diff --git a/test_data/oatkDB/dikarya_mito.fam b/test_data/oatkDB/dikarya_mito.fam new file mode 100644 index 0000000..8eee38e --- /dev/null +++ b/test_data/oatkDB/dikarya_mito.fam @@ -0,0 +1,71087 @@ +HMMER3/f [3.4 | Aug 2023] +NAME atp6 +LENG 1262 +MAXL 3026 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Wed Sep 20 15:58:12 2023 +NSEQ 5885 +EFFN 274.369293 +CKSUM 3973048843 +STATS LOCAL MSV -12.9954 0.69499 +STATS LOCAL VITERBI -13.5269 0.69499 +STATS LOCAL FORWARD -7.2595 0.69499 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.21173 1.75828 1.71124 1.05172 + 1.38629 1.38629 1.38629 1.38629 + 0.08761 3.17150 3.17150 1.46634 0.26236 0.00000 * + 1 1.05988 1.65853 1.42265 1.50504 1 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.08761 3.17150 3.17150 1.46634 0.26236 1.09861 0.40547 + 2 1.59733 1.50586 1.51432 1.03344 2 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.08761 3.17150 3.17150 1.46634 0.26236 1.09861 0.40547 + 3 1.56855 1.71240 0.92110 1.54581 3 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.08761 3.17150 3.17150 1.46634 0.26236 1.09861 0.40547 + 4 1.59733 1.50586 1.51432 1.03344 4 t - 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- - + 1.05456 1.87888 1.52181 1.27090 + 0.22906 1.59126 6.85602 1.12339 0.39330 3.70381 0.02494 + 734 1.01941 1.50974 2.47368 1.09677 1776 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.00086 7.75660 7.75660 1.46634 0.26236 3.45432 0.03212 + 735 2.93691 4.55301 1.08133 0.51535 1777 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.00086 7.75723 7.75723 1.46634 0.26236 3.70381 0.02494 + 736 3.43396 1.16836 3.04073 0.49583 1778 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.00086 7.75723 7.75723 1.46634 0.26236 3.70381 0.02494 + 737 1.94336 1.69993 3.45054 0.44262 1779 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.00086 7.75723 7.75723 1.46634 0.26236 3.70381 0.02494 + 738 0.78855 4.07264 1.05264 1.71786 1780 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.00086 7.75671 7.75671 1.46634 0.26236 3.70381 0.02494 + 739 5.62259 3.25191 5.99566 0.04584 1781 T - - - + 1.38629 1.38629 1.38629 1.38629 + 0.00086 7.75621 7.75621 1.46634 0.26236 3.70381 0.02494 + 740 0.82368 2.16603 3.61396 0.86843 1782 a - 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- - + 1.38629 1.38629 1.38629 1.38629 + 0.00085 7.75903 7.75903 1.46634 0.26236 3.58517 0.02812 + 748 6.35216 4.75105 7.61568 0.01094 1790 T - - - + 1.38629 1.38629 1.38629 1.38629 + 0.00086 7.75583 7.75583 1.46634 0.26236 3.58517 0.02812 + 749 0.30813 2.90693 3.52767 1.70833 1791 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.00086 7.75532 7.75532 1.46634 0.26236 1.07621 0.41686 + 750 0.40846 3.42286 1.74772 2.05152 1792 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.00095 7.77909 7.53278 1.46634 0.26236 3.20953 0.04121 + 751 3.91155 4.30961 6.43429 0.03568 1793 T - - - + 1.38629 1.38629 1.38629 1.38629 + 0.00084 7.77858 7.77858 1.46634 0.26236 3.21178 0.04112 + 752 0.58100 2.12285 3.58229 1.22704 1794 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.00084 7.77822 7.77822 1.46634 0.26236 3.21178 0.04112 + 