_ranges(locus, sequence, cust_seq, bracketed):
+    marker = STRMarkerObject(locus, sequence, "straitrazor", custom=True, kit="powerseq")
+    assert marker.custom_sequence == cust_seq
+    assert marker.custom_brack == bracketed