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unit tests
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‎test/padl.gff3

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##sequence-region PADLG01_00_1 792 44515
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##sequence-region PADLG01_00_10 681 29757
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##sequence-region PADLG01_00_11 4205 114172
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##sequence-region PADLG01_00_12 1 30853
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##sequence-region PADLG01_00_13 3 30891
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##sequence-region PADLG01_00_14 123 29295
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##sequence-region PADLG01_00_15 4092 27603
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##sequence-region PADLG01_00_16 1749 26301
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##sequence-region PADLG01_00_17 1175 24629
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##sequence-region PADLG01_00_18 9099 24813
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##sequence-region PADLG01_00_19 2 24131
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##sequence-region PADLG01_00_2 3553 42284
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##sequence-region PADLG01_00_20 1 20419
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##sequence-region PADLG01_00_21 11572 20821
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##sequence-region PADLG01_00_22 1 93196
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##sequence-region PADLG01_00_23 1 17679
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##sequence-region PADLG01_00_24 1429 15203
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##sequence-region PADLG01_00_25 2853 16867
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##sequence-region PADLG01_00_26 1 15059
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##sequence-region PADLG01_00_27 65 15265
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##sequence-region PADLG01_00_28 1914 15784
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##sequence-region PADLG01_00_29 188 14762
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##sequence-region PADLG01_00_3 3 41425
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##sequence-region PADLG01_00_30 1 15645
25+
##sequence-region PADLG01_00_31 1197 15558
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##sequence-region PADLG01_00_32 253 12327
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##sequence-region PADLG01_00_33 3785 86766
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##sequence-region PADLG01_00_34 950 11770
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##sequence-region PADLG01_00_35 1373 15230
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##sequence-region PADLG01_00_36 3 15070
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##sequence-region PADLG01_00_37 1763 13490
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##sequence-region PADLG01_00_38 3 6651
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##sequence-region PADLG01_00_39 301 14065
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##sequence-region PADLG01_00_4 610 40909
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##sequence-region PADLG01_00_40 2678 13141
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##sequence-region PADLG01_00_41 586 11054
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##sequence-region PADLG01_00_42 1 12143
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##sequence-region PADLG01_00_43 922 11924
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##sequence-region PADLG01_00_44 1597 66948
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##sequence-region PADLG01_00_45 7518 10612
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##sequence-region PADLG01_00_46 2586 10352
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##sequence-region PADLG01_00_47 96 10917
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##sequence-region PADLG01_00_48 4100 9563
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##sequence-region PADLG01_00_49 4742 6367
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##sequence-region PADLG01_00_5 88 39644
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##sequence-region PADLG01_00_50 4336 10077
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##sequence-region PADLG01_00_51 2263 8790
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##sequence-region PADLG01_00_52 1 8907
49+
##sequence-region PADLG01_00_53 1 8792
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##sequence-region PADLG01_00_54 2828 5520
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##sequence-region PADLG01_00_55 2335 62802
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##sequence-region PADLG01_00_56 615 7656
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##sequence-region PADLG01_00_57 1718 6012
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##sequence-region PADLG01_00_58 12 5240
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##sequence-region PADLG01_00_59 15 3268
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##sequence-region PADLG01_00_6 2809 35923
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##sequence-region PADLG01_00_60 18 6147
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##sequence-region PADLG01_00_61 3660 5756
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##sequence-region PADLG01_00_62 1 5119
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##sequence-region PADLG01_00_63 97 5175
