1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/277403d31907/ changeset: 277403d31907 user: jgoecks date: 2011-11-18 20:58:25 summary: Update Cuffcompare test data to be compatible with v1.1.0 affected #: 6 files diff -r bde09cbd60865053ffd0ab05138d6fa3e594d399 -r 277403d31907d71e5e77694c0c97c16772f23e27 test-data/cuffcompare_out1.tmap --- a/test-data/cuffcompare_out1.tmap +++ b/test-data/cuffcompare_out1.tmap @@ -1,51 +1,51 @@ ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo FPKM_conf_hi cov len major_iso_id ref_match_len -- - u CUFF.1 CUFF.1.1 100 0.000000 0.000000 0.000000 0.000000 41 CUFF.1.1 - -- - u CUFF.3 CUFF.3.1 100 0.000000 0.000000 0.000000 0.000000 31 CUFF.3.1 - -- - u CUFF.5 CUFF.5.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.5.1 - -- - u CUFF.7 CUFF.7.1 100 0.000000 0.000000 0.000000 0.000000 169 CUFF.7.1 - -- - u CUFF.9 CUFF.9.1 100 0.000000 0.000000 0.000000 0.000000 404 CUFF.9.1 - -- - u CUFF.11 CUFF.11.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.11.1 - -- - u CUFF.13 CUFF.13.1 100 0.000000 0.000000 0.000000 0.000000 79 CUFF.13.1 - -- - u CUFF.15 CUFF.15.1 100 0.000000 0.000000 0.000000 0.000000 79 CUFF.15.1 - -- - u CUFF.17 CUFF.17.1 100 0.000000 0.000000 0.000000 0.000000 97 CUFF.17.1 - -- - u CUFF.19 CUFF.19.1 100 0.000000 0.000000 0.000000 0.000000 72 CUFF.19.1 - -- - u CUFF.21 CUFF.21.1 100 0.000000 0.000000 0.000000 0.000000 61 CUFF.21.1 - -- - u CUFF.23 CUFF.23.1 100 0.000000 0.000000 0.000000 0.000000 54 CUFF.23.1 - -- - u CUFF.25 CUFF.25.1 100 0.000000 0.000000 0.000000 0.000000 290 CUFF.25.1 - -- - u CUFF.27 CUFF.27.1 100 0.000000 0.000000 0.000000 0.000000 37 CUFF.27.1 - -- - u CUFF.29 CUFF.29.1 100 0.000000 0.000000 0.000000 0.000000 142 CUFF.29.1 - -- - u CUFF.31 CUFF.31.1 100 0.000000 0.000000 0.000000 0.000000 31 CUFF.31.1 - -- - u CUFF.33 CUFF.33.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.33.1 - -- - u CUFF.35 CUFF.35.1 100 0.000000 0.000000 0.000000 0.000000 131 CUFF.35.1 - -- - u CUFF.37 CUFF.37.1 100 0.000000 0.000000 0.000000 0.000000 69 CUFF.37.1 - -- - u CUFF.39 CUFF.39.1 100 0.000000 0.000000 0.000000 0.000000 53 CUFF.39.1 - -- - u CUFF.41 CUFF.41.1 100 0.000000 0.000000 0.000000 0.000000 79 CUFF.41.1 - -- - u CUFF.43 CUFF.43.1 100 0.000000 0.000000 0.000000 0.000000 80 CUFF.43.1 - -- - u CUFF.45 CUFF.45.1 100 0.000000 0.000000 0.000000 0.000000 102 CUFF.45.1 - -- - u CUFF.47 CUFF.47.1 100 0.000000 0.000000 0.000000 0.000000 41 CUFF.47.1 - -- - u CUFF.49 CUFF.49.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.49.1 - -- - u CUFF.51 CUFF.51.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.51.1 - -- - u CUFF.53 CUFF.53.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.53.1 - -- - u CUFF.55 CUFF.55.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.55.1 - -- - u CUFF.57 CUFF.57.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.57.1 - -- - u CUFF.59 CUFF.59.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.59.1 - -- - u CUFF.61 CUFF.61.1 100 0.000000 0.000000 0.000000 0.000000 28 CUFF.61.1 - -- - u CUFF.63 CUFF.63.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.63.1 - -- - u CUFF.65 CUFF.65.1 100 0.000000 0.000000 0.000000 0.000000 55 CUFF.65.1 - -- - u CUFF.67 CUFF.67.1 100 0.000000 0.000000 0.000000 0.000000 65 CUFF.67.1 - -- - u CUFF.69 CUFF.69.1 100 0.000000 0.000000 0.000000 0.000000 84 CUFF.69.1 - -- - u CUFF.71 CUFF.71.1 100 0.000000 0.000000 0.000000 0.000000 98 CUFF.71.1 - -- - u CUFF.73 CUFF.73.1 100 0.000000 0.000000 0.000000 0.000000 55 CUFF.73.1 - -- - u CUFF.75 CUFF.75.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.75.1 - -- - u CUFF.77 CUFF.77.1 100 0.000000 0.000000 0.000000 0.000000 52 CUFF.77.1 - -- - u CUFF.79 CUFF.79.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.79.1 - -- - u CUFF.81 CUFF.81.1 100 0.000000 0.000000 0.000000 0.000000 64 CUFF.81.1 - -- - u CUFF.83 CUFF.83.1 100 0.000000 0.000000 0.000000 0.000000 96 CUFF.83.1 - -- - u CUFF.85 CUFF.85.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.85.1 - -- - u CUFF.87 CUFF.87.1 100 0.000000 0.000000 0.000000 0.000000 49 CUFF.87.1 - -- - u CUFF.89 CUFF.89.1 100 0.000000 0.000000 0.000000 0.000000 51 CUFF.89.1 - -- - u CUFF.91 CUFF.91.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.91.1 - -- - u CUFF.93 CUFF.93.1 100 0.000000 0.000000 0.000000 0.000000 39 CUFF.93.1 - -- - u CUFF.95 CUFF.95.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.95.1 - -- - u CUFF.97 CUFF.97.1 100 0.000000 0.000000 0.000000 0.000000 59 CUFF.97.1 - -- - u CUFF.99 CUFF.99.1 100 0.000000 0.000000 0.000000 0.000000 58 CUFF.99.1 - +- - u CUFF.1 CUFF.1.1 100 20.607936 0.000000 49.751960 1.317073 41 CUFF.1.1 - +- - u CUFF.3 CUFF.3.1 100 27.255658 0.000000 65.800979 1.741935 31 CUFF.3.1 - +- - u CUFF.5 CUFF.5.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.5.1 - +- - u CUFF.7 CUFF.7.1 100 9.999117 0.000000 19.998234 0.639053 169 CUFF.7.1 - +- - u CUFF.9 CUFF.9.1 100 17.776896 9.153835 26.399957 1.136139 404 CUFF.9.1 - +- - u CUFF.11 CUFF.11.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.11.1 - +Xkr4 Xkr4 c CUFF.13 CUFF.13.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.13.1 3634 +Xkr4 Xkr4 i CUFF.15 CUFF.15.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.15.1 3634 +Xkr4 Xkr4 i CUFF.17 CUFF.17.1 100 8.710571 0.000000 21.029179 0.556701 97 CUFF.17.1 3634 +Xkr4 Xkr4 i CUFF.19 CUFF.19.1 100 29.337687 3.097262 55.578113 1.875000 72 CUFF.19.1 3634 +Xkr4 Xkr4 i CUFF.21 CUFF.21.1 100 13.851236 0.000000 33.439842 0.885246 61 CUFF.21.1 3634 +Xkr4 Xkr4 i CUFF.23 CUFF.23.1 100 23.470150 0.000000 50.571145 1.500000 54 CUFF.23.1 3634 +Xkr4 Xkr4 i CUFF.25 CUFF.25.1 100 14.567679 5.354270 23.781089 0.931034 290 CUFF.25.1 3634 +Xkr4 Xkr4 i CUFF.27 CUFF.27.1 100 34.253732 0.000000 73.806535 2.189189 37 CUFF.27.1 3634 +- - u CUFF.29 CUFF.29.1 100 107.103219 71.402146 142.804292 6.845070 142 CUFF.29.1 - +- - u CUFF.31 CUFF.31.1 100 122.650461 40.883487 204.417435 7.838710 31 CUFF.31.1 - +- - u CUFF.33 CUFF.33.1 100 109.527366 26.732460 192.322273 7.000000 27 CUFF.33.1 - +- - u CUFF.35 CUFF.35.1 100 96.747183 61.420107 132.074259 6.183206 131 CUFF.35.1 - +- - u CUFF.37 CUFF.37.1 100 104.085013 53.596365 154.573660 6.652174 69 CUFF.37.1 - +- - u CUFF.39 CUFF.39.1 100 23.912983 0.000000 51.525317 1.528302 53 CUFF.39.1 - +- - u CUFF.41 CUFF.41.