753 4.40819 0.08482 3.96332 2.99291 1795 C - - - + 1.38629 1.38629 1.38629 1.38629 + 0.00084 7.77801 7.77801 1.46634 0.26236 3.21178 0.04112 + 754 3.45273 0.07927 3.96309 3.66732 1796 C - 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- - + 1.38629 1.38629 1.38629 1.38629 + 0.00111 7.72626 7.31808 1.46634 0.26236 3.59627 0.02781 + 762 1.20709 2.52857 1.86511 0.76297 1892 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.00088 7.72632 7.72632 1.46634 0.26236 3.34688 0.03583 + 763 6.22332 3.20412 2.93100 0.10084 1893 T - - - + 1.38629 1.38629 1.38629 1.38629 + 0.00088 7.72562 7.72562 1.46634 0.26236 3.83050 0.02194 + 764 1.10249 1.90093 3.48710 0.71756 1894 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.00088 7.72535 7.72535 1.46634 0.26236 2.65149 0.07316 + 765 1.12439 3.07407 2.46727 0.60862 1895 t - - - + 0.82562 2.36565 1.78370 1.20353 + 0.05751 3.34538 3.88060 3.83270 0.02189 3.78042 0.02308 + 766 6.54044 6.09480 5.82813 0.00666 1974 T - - - + 1.38629 1.38629 1.38629 1.38629 + 0.00090 7.70941 7.70941 1.46634 0.26236 3.97082 0.01904 + 767 1.78102 1.21201 4.79775 0.64305 1975 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.00090 7.70806 7.70806 1.46634 0.26236 3.97082 0.01904 + 768 0.86104 2.83625 1.64082 1.12451 1976 a - 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- - + 0.88282 1.64823 1.21891 2.31830 + 0.11352 2.23202 * 1.54458 0.24004 0.00000 * +// +HMMER3/f [3.4 | Aug 2023] +NAME trnE-UUC +LENG 72 +MAXL 139 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Wed Sep 20 15:58:13 2023 +NSEQ 354 +EFFN 17.217636 +CKSUM 1857761641 +STATS LOCAL MSV -8.1042 0.71870 +STATS LOCAL VITERBI -8.8779 0.71870 +STATS LOCAL FORWARD -4.0402 0.71870 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.38869 1.58562 1.51189 1.12305 + 1.89134 2.62157 1.89134 0.46909 + 0.08043 2.74075 4.36124 2.08867 0.13222 0.00000 * + 1 2.88594 4.18145 0.14661 2.72893 10 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.01043 5.26113 5.26113 1.46634 0.26236 0.93360 0.49945 + 2 1.27014 3.63303 0.39988 3.79988 11 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.01035 5.26877 5.26877 1.46634 0.26236 1.09861 0.40547 + 3 1.64638 0.71847 3.25274 1.26908 12 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.01035 5.26877 5.26877 1.46634 0.26236 1.09861 0.40547 + 4 4.48816 0.50462 4.71479 0.97800 13 c - 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- - + 0.37117 1.94441 2.03353 3.32060 + 0.10053 2.34718 * 2.03825 0.13956 0.00000 * +// +HMMER3/f [3.4 | Aug 2023] +NAME trnL-UAA +LENG 83 +MAXL 154 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Wed Sep 20 15:58:13 2023 +NSEQ 302 +EFFN 11.912079 +CKSUM 2689876209 +STATS LOCAL MSV -8.5587 0.71851 +STATS LOCAL VITERBI -9.4720 0.71851 +STATS LOCAL FORWARD -3.6833 0.71851 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.23755 1.76862 1.44861 1.18928 + 1.43256 1.43256 1.43256 1.25911 + 0.08839 3.88698 2.74748 0.82979 0.57295 0.00000 * + 1 1.27033 3.96649 0.39102 3.73162 2 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.01514 4.89092 4.89092 1.46634 0.26236 1.52798 0.24459 + 2 1.86910 0.90869 2.85734 0.95383 