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##sequence-region PADLG01_00_64 384 3964
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##sequence-region PADLG01_00_66 5566 58455
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##sequence-region PADLG01_00_7 6325 37983
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##sequence-region PADLG01_00_77 254 49660
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##sequence-region PADLG01_00_78 287 38658
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##sequence-region PADLG01_00_79 1 42271
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##sequence-region PADLG01_00_8 215 37330
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##sequence-region PADLG01_00_9 104 30698
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##sequence-region PADLG01_01 4634 477637
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##sequence-region PADLG01_02 3420 706137
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##sequence-region PADLG01_03 1771 918026
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##sequence-region PADLG01_04 2330 1019821
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##sequence-region PADLG01_05 239 1247804
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##sequence-region PADLG01_06 22 1167056
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##sequence-region PADLG01_07 7793 1271718
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##sequence-region PADLG01_08 3768 1233060
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##sequence-region PADLG01_09 665 1315495
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##sequence-region PADLG01_10 5865 1403666
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##sequence-region PADLG01_11 4178 1779290
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##sequence-region PADLG01_12 2478 2137346
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##sequence-region PADLG01_13 5310 2653824
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##sequence-region PADLG01_14 56 3041661

‎test/pfal.gff3

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1+
##sequence-region Pf3D7_01_v3 29510 614893
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##sequence-region Pf3D7_02_v3 25232 923648
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##sequence-region Pf3D7_03_v3 36965 1038254
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##sequence-region Pf3D7_04_v3 28706 1180226
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##sequence-region Pf3D7_05_v3 20929 1342964
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##sequence-region Pf3D7_06_v3 653 1382627
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##sequence-region Pf3D7_07_v3 20307 1426234
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##sequence-region Pf3D7_08_v3 21361 1443449
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##sequence-region Pf3D7_09_v3 20080 1503336
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##sequence-region Pf3D7_10_v3 28490 1649948
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##sequence-region Pf3D7_11_v3 24160 2035886
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##sequence-region Pf3D7_12_v3 16973 2248962
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##sequence-region Pf3D7_13_v3 21364 2892340
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##sequence-region Pf3D7_14_v3 1393 3291501
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##sequence-region Pf3D7_API_v3 1 34225
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##sequence-region Pf3D7_MIT_v3 3 5954

‎test/pviv.gff3

Lines changed: 178 additions & 0 deletions
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##sequence-region PvP01_01_v2 2235 1019504
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##sequence-region PvP01_02_v2 420 953393
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##sequence-region PvP01_03_v2 5662 895347
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##sequence-region PvP01_04_v2 1812 1012024
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##sequence-region PvP01_05_v2 97 1524814
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##sequence-region PvP01_06_v2 27 1038726
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##sequence-region PvP01_07_v2 1 1651798
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##sequence-region PvP01_08_v2 3113 1759241
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##sequence-region PvP01_09_v2 573 2235640
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##sequence-region PvP01_10_v2 4247 1546921
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##sequence-region PvP01_11_v2 2476 2131037
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##sequence-region PvP01_12_v2 2 3179176
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##sequence-region PvP01_13_v2 4952 2086226
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##sequence-region PvP01_14_v2 4 3147656
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##sequence-region PvP01_API_v2 9 29321
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##sequence-region PvP01_MIT_v2 16 5985
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##sequence-region Transfer.PvP01_00_1.final 53 401003
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##sequence-region Transfer.PvP01_00_10.final 1402 130384
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##sequence-region Transfer.PvP01_00_101.final 2599 3600
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##sequence-region Transfer.PvP01_00_103.final 646 3551