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.41.1 - +- - u CUFF.43 CUFF.43.1 100 10.561567 0.000000 25.497879 0.675000 80 CUFF.43.1 - +- - u CUFF.45 CUFF.45.1 100 20.708956 2.186303 39.231609 1.323529 102 CUFF.45.1 - +- - u CUFF.47 CUFF.47.1 100 20.607936 0.000000 49.751960 1.317073 41 CUFF.47.1 - +- - u CUFF.49 CUFF.49.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.49.1 - +- - u CUFF.51 CUFF.51.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.51.1 - +- - u CUFF.53 CUFF.53.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.53.1 - +- - u CUFF.55 CUFF.55.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.55.1 - +- - u CUFF.57 CUFF.57.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.57.1 - +- - u CUFF.59 CUFF.59.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.59.1 - +Xkr4 Xkr4 i CUFF.61 CUFF.61.1 100 45.263860 0.000000 97.530065 2.892857 28 CUFF.61.1 3634 +Xkr4 Xkr4 i CUFF.63 CUFF.63.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.63.1 3634 +Xkr4 Xkr4 i CUFF.65 CUFF.65.1 100 15.362280 0.000000 37.087825 0.981818 55 CUFF.65.1 3634 +Xkr4 Xkr4 i CUFF.67 CUFF.67.1 100 12.998852 0.000000 31.382005 0.830769 65 CUFF.67.1 3634 +Xkr4 Xkr4 i CUFF.69 CUFF.69.1 100 10.058636 0.000000 24.283695 0.642857 84 CUFF.69.1 3634 +Xkr4 Xkr4 i CUFF.71 CUFF.71.1 100 8.621688 0.000000 20.814595 0.551020 98 CUFF.71.1 3634 +Xkr4 Xkr4 i CUFF.73 CUFF.73.1 100 15.362280 0.000000 37.087825 0.981818 55 CUFF.73.1 3634 +Xkr4 Xkr4 i CUFF.75 CUFF.75.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.75.1 3634 +Xkr4 Xkr4 i CUFF.77 CUFF.77.1 100 16.248565 0.000000 39.227507 1.038462 52 CUFF.77.1 3634 +Xkr4 Xkr4 i CUFF.79 CUFF.79.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.79.1 3634 +Xkr4 Xkr4 i CUFF.81 CUFF.81.1 100 13.201959 0.000000 31.872349 0.843750 64 CUFF.81.1 3634 +Xkr4 Xkr4 i CUFF.83 CUFF.83.1 100 13.201959 0.000000 28.446269 0.843750 96 CUFF.83.1 3634 +Xkr4 Xkr4 i CUFF.85 CUFF.85.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.85.1 3634 +Xkr4 Xkr4 i CUFF.87 CUFF.87.1 100 17.243375 0.000000 41.629191 1.102041 49 CUFF.87.1 3634 +Xkr4 Xkr4 i CUFF.89 CUFF.89.1 100 16.567165 0.000000 39.996674 1.058824 51 CUFF.89.1 3634 +Xkr4 Xkr4 i CUFF.91 CUFF.91.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.91.1 3634 +Xkr4 Xkr4 i CUFF.93 CUFF.93.1 100 21.664754 0.000000 52.303342 1.384615 39 CUFF.93.1 3634 +Xkr4 Xkr4 i CUFF.95 CUFF.95.1 100 46.940300 0.000000 101.142289 3.000000 27 CUFF.95.1 3634 +Xkr4 Xkr4 i CUFF.97 CUFF.97.1 100 21.481154 0.000000 46.285454 1.372881 59 CUFF.97.1 3634 +Xkr4 Xkr4 i CUFF.99 CUFF.99.1 100 14.567679 0.000000 35.169489 0.931034 58 CUFF.99.1 3634 diff -r bde09cbd60865053ffd0ab05138d6fa3e594d399 -r 277403d31907d71e5e77694c0c97c16772f23e27 test-data/cuffcompare_out2.refmap --- a/test-data/cuffcompare_out2.refmap +++ b/test-data/cuffcompare_out2.refmap @@ -1,1 +1,2 @@ ref_gene_id ref_id class_code cuff_id_list +Xkr4 Xkr4 c CUFF.13|CUFF.13.1 diff -r bde09cbd60865053ffd0ab05138d6fa3e594d399 -r 277403d31907d71e5e77694c0c97c16772f23e27 test-data/cuffcompare_out3.tmap --- a/test-data/cuffcompare_out3.tmap +++ b/test-data/cuffcompare_out3.tmap @@ -1,51 +1,51 @@ ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo FPKM_conf_hi cov len major_iso_id ref_match_len -- - u CUFF.1 CUFF.1.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.1.1 - -- - u CUFF.3 CUFF.3.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.3.1 - -- - u CUFF.5 CUFF.5.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.5.1 - -- - u CUFF.7 CUFF.7.1 100 0.000000 0.000000 0.000000 0.000000 576 CUFF.7.1 - -- - u CUFF.9 CUFF.9.1 100 0.000000 0.000000 0.000000 0.000000 565 CUFF.9.1 - -- - u CUFF.11 CUFF.11.1 100 0.000000 0.000000 0.000000 0.000000 979 CUFF.11.1 - -- - u CUFF.13 CUFF.13.1 100 0.000000 0.000000 0.000000 0.000000 86 CUFF.13.1 - -- - u CUFF.15 CUFF.15.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.15.1 - -- - u CUFF.17 CUFF.17.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.17.1 - -- - u CUFF.19 CUFF.19.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.19.1 - -- - u CUFF.21 CUFF.21.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.21.1 - -- - u CUFF.23 CUFF.23.1 100 0.000000 0.000000 0.000000 0.000000 88 CUFF.23.1 - -- - u CUFF.25 CUFF.25.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.25.1 - -- - u CUFF.26 CUFF.26.1 100 0.000000 0.000000 0.000000 0.000000 32 CUFF.26.1 - -- - u CUFF.29 CUFF.29.1 100 0.000000 0.000000 0.000000 0.000000 70 CUFF.29.1 - -- - u CUFF.31 CUFF.31.1 100 0.000000 0.000000 0.000000 0.000000 84 CUFF.31.1 - -- - u CUFF.33 CUFF.33.1 100 0.000000 0.000000 0.000000 0.000000 40 CUFF.33.1 - -- - u CUFF.35 CUFF.35.1 100 0.000000 0.000000 0.000000 0.000000 84 CUFF.35.1 - -- - u CUFF.37 CUFF.37.1 100 0.000000 0.000000 0.000000 0.000000 124 CUFF.37.1 - -- - u CUFF.39 CUFF.39.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.39.1 - -- - u CUFF.41 CUFF.41.1 100 0.000000 0.000000 0.000000 0.000000 33 CUFF.41.1 - -- - u CUFF.43 CUFF.43.1 100 0.000000 0.000000 0.000000 0.000000 81 CUFF.43.1 - -- - u CUFF.45 CUFF.45.1 100 0.000000 0.000000 0.000000 0.000000 46 CUFF.45.1 - -- - u CUFF.47 CUFF.47.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.47.1 - -- - u CUFF.49 CUFF.49.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.49.1 - -- - u CUFF.51 CUFF.51.1 100 0.000000 0.000000 0.000000 0.000000 477 CUFF.51.1 - -- - u CUFF.53 CUFF.53.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.53.1 - -- - u CUFF.55 CUFF.55.