3 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.01514 4.89092 4.89092 1.46634 0.26236 1.52798 0.24459 + 3 1.71958 0.78457 1.50748 1.94437 4 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.01514 4.89092 4.89092 1.46634 0.26236 1.52798 0.24459 + 4 1.00160 1.27786 2.26943 1.38349 5 a - 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- - + 1.47675 1.26503 1.33563 1.48546 + 0.02042 3.90155 * 0.39398 1.12199 0.00000 * +// +HMMER3/f [3.4 | Aug 2023] +NAME trnQ-UUG +LENG 73 +MAXL 147 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Wed Sep 20 15:58:13 2023 +NSEQ 348 +EFFN 8.567780 +CKSUM 1234092129 +STATS LOCAL MSV -8.1766 0.71868 +STATS LOCAL VITERBI -9.0345 0.71868 +STATS LOCAL FORWARD -4.3103 0.71868 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.32439 1.73719 1.49665 1.09619 + 1.32178 1.41434 1.41434 1.39770 + 0.03671 3.91947 4.12324 0.99738 0.46020 0.00000 * + 1 4.15582 3.69396 4.29984 0.05564 2 T - - - + 1.38629 1.38629 1.38629 1.38629 + 0.01888 4.67221 4.67221 1.46634 0.26236 1.00836 0.45384 + 2 1.07315 2.42598 0.81655 2.05788 3 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.01875 4.67914 4.67914 1.46634 0.26236 1.09861 0.40547 + 3 1.22803 2.14824 1.58777 0.95176 4 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.01875 4.67914 4.67914 1.46634 0.26236 1.09861 0.40547 + 4 1.86170 2.19285 0.43095 2.48773 5 g - 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- - + 1.38629 1.38629 1.38629 1.38629 + 0.01273 5.06324 5.06324 1.46634 0.26236 1.09861 0.40547 + 82 4.31482 0.25489 4.54687 1.60430 89 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.01273 5.06324 5.06324 1.46634 0.26236 1.09861 0.40547 + 83 4.07786 0.81805 4.27716 0.63888 90 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.01273 5.06324 5.06324 1.46634 0.26236 1.09861 0.40547 + 84 2.48983 0.74278 3.39702 0.89695 91 c - - - + 1.38629 1.38629 1.38629 1.38629 + 0.02533 5.06324 3.98019 1.46634 0.26236 1.09861 0.40547 + 85 0.17245 3.64027 2.75486 2.68041 92 a - - - + 0.85380 2.38047 2.79201 0.86654 + 0.09665 2.38456 * 2.18095 0.11984 0.00000 * +// diff --git a/test_data/oatkDB/dikarya_mito.fam.h3f b/test_data/oatkDB/dikarya_mito.fam.h3f new file mode 100644 index 0000000..f45256d Binary files /dev/null and b/test_data/oatkDB/dikarya_mito.fam.h3f differ diff --git a/test_data/oatkDB/dikarya_mito.fam.h3i b/test_data/oatkDB/dikarya_mito.fam.h3i new file mode 100644 index 0000000..31317e1 Binary files /dev/null and b/test_data/oatkDB/dikarya_mito.fam.h3i differ diff --git a/test_data/oatkDB/dikarya_mito.fam.h3m b/test_data/oatkDB/dikarya_mito.fam.h3m new file mode 100644 index 0000000..147c7d7 Binary files /dev/null and b/test_data/oatkDB/dikarya_mito.fam.h3m differ diff --git a/test_data/oatkDB/dikarya_mito.fam.h3p b/test_data/oatkDB/dikarya_mito.fam.h3p new file mode 100644 index 0000000..37a50a9 Binary files /dev/null and b/test_data/oatkDB/dikarya_mito.fam.h3p differ diff --git a/test_data/oatkDB/mito.fam b/test_data/oatkDB/mito.fam deleted file mode 100644 index e69de29..0000000 diff --git a/test_data/oatkDB/mito.fam.h3f b/test_data/oatkDB/mito.fam.h3f deleted file