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##sequence-region Transfer.PvP01_00_104.final 824 2889
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##sequence-region Transfer.PvP01_00_106.final 2631 3714
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##sequence-region Transfer.PvP01_00_107.final 70 3768
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##sequence-region Transfer.PvP01_00_108.final 1827 3717
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##sequence-region Transfer.PvP01_00_11.final 8335 114064
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##sequence-region Transfer.PvP01_00_110.final 175 3619
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##sequence-region Transfer.PvP01_00_111.final 3314 3475
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##sequence-region Transfer.PvP01_00_113.final 297 1686
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##sequence-region Transfer.PvP01_00_114.final 1655 2473
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##sequence-region Transfer.PvP01_00_119.final 1 1881
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##sequence-region Transfer.PvP01_00_12.final 3689 117582
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##sequence-region Transfer.PvP01_00_121.final 586 1809
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##sequence-region Transfer.PvP01_00_123.final 1754 2164
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##sequence-region Transfer.PvP01_00_124.final 559 2138
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##sequence-region Transfer.PvP01_00_125.final 1281 1696
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##sequence-region Transfer.PvP01_00_127.final 1049 2028
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##sequence-region Transfer.PvP01_00_129.final 121 1623
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##sequence-region Transfer.PvP01_00_13.final 344 111332
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##sequence-region Transfer.PvP01_00_131.final 1 1662
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##sequence-region Transfer.PvP01_00_136.final 1 1021
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##sequence-region Transfer.PvP01_00_137.final 410 1701
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##sequence-region Transfer.PvP01_00_138.final 1123 1526
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##sequence-region Transfer.PvP01_00_14.final 2 101402
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##sequence-region Transfer.PvP01_00_140.final 1 1769
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##sequence-region Transfer.PvP01_00_141.final 1438 1738
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##sequence-region Transfer.PvP01_00_143.final 1092 1595
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##sequence-region Transfer.PvP01_00_147.final 1079 1624
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##sequence-region Transfer.PvP01_00_148.final 689 1615
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##sequence-region Transfer.PvP01_00_15.final 245 98239
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##sequence-region Transfer.PvP01_00_150.final 1 367
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##sequence-region Transfer.PvP01_00_152.final 352 1308
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##sequence-region Transfer.PvP01_00_153.final 123 1230
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##sequence-region Transfer.PvP01_00_156.final 2 1262
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##sequence-region Transfer.PvP01_00_157.final 74 727
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##sequence-region Transfer.PvP01_00_158.final 264 1325
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##sequence-region Transfer.PvP01_00_16.final 216 95157
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##sequence-region Transfer.PvP01_00_160.final 870 1482
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##sequence-region Transfer.PvP01_00_161.final 1 1453
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##sequence-region Transfer.PvP01_00_169.final 1 704
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##sequence-region Transfer.PvP01_00_17.final 161 90239
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##sequence-region Transfer.PvP01_00_170.final 111 1405
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##sequence-region Transfer.PvP01_00_172.final 3 356
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##sequence-region Transfer.PvP01_00_173.final 577 1248
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##sequence-region Transfer.PvP01_00_174.final 3 708
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##sequence-region Transfer.PvP01_00_175.final 906 1358
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##sequence-region Transfer.PvP01_00_176.final 642 1357
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##sequence-region Transfer.PvP01_00_177.final 274 1169
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##sequence-region Transfer.PvP01_00_179.final 1 478
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##sequence-region Transfer.PvP01_00_18.final 836 87867
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##sequence-region Transfer.PvP01_00_180.final 996 1346
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##sequence-region Transfer.PvP01_00_186.final 62 816
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##sequence-region Transfer.PvP01_00_187.final 25 1288
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##sequence-region Transfer.PvP01_00_19.final 930 86064