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.55.1 - -- - u CUFF.57 CUFF.57.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.57.1 - -- - u CUFF.59 CUFF.59.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.59.1 - -- - u CUFF.61 CUFF.61.1 100 0.000000 0.000000 0.000000 0.000000 72 CUFF.61.1 - -- - u CUFF.63 CUFF.63.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.63.1 - -- - u CUFF.65 CUFF.65.1 100 0.000000 0.000000 0.000000 0.000000 61 CUFF.65.1 - -- - u CUFF.67 CUFF.67.1 100 0.000000 0.000000 0.000000 0.000000 197 CUFF.67.1 - -- - u CUFF.69 CUFF.69.1 100 0.000000 0.000000 0.000000 0.000000 354 CUFF.69.1 - -- - u CUFF.71 CUFF.71.1 100 0.000000 0.000000 0.000000 0.000000 42 CUFF.71.1 - -- - u CUFF.73 CUFF.73.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.73.1 - -- - u CUFF.75 CUFF.75.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.75.1 - -- - u CUFF.77 CUFF.77.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.77.1 - -- - u CUFF.79 CUFF.79.1 100 0.000000 0.000000 0.000000 0.000000 71 CUFF.79.1 - -- - u CUFF.81 CUFF.81.1 100 0.000000 0.000000 0.000000 0.000000 212 CUFF.81.1 - -- - u CUFF.83 CUFF.83.1 100 0.000000 0.000000 0.000000 0.000000 45 CUFF.83.1 - -- - u CUFF.85 CUFF.85.1 100 0.000000 0.000000 0.000000 0.000000 100 CUFF.85.1 - -- - u CUFF.87 CUFF.87.1 100 0.000000 0.000000 0.000000 0.000000 59 CUFF.87.1 - -- - u CUFF.89 CUFF.89.1 100 0.000000 0.000000 0.000000 0.000000 48 CUFF.89.1 - -- - u CUFF.91 CUFF.91.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.91.1 - -- - u CUFF.93 CUFF.93.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.93.1 - -- - u CUFF.95 CUFF.95.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.95.1 - -- - u CUFF.97 CUFF.97.1 100 0.000000 0.000000 0.000000 0.000000 27 CUFF.97.1 - -- - u CUFF.99 CUFF.99.1 100 0.000000 0.000000 0.000000 0.000000 97 CUFF.99.1 - +- - u CUFF.1 CUFF.1.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.1.1 - +- - u CUFF.3 CUFF.3.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.3.1 - +- - u CUFF.5 CUFF.5.1 100 21.226627 0.000000 59.889707 1.205672 27 CUFF.5.1 - +- - u CUFF.7 CUFF.7.1 100 29.709524 19.806349 39.612698 1.687500 576 CUFF.7.1 - +- - u CUFF.9 CUFF.9.1 100 34.072933 23.364686 44.781179 1.935341 565 CUFF.9.1 - +- - u CUFF.11 CUFF.11.1 100 32.531777 24.582998 40.480555 1.847804 979 CUFF.11.1 - +- - u CUFF.13 CUFF.13.1 100 16.582060 0.000000 35.729373 0.941860 86 CUFF.13.1 - +- - u CUFF.15 CUFF.15.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.15.1 - +- - u CUFF.17 CUFF.17.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.17.1 - +- - u CUFF.19 CUFF.19.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.19.1 - +- - u CUFF.21 CUFF.21.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.21.1 - +- - u CUFF.23 CUFF.23.1 100 16.205195 0.000000 34.917342 0.920455 88 CUFF.23.1 - +- - u CUFF.25 CUFF.25.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.25.1 - +- - u CUFF.26 CUFF.26.1 100 29.709524 0.000000 71.725135 1.687500 32 CUFF.26.1 - +- - u CUFF.29 CUFF.29.1 100 13.581496 0.000000 32.788633 0.771429 70 CUFF.29.1 - +- - u CUFF.31 CUFF.31.1 100 22.635827 0.000000 45.271655 1.285714 84 CUFF.31.1 - +Xkr4 Xkr4 i CUFF.33 CUFF.33.1 100 23.767619 0.000000 57.380108 1.350000 40 CUFF.33.1 3634 +Xkr4 Xkr4 i CUFF.35 CUFF.35.1 100 11.317914 0.000000 27.323861 0.642857 84 CUFF.35.1 3634 +Xkr4 Xkr4 i CUFF.37 CUFF.37.1 100 11.500461 0.000000 24.780049 0.653226 124 CUFF.37.1 3634 +Xkr4 Xkr4 i CUFF.39 CUFF.39.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.39.1 3634 +Xkr4 Xkr4 i CUFF.41 CUFF.41.1 100 43.213852 0.000000 93.112911 2.454545 33 CUFF.41.1 3634 +Xkr4 Xkr4 i CUFF.43 CUFF.43.1 100 23.474191 0.000000 46.948383 1.333333 81 CUFF.43.1 3634 +Xkr4 Xkr4 i CUFF.45 CUFF.45.1 100 20.667495 0.000000 49.895746 1.173913 46 CUFF.45.1 3634 +Xkr4 Xkr4 i CUFF.47 CUFF.47.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.47.1 3634 +Xkr4 Xkr4 i CUFF.49 CUFF.49.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.49.1 3634 +Xkr4 Xkr4 i CUFF.51 CUFF.51.1 100 14.948188 7.228977 22.667399 0.849057 477 CUFF.51.1 3634 +Xkr4 Xkr4 i CUFF.53 CUFF.53.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.53.1 3634 +Xkr4 Xkr4 i CUFF.55 CUFF.55.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.55.1 3634 +Xkr4 Xkr4 i CUFF.57 CUFF.57.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.57.1 3634 +Xkr4 Xkr4 i CUFF.59 CUFF.59.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.59.1 3634 +Xkr4 Xkr4 i CUFF.61 CUFF.61.1 100 13.204233 0.000000 31.877838 0.750000 72 CUFF.61.1 3634 +Xkr4 Xkr4 i CUFF.63 CUFF.63.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.63.1 3634 +Xkr4 Xkr4 i CUFF.65 CUFF.65.1 100 31.170648 0.000000 62.341295 1.770492 61 CUFF.65.1 3634 +Xkr4 Xkr4 i CUFF.67 CUFF.67.1 100 15.681351 3.378764 27.983938 0.890700 197 CUFF.67.1 3634 +Xkr4 Xkr4 i CUFF.69 CUFF.69.1 100 18.799247 8.750627 28.847866 1.067797 354 CUFF.69.1 3634 +Xkr4 Xkr4 i CUFF.71 CUFF.71.1 100 22.635827 0.000000 54.647722 1.285714 42 CUFF.71.1 3634 +Xkr4 Xkr4 i CUFF.73 CUFF.73.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.73.1 3634 +Xkr4 Xkr4 i CUFF.75 CUFF.75.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.75.1 3634 +Xkr4 Xkr4 i CUFF.77 CUFF.77.1 100 17.605644 0.000000 52.816931 1.000000 27 CUFF.77.1 3634 +Xkr4 Xkr4 i CUFF.79 CUFF.79.1 100 13.390208 0.000000 32.326821 0.760563 71 CUFF.79.1 3634 +Xkr4 Xkr4 i CUFF.81 CUFF.81.1 100 11.211141 1.183592 21.238690 0.636792 212 CUFF.81.1 3634 +Xkr4 Xkr4 i CUFF.83 CUFF.83.1 100 21.126772 0.000000 51.004540 1.200000 45 CUFF.83.1 3634 +Xkr4 Xkr4 i CUFF.85 CUFF.85.1 100 19.014095 0.000000 38.028190 1.080000 100 CUFF.85.1 3634 +Xkr4 Xkr4 i CUFF.87 CUFF.87.1 100 24.170460 0.000000 52.080103 1.372881 59 CUFF.87.1 3634 +Xkr4 Xkr4 i CUFF.89 CUFF.89.1 100 29.709524 0.000000 64.015126 1.687500 48 CUFF.89.1 3634 +Xkr4 Xkr4 i CUFF.91 CUFF.91.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.91.1 3634 +Xkr4 Xkr4 i CUFF.93 CUFF.93.