mode 100644 index e69de29..0000000 diff --git a/test_data/oatkDB/mito.fam.h3i b/test_data/oatkDB/mito.fam.h3i deleted file mode 100644 index e69de29..0000000 diff --git a/test_data/oatkDB/mito.fam.h3m b/test_data/oatkDB/mito.fam.h3m deleted file mode 100644 index e69de29..0000000 diff --git a/test_data/oatkDB/mito.fam.h3p b/test_data/oatkDB/mito.fam.h3p deleted file mode 100644 index e69de29..0000000 diff --git a/test_data/raw_hic/hic_test_1.fastq.gz b/test_data/raw_hic/hic_test_1.fastq.gz deleted file mode 100644 index e69de29..0000000 diff --git a/test_data/raw_hic/hic_test_2.fastq.gz b/test_data/raw_hic/hic_test_2.fastq.gz deleted file mode 100644 index e69de29..0000000 diff --git a/test_data/raw_hic/sorted_hic_test_YBP2_SRR27548905_PRJNA1013711_1.fastq.gz b/test_data/raw_hic/sorted_hic_test_YBP2_SRR27548905_PRJNA1013711_1.fastq.gz new file mode 100644 index 0000000..7c5ef0f Binary files /dev/null and b/test_data/raw_hic/sorted_hic_test_YBP2_SRR27548905_PRJNA1013711_1.fastq.gz differ diff --git a/test_data/raw_hic/sorted_hic_test_YBP2_SRR27548905_PRJNA1013711_2.fastq.gz b/test_data/raw_hic/sorted_hic_test_YBP2_SRR27548905_PRJNA1013711_2.fastq.gz new file mode 100644 index 0000000..02c4b43 Binary files /dev/null and b/test_data/raw_hic/sorted_hic_test_YBP2_SRR27548905_PRJNA1013711_2.fastq.gz differ diff --git a/test_data/raw_hifi/hifi_test.fastq.gz b/test_data/raw_hifi/hifi_test.fastq.gz deleted file mode 100644 index e69de29..0000000 diff --git a/test_data/raw_hifi/hifi_test_SPSC01_SRR27947616_PRJNA1075684aa.fastq.gz b/test_data/raw_hifi/hifi_test_SPSC01_SRR27947616_PRJNA1075684aa.fastq.gz new file mode 100644 index 0000000..d24b1a4 Binary files /dev/null and b/test_data/raw_hifi/hifi_test_SPSC01_SRR27947616_PRJNA1075684aa.fastq.gz differ diff --git a/test_data/raw_hifi/hifi_test_SPSC01_SRR27947616_PRJNA1075684ab.fastq.gz b/test_data/raw_hifi/hifi_test_SPSC01_SRR27947616_PRJNA1075684ab.fastq.gz new file mode 100644 index 0000000..c9411cb Binary files /dev/null and b/test_data/raw_hifi/hifi_test_SPSC01_SRR27947616_PRJNA1075684ab.fastq.gz differ diff --git a/test_data/raw_ont/ont_test.fastq.gz b/test_data/raw_ont/ont_test.fastq.gz deleted file mode 100644 index e69de29..0000000 diff --git a/test_data/raw_ont/ont_test_SPSC01_SRR27947616_PRJNA1075684aa.fastq.gz b/test_data/raw_ont/ont_test_SPSC01_SRR27947616_PRJNA1075684aa.fastq.gz new file mode 100644 index 0000000..5147062 Binary files /dev/null and b/test_data/raw_ont/ont_test_SPSC01_SRR27947616_PRJNA1075684aa.fastq.gz differ diff --git a/test_data/raw_ont/ont_test_SPSC01_SRR27947616_PRJNA1075684ab.fastq.gz b/test_data/raw_ont/ont_test_SPSC01_SRR27947616_PRJNA1075684ab.fastq.gz new file mode 100644 index 0000000..861b6d1 Binary files /dev/null and b/test_data/raw_ont/ont_test_SPSC01_SRR27947616_PRJNA1075684ab.fastq.gz differ diff --git a/test_data/raw_ont/ont_test_SPSC01_SRR27947616_PRJNA1075684ac.fastq.gz b/test_data/raw_ont/ont_test_SPSC01_SRR27947616_PRJNA1075684ac.fastq.gz new file mode 100644 index 0000000..9500878 Binary files /dev/null and b/test_data/raw_ont/ont_test_SPSC01_SRR27947616_PRJNA1075684ac.fastq.gz differ