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##sequence-region Transfer.PvP01_00_192.final 256 823
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##sequence-region Transfer.PvP01_00_196.final 64 385
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##sequence-region Transfer.PvP01_00_197.final 201 869
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##sequence-region Transfer.PvP01_00_199.final 117 1200
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##sequence-region Transfer.PvP01_00_2.final 3 329065
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##sequence-region Transfer.PvP01_00_20.final 186 69669
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##sequence-region Transfer.PvP01_00_200.final 506 1200
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##sequence-region Transfer.PvP01_00_201.final 23 722
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##sequence-region Transfer.PvP01_00_203.final 1 1104
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##sequence-region Transfer.PvP01_00_204.final 3 1173
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##sequence-region Transfer.PvP01_00_205.final 341 880
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##sequence-region Transfer.PvP01_00_208.final 2 925
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##sequence-region Transfer.PvP01_00_209.final 20 496
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##sequence-region Transfer.PvP01_00_21.final 1 65865
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##sequence-region Transfer.PvP01_00_211.final 1 788
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##sequence-region Transfer.PvP01_00_212.final 669 1130
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##sequence-region Transfer.PvP01_00_214.final 472 1084
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##sequence-region Transfer.PvP01_00_215.final 285 1113
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##sequence-region Transfer.PvP01_00_217.final 42 1024
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##sequence-region Transfer.PvP01_00_22.final 2490 60938
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##sequence-region Transfer.PvP01_00_221.final 1 1073
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##sequence-region Transfer.PvP01_00_222.final 110 1070
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##sequence-region Transfer.PvP01_00_223.final 1 1070
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##sequence-region Transfer.PvP01_00_225.final 1 147
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##sequence-region Transfer.PvP01_00_226.final 75 970
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##sequence-region Transfer.PvP01_00_227.final 73 1060
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##sequence-region Transfer.PvP01_00_23.final 2213 62799
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##sequence-region Transfer.PvP01_00_233.final 1 863
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##sequence-region Transfer.PvP01_00_234.final 2 603
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##sequence-region Transfer.PvP01_00_238.final 124 348
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##sequence-region Transfer.PvP01_00_24.final 3926 64114
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##sequence-region Transfer.PvP01_00_25.final 1867 56184
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##sequence-region Transfer.PvP01_00_26.final 2613 57857
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##sequence-region Transfer.PvP01_00_27.final 3848 54181
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##sequence-region Transfer.PvP01_00_28.final 506 45676
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##sequence-region Transfer.PvP01_00_29.final 3016 42965
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##sequence-region Transfer.PvP01_00_3.final 4464 210234
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##sequence-region Transfer.PvP01_00_30.final 1650 43062
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##sequence-region Transfer.PvP01_00_300.final 676 42148
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##sequence-region Transfer.PvP01_00_301.final 177 1546
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##sequence-region Transfer.PvP01_00_31.final 1306 39127
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##sequence-region Transfer.PvP01_00_32.final 3979 38918
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##sequence-region Transfer.PvP01_00_33.final 3007 39243
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##sequence-region Transfer.PvP01_00_34.final 2501 36817
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##sequence-region Transfer.PvP01_00_35.final 2663 34384
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##sequence-region Transfer.PvP01_00_36.final 49 34033
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##sequence-region Transfer.PvP01_00_37.final 1694 34237
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##sequence-region Transfer.PvP01_00_38.final 1692 33209
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##sequence-region Transfer.PvP01_00_39.final 352 30514
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##sequence-region Transfer.PvP01_00_4.final 4365 164315
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##sequence-region Transfer.PvP01_00_40.final 549 27136
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##sequence-region Transfer.PvP01_00_41.final 2514 26520
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##sequence-region Transfer.PvP01_00_42.final 2825 26582