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.93.1 3634 +Xkr4 Xkr4 i CUFF.95 CUFF.95.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.95.1 3634 +Xkr4 Xkr4 i CUFF.97 CUFF.97.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.97.1 3634 +Xkr4 Xkr4 i CUFF.99 CUFF.99.1 100 19.602160 0.000000 39.204320 1.113402 97 CUFF.99.1 3634 diff -r bde09cbd60865053ffd0ab05138d6fa3e594d399 -r 277403d31907d71e5e77694c0c97c16772f23e27 test-data/cuffcompare_out5.gtf --- a/test-data/cuffcompare_out5.gtf +++ b/test-data/cuffcompare_out5.gtf @@ -1,90 +1,90 @@ -chr1 Cufflinks exon 3111450 3111490 . . . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; -chr1 Cufflinks exon 3111546 3111576 . . . gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; -chr1 Cufflinks exon 3174766 3174792 . . . gene_id "XLOC_000003"; transcript_id "TCONS_00000051"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; -chr1 Cufflinks exon 3187402 3187428 . . . gene_id "XLOC_000004"; transcript_id "TCONS_00000052"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; -chr1 Cufflinks exon 3188522 3188548 . . . gene_id "XLOC_000005"; transcript_id "TCONS_00000053"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; -chr1 Cufflinks exon 3189811 3190789 . . . gene_id "XLOC_000006"; transcript_id "TCONS_00000054"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; -chr1 Cufflinks exon 3190859 3191434 . . . gene_id "XLOC_000007"; transcript_id "TCONS_00000055"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; -chr1 Cufflinks exon 3191513 3192077 . . . gene_id "XLOC_000008"; transcript_id "TCONS_00000056"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; -chr1 Cufflinks exon 3192251 3192336 . . . gene_id "XLOC_000009"; transcript_id "TCONS_00000057"; exon_number "1"; oId "CUFF.13.1"; class_code "u"; -chr1 Cufflinks exon 3192442 3192494 . . . gene_id "XLOC_000010"; transcript_id "TCONS_00000008"; exon_number "1"; oId "CUFF.39.1"; class_code "u"; -chr1 Cufflinks exon 3192551 3192629 . . . gene_id "XLOC_000011"; transcript_id "TCONS_00000009"; exon_number "1"; oId "CUFF.41.1"; class_code "u"; -chr1 Cufflinks exon 3192650 3192676 . . . gene_id "XLOC_000012"; transcript_id "TCONS_00000058"; exon_number "1"; oId "CUFF.15.1"; class_code "u"; -chr1 Cufflinks exon 3192732 3192811 . . . gene_id "XLOC_000013"; transcript_id "TCONS_00000010"; exon_number "1"; oId "CUFF.43.1"; class_code "u"; -chr1 Cufflinks exon 3192941 3193042 . . . gene_id "XLOC_000014"; transcript_id "TCONS_00000011"; exon_number "1"; oId "CUFF.45.1"; class_code "u"; -chr1 Cufflinks exon 3194186 3194226 . . . gene_id "XLOC_000015"; transcript_id "TCONS_00000012"; exon_number "1"; oId "CUFF.47.1"; class_code "u"; -chr1 Cufflinks exon 3194303 3194329 . . . gene_id "XLOC_000016"; transcript_id "TCONS_00000013"; exon_number "1"; oId "CUFF.49.1"; class_code "u"; -chr1 Cufflinks exon 3194707 3194733 . . . gene_id "XLOC_000017"; transcript_id "TCONS_00000059"; exon_number "1"; oId "CUFF.17.1"; class_code "u"; -chr1 Cufflinks exon 3195084 3195110 . . . gene_id "XLOC_000018"; transcript_id "TCONS_00000014"; exon_number "1"; oId "CUFF.51.1"; class_code "u"; -chr1 Cufflinks exon 3195451 3195477 . . . gene_id "XLOC_000019"; transcript_id "TCONS_00000015"; exon_number "1"; oId "CUFF.53.1"; class_code "u"; -chr1 Cufflinks exon 3197090 3197116 . . . gene_id "XLOC_000020"; transcript_id "TCONS_00000016"; exon_number "1"; oId "CUFF.55.1"; class_code "u"; -chr1 Cufflinks exon 3197247 3197273 . . . gene_id "XLOC_000021"; transcript_id "TCONS_00000017"; exon_number "1"; oId "CUFF.57.1"; class_code "u"; -chr1 Cufflinks exon 3197347 3197373 . . . gene_id "XLOC_000022"; transcript_id "TCONS_00000018"; exon_number "1"; oId "CUFF.59.1"; class_code "u"; -chr1 Cufflinks exon 3197426 3197452 . . . gene_id "XLOC_000023"; transcript_id "TCONS_00000060"; exon_number "1"; oId "CUFF.19.1"; class_code "u"; -chr1 Cufflinks exon 3200023 3200191 . . . gene_id "XLOC_000024"; transcript_id "TCONS_00000019"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; -chr1 Cufflinks exon 3200326 3200352 . . . gene_id "XLOC_000025"; transcript_id "TCONS_00000020"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; -chr1 Cufflinks exon 3200431 3200457 . . . gene_id "XLOC_000026"; transcript_id "TCONS_00000062"; exon_number "1"; oId "CUFF.21.1"; class_code "u"; -chr1 Cufflinks exon 3201008 3201039 . . . gene_id "XLOC_000027"; transcript_id "TCONS_00000063"; exon_number "1"; oId "CUFF.26.1"; class_code "u"; -chr1 Cufflinks exon 3201078 3201481 . . . gene_id "XLOC_000028"; transcript_id "TCONS_00000021"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; -chr1 Cufflinks exon 3201597 3201666 . . . gene_id "XLOC_000029"; transcript_id "TCONS_00000065"; exon_number "1"; oId "CUFF.29.1"; class_code "u"; -chr1 Cufflinks exon 3201673 3201699 . . . gene_id "XLOC_000030"; transcript_id "TCONS_00000022"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; -chr1 Cufflinks exon 3201726 3201809 . . . gene_id "XLOC_000031"; transcript_id "TCONS_00000066"; exon_number "1"; oId "CUFF.31.1"; class_code "u"; -chr1 Cufflinks exon 3204755 3204833 . . . gene_id "XLOC_000032"; transcript_id "TCONS_00000023"; exon_number "1"; oId "CUFF.13.1"; class_code "u"; -chr1 Cufflinks exon 3211522 3211561 . . . gene_id "XLOC_000033"; transcript_id "TCONS_00000067"; exon_number "1"; oId "CUFF.33.1"; class_code "u"; -chr1 Cufflinks exon 3212214 3212292 . . . gene_id "XLOC_000034"; transcript_id "TCONS_00000024"; exon_number "1"; oId "CUFF.15.1"; class_code "u"; -chr1 Cufflinks exon 3212368 3212439 . . . gene_id "XLOC_000035"; transcript_id "TCONS_00000025"; exon_number "1"; oId "CUFF.19.1"; class_code "u"; -chr1 Cufflinks exon 3212718 3212801 . . . gene_id "XLOC_000036"; transcript_id "TCONS_00000068"; exon_number "1"; oId "CUFF.35.1"; class_code "u"; -chr1 Cufflinks exon 3213096 3213192 . . . gene_id "XLOC_000037"; transcript_id "TCONS_00000026"; exon_number "1"; oId "CUFF.17.1"; class_code "u"; -chr1 Cufflinks exon 3213119 3213242 . . . gene_id "XLOC_000037"; transcript_id "TCONS_00000069"; exon_number "1"; oId "CUFF.37.1"; class_code "u"; -chr1 Cufflinks exon 3240607 3240633 . . . gene_id "XLOC_000038"; transcript_id "TCONS_00000070"; exon_number "1"; oId "CUFF.39.1"; class_code "u"; -chr1 Cufflinks exon 3242480 3242512 . . . gene_id "XLOC_000039"; transcript_id "TCONS_00000071"; exon_number "1"; oId "CUFF.41.1"; class_code "u"; -chr1 Cufflinks exon 3242634 3242923 . . . gene_id "XLOC_000040"; transcript_id "TCONS_00000027"; exon_number "1"; oId "CUFF.25.1"; class_code "u"; -chr1 Cufflinks exon 3242925 3243005 . . . gene_id "XLOC_000041"; transcript_id "TCONS_00000072"; exon_number "1"; oId "CUFF.43.1"; class_code "u"; -chr1 Cufflinks exon 3243019 3243079 . . . gene_id "XLOC_000042"; transcript_id "TCONS_00000028"; exon_number "1"; oId "CUFF.21.1"; class_code "u"; -chr1 Cufflinks exon 3243109 3243154 . . . gene_id "XLOC_000043"; transcript_id "TCONS_00000073"; exon_number "1"; oId "CUFF.45.1"; class_code "u"; -chr1 Cufflinks exon 3243348 3243401 . . . gene_id "XLOC_000044"; transcript_id "TCONS_00000029"; exon_number "1"; oId "CUFF.23.1"; class_code "u"; -chr1 Cufflinks exon 3254080 3254106 . . . gene_id "XLOC_000045"; transcript_id "TCONS_00000074"; exon_number "1"; oId "CUFF.47.1"; class_code "u"; -chr1 Cufflinks exon 3256975 3257011 . . . gene_id "XLOC_000046"; transcript_id "TCONS_00000030"; exon_number "1"; oId "CUFF.27.1"; class_code "u"; -chr1 Cufflinks exon 3277156 3277182 . . . gene_id "XLOC_000047"; transcript_id "TCONS_00000075"; exon_number "1"; oId "CUFF.49.1"; class_code "u"; -chr1 Cufflinks exon 3277191 3277218 . . . gene_id "XLOC_000048"; transcript_id "TCONS_00000031"; exon_number "1"; oId "CUFF.61.1"; class_code "u"; -chr1 Cufflinks exon 3277914 3278390 . . . gene_id "XLOC_000049"; transcript_id "TCONS_00000076"; exon_number "1"; oId "CUFF.51.1"; class_code "u"; -chr1 Cufflinks exon 3280118 3280144 . . . gene_id "XLOC_000050"; transcript_id "TCONS_00000077"; exon_number "1"; oId "CUFF.53.1"; class_code "u"; -chr1 Cufflinks exon 3280499 3280525 . . . gene_id "XLOC_000051"; transcript_id "TCONS_00000078"; exon_number "1"; oId "CUFF.55.1"; class_code "u"; -chr1 Cufflinks exon 3280687 3280741 . . . gene_id "XLOC_000052"; transcript_id "TCONS_00000033"; exon_number "1"; oId "CUFF.65.1"; class_code "u"; -chr1 Cufflinks exon 3282505 3282531 . . . gene_id "XLOC_000053"; transcript_id "TCONS_00000079"; exon_number "1"; oId "CUFF.57.1"; class_code "u"; -chr1 Cufflinks exon 3282651 3282677 . . . gene_id "XLOC_000054"; transcript_id "TCONS_00000080"; exon_number "1"; oId "CUFF.59.1"; class_code "u"; -chr1 Cufflinks exon 3282761 3282832 . . . gene_id "XLOC_000055"; transcript_id "TCONS_00000081"; exon_number "1"; oId "CUFF.61.1"; class_code "u"; -chr1 Cufflinks exon 3284967 3284993 . . . gene_id "XLOC_000056"; transcript_id "TCONS_00000082"; exon_number "1"; oId "CUFF.63.1"; class_code "u"; -chr1 Cufflinks exon 3290489 3290553 . . . gene_id "XLOC_000057"; transcript_id "TCONS_00000034"; exon_number "1"; oId "CUFF.67.1"; class_code "u"; -chr1 Cufflinks exon 3290799 3290859 . . . gene_id "XLOC_000058"; transcript_id "TCONS_00000083"; exon_number "1"; oId "CUFF.65.1"; class_code "u"; -chr1 Cufflinks exon 3290920 3291273 . . . gene_id "XLOC_000059"; transcript_id "TCONS_00000084"; exon_number "1"; oId "CUFF.69.1"; class_code "u"; -chr1 Cufflinks exon 3299444 3299640 . . . gene_id "XLOC_000060"; transcript_id "TCONS_00000085"; exon_number "1"; oId "CUFF.67.1"; class_code "u"; -chr1 Cufflinks exon 3299610 3299664 . . . gene_id "XLOC_000060"; transcript_id "TCONS_00000037"; exon_number "1"; oId "CUFF.73.1"; class_code "u"; -chr1 Cufflinks exon 3299692 3299733 . . . gene_id "XLOC_000061"; transcript_id "TCONS_00000086"; exon_number "1"; oId "CUFF.71.1"; class_code "u"; -chr1 Cufflinks exon 3300052 3300078 . . . gene_id "XLOC_000062"; transcript_id "TCONS_00000038"; exon_number "1"; oId "CUFF.75.1"; class_code "u"; -chr1 Cufflinks exon 3307749 3307775 . . . gene_id "XLOC_000063"; transcript_id "TCONS_00000087"; exon_number "1"; oId "CUFF.73.1"; class_code "u"; -chr1 Cufflinks exon 3318621 3318647 . . . gene_id "XLOC_000064"; transcript_id "TCONS_00000088"; exon_number "1"; oId "CUFF.75.1"; class_code "u"; -chr1 Cufflinks exon 3319000 3319051 . . . gene_id "XLOC_000065"; transcript_id "TCONS_00000039"; exon_number "1"; oId "CUFF.77.1"; class_code "u"; -chr1 Cufflinks exon 3330528 3330554 . . . gene_id "XLOC_000066"; transcript_id "TCONS_00000089"; exon_number "1"; oId "CUFF.77.1"; class_code "u"; -chr1 Cufflinks exon 3351241 3351311 . . . gene_id "XLOC_000067"; transcript_id "TCONS_00000090"; exon_number "1"; oId "CUFF.79.1"; class_code "u"; -chr1 Cufflinks exon 3355888 3355914 . . . gene_id "XLOC_000068"; transcript_id "TCONS_00000040"; exon_number "1"; oId "CUFF.79.1"; class_code "u"; -chr1 Cufflinks exon 3355908 3356119 . . . gene_id "XLOC_000068"; transcript_id "TCONS_00000091"; exon_number "1"; oId "CUFF.81.1"; class_code "u"; -chr1 Cufflinks exon 3356181 3356225 . . . gene_id "XLOC_000069"; transcript_id "TCONS_00000092"; exon_number "1"; oId "CUFF.83.1"; class_code "u"; -chr1 Cufflinks exon 3363077 3363176 . . . gene_id "XLOC_000070"; transcript_id "TCONS_00000093"; exon_number "1"; oId "CUFF.85.1"; class_code "u"; -chr1 Cufflinks exon 3363215 3363278 . . . gene_id "XLOC_000071"; transcript_id "TCONS_00000041"; exon_number "1"; oId "CUFF.81.1"; class_code "u"; -chr1 Cufflinks exon 3363388 3363446 . . . gene_id "XLOC_000072"; transcript_id "TCONS_00000094"; exon_number "1"; oId "CUFF.87.1"; class_code "u"; -chr1 Cufflinks exon 3363754 3363849 . . . gene_id "XLOC_000073"; transcript_id "TCONS_00000042"; exon_number "1"; oId "CUFF.83.1"; class_code "u"; -chr1 Cufflinks exon 3364872 3364919 . . . gene_id "XLOC_000074"; transcript_id "TCONS_00000095"; exon_number "1"; oId "CUFF.89.1"; class_code "u"; -chr1 Cufflinks exon 3367136 3367162 . . . gene_id "XLOC_000075"; transcript_id "TCONS_00000043"; exon_number "1"; oId "CUFF.85.1"; class_code "u"; -chr1 Cufflinks exon 3367211 3367237 . . . gene_id "XLOC_000076"; transcript_id "TCONS_00000096"; exon_number "1"; oId "CUFF.91.1"; class_code "u"; -chr1 Cufflinks exon 3367334 3367382 . . . gene_id "XLOC_000077"; transcript_id "TCONS_00000044"; exon_number "1"; oId "CUFF.87.1"; class_code "u"; -chr1 Cufflinks exon 3369581 3369607 . . . gene_id "XLOC_000078"; transcript_id "TCONS_00000097"; exon_number "1"; oId "CUFF.93.1"; class_code "u"; -chr1 Cufflinks exon 3375002 3375028 . . . gene_id "XLOC_000079"; transcript_id "TCONS_00000098"; exon_number "1"; oId "CUFF.95.1"; class_code "u"; -chr1 Cufflinks exon 3377212 3377262 . . . gene_id "XLOC_000080"; transcript_id "TCONS_00000045"; exon_number "1"; oId "CUFF.89.1"; class_code "u"; -chr1 Cufflinks exon 3379889 3379915 . . . gene_id "XLOC_000081"; transcript_id "TCONS_00000099"; exon_number "1"; oId "CUFF.97.1"; class_code "u"; -chr1 Cufflinks exon 3386740 3386836 . . . gene_id "XLOC_000082"; transcript_id "TCONS_00000100"; exon_number "1"; oId "CUFF.99.1"; class_code "u"; -chr1 Cufflinks exon 3391326 3391352 . . . gene_id "XLOC_000083"; transcript_id "TCONS_00000046"; exon_number "1"; oId "CUFF.91.1"; class_code "u"; -chr1 Cufflinks exon 3435842 3435880 . . . gene_id "XLOC_000084"; transcript_id "TCONS_00000047"; exon_number "1"; oId "CUFF.93.1"; class_code "u"; -chr1 Cufflinks exon 3447762 3447788 . . . gene_id "XLOC_000085"; transcript_id "TCONS_00000048"; exon_number "1"; oId "CUFF.95.1"; class_code "u"; -chr1 Cufflinks exon 3450907 3450965 . . . gene_id "XLOC_000086"; transcript_id "TCONS_00000049"; exon_number "1"; oId "CUFF.97.1"; class_code "u"; -chr1 Cufflinks exon 3451052 3451109 . . . gene_id "XLOC_000087"; transcript_id "TCONS_00000050"; exon_number "1"; oId "CUFF.99.1"; class_code "u"; +chr1 Cufflinks exon 3204755 3204833 . - . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.13.1"; nearest_ref "Xkr4"; class_code "c"; tss_id "TSS1"; +chr1 Cufflinks exon 3111450 3111490 . . . gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS2"; +chr1 Cufflinks exon 3111546 3111576 . . . gene_id "XLOC_000003"; transcript_id "TCONS_00000003"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS3"; +chr1 Cufflinks exon 3174766 3174792 . . . gene_id "XLOC_000004"; transcript_id "TCONS_00000051"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS4"; +chr1 Cufflinks exon 3187402 3187428 . . . gene_id "XLOC_000005"; transcript_id "TCONS_00000052"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS5"; +chr1 Cufflinks exon 3188522 3188548 . . . gene_id "XLOC_000006"; transcript_id "TCONS_00000053"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS6"; +chr1 Cufflinks exon 3189811 3190789 . . . gene_id "XLOC_000007"; transcript_id "TCONS_00000054"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS7"; +chr1 Cufflinks exon 3190859 3191434 . . . gene_id "XLOC_000008"; transcript_id "TCONS_00000055"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS11"; +chr1 Cufflinks exon 3191513 3192077 . . . gene_id "XLOC_000009"; transcript_id "TCONS_00000056"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS12"; +chr1 Cufflinks exon 3192251 3192336 . . . gene_id "XLOC_000010"; transcript_id "TCONS_00000057"; exon_number "1"; oId "CUFF.13.1"; class_code "u"; tss_id "TSS15"; +chr1 Cufflinks exon 3192442 3192494 . . . gene_id "XLOC_000011"; transcript_id "TCONS_00000009"; exon_number "1"; oId "CUFF.39.1"; class_code "u"; tss_id "TSS16"; +chr1 Cufflinks exon 3192551 3192629 . . . gene_id "XLOC_000012"; transcript_id "TCONS_00000010"; exon_number "1"; oId "CUFF.41.1"; class_code "u"; tss_id "TSS17"; +chr1 Cufflinks exon 3192650 3192676 . . . gene_id "XLOC_000013"; transcript_id "TCONS_00000058"; exon_number "1"; oId "CUFF.15.1"; class_code "u"; tss_id "TSS18"; +chr1 Cufflinks exon 3192732 3192811 . . . gene_id "XLOC_000014"; transcript_id "TCONS_00000011"; exon_number "1"; oId "CUFF.43.1"; class_code "u"; tss_id "TSS19"; +chr1 Cufflinks exon 3192941 3193042 . . . gene_id "XLOC_000015"; transcript_id "TCONS_00000012"; exon_number "1"; oId "CUFF.45.1"; class_code "u"; tss_id "TSS20"; +chr1 Cufflinks exon 3194186 3194226 . . . gene_id "XLOC_000016"; transcript_id "TCONS_00000013"; exon_number "1"; oId "CUFF.47.1"; class_code "u"; tss_id "TSS21"; +chr1 Cufflinks exon 3194303 3194329 . . . gene_id "XLOC_000017"; transcript_id "TCONS_00000014"; exon_number "1"; oId "CUFF.49.1"; class_code "u"; tss_id "TSS22"; +chr1 Cufflinks exon 3194707 3194733 . . . gene_id "XLOC_000018"; transcript_id "TCONS_00000059"; exon_number "1"; oId "CUFF.17.1"; class_code "u"; tss_id "TSS23"; +chr1 Cufflinks exon 3195084 3195110 . . . gene_id "XLOC_000019"; transcript_id "TCONS_00000015"; exon_number "1"; oId "CUFF.51.1"; class_code "u"; tss_id "TSS24"; +chr1 Cufflinks exon 3195451 3195477 . . . gene_id "XLOC_000020"; transcript_id "TCONS_00000016"; exon_number "1"; oId "CUFF.53.1"; class_code "u"; tss_id "TSS25"; +chr1 Cufflinks exon 3197090 3197116 . . . gene_id "XLOC_000021"; transcript_id "TCONS_00000017"; exon_number "1"; oId "CUFF.55.1"; class_code "u"; tss_id "TSS26"; +chr1 Cufflinks exon 3197247 3197273 . . . gene_id "XLOC_000022"; transcript_id "TCONS_00000018"; exon_number "1"; oId "CUFF.57.1"; class_code "u"; tss_id "TSS27"; +chr1 Cufflinks exon 3197347 3197373 . . . gene_id "XLOC_000023"; transcript_id "TCONS_00000019"; exon_number "1"; oId "CUFF.59.1"; class_code "u"; tss_id "TSS28"; +chr1 Cufflinks exon 3197426 3197452 . . . gene_id "XLOC_000024"; transcript_id "TCONS_00000060"; exon_number "1"; oId "CUFF.19.1"; class_code "u"; tss_id "TSS29"; +chr1 Cufflinks exon 3200023 3200191 . . . gene_id "XLOC_000025"; transcript_id "TCONS_00000020"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS30"; +chr1 Cufflinks exon 3200326 3200352 . . . gene_id "XLOC_000026"; transcript_id "TCONS_00000021"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS32"; +chr1 Cufflinks exon 3200431 3200457 . . . gene_id "XLOC_000027"; transcript_id "TCONS_00000062"; exon_number "1"; oId "CUFF.21.1"; class_code "u"; tss_id "TSS33"; +chr1 Cufflinks exon 3201008 3201039 . . . gene_id "XLOC_000028"; transcript_id "TCONS_00000063"; exon_number "1"; oId "CUFF.26.1"; class_code "u"; tss_id "TSS34"; +chr1 Cufflinks exon 3201078 3201481 . . . gene_id "XLOC_000029"; transcript_id "TCONS_00000022"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS35"; +chr1 Cufflinks exon 3201597 3201666 . . . gene_id "XLOC_000030"; transcript_id "TCONS_00000065"; exon_number "1"; oId "CUFF.29.1"; class_code "u"; tss_id "TSS37"; +chr1 Cufflinks exon 3201673 3201699 . . . gene_id "XLOC_000031"; transcript_id "TCONS_00000023"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS38"; +chr1 Cufflinks exon 3201726 3201809 . . . gene_id "XLOC_000032"; transcript_id "TCONS_00000066"; exon_number "1"; oId "CUFF.31.1"; class_code "u"; tss_id "TSS39"; +chr1 Cufflinks exon 3211522 3211561 . . . gene_id "XLOC_000033"; transcript_id "TCONS_00000067"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.33.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS40"; +chr1 Cufflinks exon 3212214 3212292 . . . gene_id "XLOC_000034"; transcript_id "TCONS_00000024"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.15.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS41"; +chr1 Cufflinks exon 3212368 3212439 . . . gene_id "XLOC_000035"; transcript_id "TCONS_00000025"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.19.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS42"; +chr1 Cufflinks exon 3212718 3212801 . . . gene_id "XLOC_000036"; transcript_id "TCONS_00000068"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.35.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS43"; +chr1 Cufflinks exon 3213096 3213192 . . . gene_id "XLOC_000037"; transcript_id "TCONS_00000026"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.17.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS44"; +chr1 Cufflinks exon 3213119 3213242 . . . gene_id "XLOC_000037"; transcript_id "TCONS_00000069"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.37.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS45"; +chr1 Cufflinks exon 3240607 3240633 . . . gene_id "XLOC_000038"; transcript_id "TCONS_00000070"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.39.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS46"; +chr1 Cufflinks exon 3242480 3242512 . . . gene_id "XLOC_000039"; transcript_id "TCONS_00000071"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.41.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS47"; +chr1 Cufflinks exon 3242634 3242923 . . . gene_id "XLOC_000040"; transcript_id "TCONS_00000027"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.25.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS48"; +chr1 Cufflinks exon 3242925 3243005 . . . gene_id "XLOC_000041"; transcript_id "TCONS_00000072"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.43.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS49"; +chr1 Cufflinks exon 3243019 3243079 . . . gene_id "XLOC_000042"; transcript_id "TCONS_00000028"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.21.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS50"; +chr1 Cufflinks exon 3243109 3243154 . . . gene_id "XLOC_000043"; transcript_id "TCONS_00000073"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.45.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS51"; +chr1 Cufflinks exon 3243348 3243401 . . . gene_id "XLOC_000044"; transcript_id "TCONS_00000029"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.23.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS52"; +chr1 Cufflinks exon 3254080 3254106 . . . gene_id "XLOC_000045"; transcript_id "TCONS_00000074"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.47.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS53"; +chr1 Cufflinks exon 3256975 3257011 . . . gene_id "XLOC_000046"; transcript_id "TCONS_00000030"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.27.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS54"; +chr1 Cufflinks exon 3277156 3277182 . . . gene_id "XLOC_000047"; transcript_id "TCONS_00000075"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.49.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS55"; +chr1 Cufflinks exon 3277191 3277218 . . . gene_id "XLOC_000048"; transcript_id "TCONS_00000031"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.61.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS56"; +chr1 Cufflinks exon 3277914 3278390 . . . gene_id "XLOC_000049"; transcript_id "TCONS_00000076"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.51.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS57"; +chr1 Cufflinks exon 3280118 3280144 . . . gene_id "XLOC_000050"; transcript_id "TCONS_00000077"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.53.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS59"; +chr1 Cufflinks exon 3280499 3280525 . . . gene_id "XLOC_000051"; transcript_id "TCONS_00000078"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.55.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS60"; +chr1 Cufflinks exon 3280687 3280741 . . . gene_id "XLOC_000052"; transcript_id "TCONS_00000033"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.65.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS61"; +chr1 Cufflinks exon 3282505 3282531 . . . gene_id "XLOC_000053"; transcript_id "TCONS_00000079"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.57.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS62"; +chr1 Cufflinks exon 3282651 3282677 . . . gene_id "XLOC_000054"; transcript_id "TCONS_00000080"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.59.