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##sequence-region Transfer.PvP01_00_43.final 572 25894
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##sequence-region Transfer.PvP01_00_44.final 1235 23031
129+
##sequence-region Transfer.PvP01_00_45.final 1216 24451
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##sequence-region Transfer.PvP01_00_46.final 321 23475
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##sequence-region Transfer.PvP01_00_47.final 6266 20601
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##sequence-region Transfer.PvP01_00_48.final 1 21005
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##sequence-region Transfer.PvP01_00_49.final 4805 21386
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##sequence-region Transfer.PvP01_00_5.final 3325 148885
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##sequence-region Transfer.PvP01_00_50.final 1 20540
136+
##sequence-region Transfer.PvP01_00_51.final 2878 20611
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##sequence-region Transfer.PvP01_00_52.final 138 18656
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##sequence-region Transfer.PvP01_00_53.final 62 15538
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##sequence-region Transfer.PvP01_00_54.final 112 17847
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##sequence-region Transfer.PvP01_00_55.final 1611 10292
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##sequence-region Transfer.PvP01_00_56.final 943 16621
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##sequence-region Transfer.PvP01_00_57.final 3819 13692
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##sequence-region Transfer.PvP01_00_59.final 91 10423
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##sequence-region Transfer.PvP01_00_6.final 5940 146288
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##sequence-region Transfer.PvP01_00_60.final 1 10792
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##sequence-region Transfer.PvP01_00_61.final 1888 12627
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##sequence-region Transfer.PvP01_00_63.final 1368 4163
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##sequence-region Transfer.PvP01_00_64.final 1717 12076
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##sequence-region Transfer.PvP01_00_65.final 209 11591
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##sequence-region Transfer.PvP01_00_66.final 185 8028
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##sequence-region Transfer.PvP01_00_67.final 1470 8986
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##sequence-region Transfer.PvP01_00_69.final 2 10394
153+
##sequence-region Transfer.PvP01_00_7.final 332 135793
154+
##sequence-region Transfer.PvP01_00_70.final 16 6908
155+
##sequence-region Transfer.PvP01_00_71.final 133 5867
156+
##sequence-region Transfer.PvP01_00_73.final 2406 7486
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##sequence-region Transfer.PvP01_00_74.final 3062 7695
158+
##sequence-region Transfer.PvP01_00_75.final 2138 7201
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##sequence-region Transfer.PvP01_00_77.final 1021 7582
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##sequence-region Transfer.PvP01_00_78.final 2635 8042
161+
##sequence-region Transfer.PvP01_00_79.final 1901 7828
162+
##sequence-region Transfer.PvP01_00_8.final 382 136930
163+
##sequence-region Transfer.PvP01_00_80.final 350 5723
164+
##sequence-region Transfer.PvP01_00_81.final 53 5418
165+
##sequence-region Transfer.PvP01_00_82.final 2536 3227
166+
##sequence-region Transfer.PvP01_00_83.final 3177 6831
167+
##sequence-region Transfer.PvP01_00_84.final 2771 3966
168+
##sequence-region Transfer.PvP01_00_85.final 5209 6500
169+
##sequence-region Transfer.PvP01_00_86.final 1198 2533
170+
##sequence-region Transfer.PvP01_00_88.final 1081 5835
171+
##sequence-region Transfer.PvP01_00_89.final 1 5697
172+
##sequence-region Transfer.PvP01_00_9.final 3963 132256
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##sequence-region Transfer.PvP01_00_90.final 388 4790
174+
##sequence-region Transfer.PvP01_00_93.final 2840 4264
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##sequence-region Transfer.PvP01_00_94.final 66 4272
176+
##sequence-region Transfer.PvP01_00_95.final 1609 2480
177+
##sequence-region Transfer.PvP01_00_96.final 165 1673
178+
##sequence-region Transfer.PvP01_00_98.final 290 913

‎test/test.py

Lines changed: 34 additions & 0 deletions
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import glob
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import os.path
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import unittest
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5+
from bin.parse_chromosomes import parse_chromosomes
6+
7+
8+
expected_pattern = {
9+
"pviv.gff3": "PvP01_([0-9][0-9])_v2",
10+
"padl.gff3": "PADLG01_([0-9][0-9])",
11+
"pfal.gff3": "Pf3D7_([0-9][0-9])_v3",
12+
"tgon.gff3": "TGME49_chr(.*)",
13+
}
14+
15+
class TestParseChromosomes(unittest.TestCase):
16+
def setUp(self):
17+
self.test_files = glob.glob("test/*.gff3")
18+
self.verification_errors = []
19+
20+
def tearDown(self):
21+
self.assertEqual([], self.verification_errors)
22+
23+
def test_parse_examples(self):
24+
for tf in self.test_files:
25+
p = parse_chromosomes(tf)
26+
try:
27+
self.assertEqual(len(p.split("\t")), 2)
28+
self.assertEqual(p.split("\t")[1], expected_pattern[os.path.basename(tf)])
29+
except AssertionError as e:
30+
self.verification_errors.append(str(e))
31+
32+
33+
if __name__ == "__main__":
34+
unittest.main()

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