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS63"; +chr1 Cufflinks exon 3282761 3282832 . . . gene_id "XLOC_000055"; transcript_id "TCONS_00000081"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.61.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS64"; +chr1 Cufflinks exon 3284967 3284993 . . . gene_id "XLOC_000056"; transcript_id "TCONS_00000082"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.63.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS65"; +chr1 Cufflinks exon 3290489 3290553 . . . gene_id "XLOC_000057"; transcript_id "TCONS_00000034"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.67.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS66"; +chr1 Cufflinks exon 3290799 3290859 . . . gene_id "XLOC_000058"; transcript_id "TCONS_00000083"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.65.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS67"; +chr1 Cufflinks exon 3290920 3291273 . . . gene_id "XLOC_000059"; transcript_id "TCONS_00000084"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.69.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS68"; +chr1 Cufflinks exon 3299444 3299640 . . . gene_id "XLOC_000060"; transcript_id "TCONS_00000085"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.67.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS70"; +chr1 Cufflinks exon 3299610 3299664 . . . gene_id "XLOC_000060"; transcript_id "TCONS_00000037"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.73.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS71"; +chr1 Cufflinks exon 3299692 3299733 . . . gene_id "XLOC_000061"; transcript_id "TCONS_00000086"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.71.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS72"; +chr1 Cufflinks exon 3300052 3300078 . . . gene_id "XLOC_000062"; transcript_id "TCONS_00000038"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.75.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS73"; +chr1 Cufflinks exon 3307749 3307775 . . . gene_id "XLOC_000063"; transcript_id "TCONS_00000087"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.73.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS74"; +chr1 Cufflinks exon 3318621 3318647 . . . gene_id "XLOC_000064"; transcript_id "TCONS_00000088"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.75.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS75"; +chr1 Cufflinks exon 3319000 3319051 . . . gene_id "XLOC_000065"; transcript_id "TCONS_00000039"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.77.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS76"; +chr1 Cufflinks exon 3330528 3330554 . . . gene_id "XLOC_000066"; transcript_id "TCONS_00000089"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.77.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS77"; +chr1 Cufflinks exon 3351241 3351311 . . . gene_id "XLOC_000067"; transcript_id "TCONS_00000090"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.79.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS78"; +chr1 Cufflinks exon 3355888 3355914 . . . gene_id "XLOC_000068"; transcript_id "TCONS_00000040"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.79.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS79"; +chr1 Cufflinks exon 3355908 3356119 . . . gene_id "XLOC_000068"; transcript_id "TCONS_00000091"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.81.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS80"; +chr1 Cufflinks exon 3356181 3356225 . . . gene_id "XLOC_000069"; transcript_id "TCONS_00000092"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.83.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS81"; +chr1 Cufflinks exon 3363077 3363176 . . . gene_id "XLOC_000070"; transcript_id "TCONS_00000093"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.85.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS82"; +chr1 Cufflinks exon 3363215 3363278 . . . gene_id "XLOC_000071"; transcript_id "TCONS_00000041"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.81.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS83"; +chr1 Cufflinks exon 3363388 3363446 . . . gene_id "XLOC_000072"; transcript_id "TCONS_00000094"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.87.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS84"; +chr1 Cufflinks exon 3363754 3363849 . . . gene_id "XLOC_000073"; transcript_id "TCONS_00000042"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.83.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS85"; +chr1 Cufflinks exon 3364872 3364919 . . . gene_id "XLOC_000074"; transcript_id "TCONS_00000095"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.89.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS86"; +chr1 Cufflinks exon 3367136 3367162 . . . gene_id "XLOC_000075"; transcript_id "TCONS_00000043"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.85.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS87"; +chr1 Cufflinks exon 3367211 3367237 . . . gene_id "XLOC_000076"; transcript_id "TCONS_00000096"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.91.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS88"; +chr1 Cufflinks exon 3367334 3367382 . . . gene_id "XLOC_000077"; transcript_id "TCONS_00000044"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.87.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS89"; +chr1 Cufflinks exon 3369581 3369607 . . . gene_id "XLOC_000078"; transcript_id "TCONS_00000097"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.93.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS90"; +chr1 Cufflinks exon 3375002 3375028 . . . gene_id "XLOC_000079"; transcript_id "TCONS_00000098"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.95.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS91"; +chr1 Cufflinks exon 3377212 3377262 . . . gene_id "XLOC_000080"; transcript_id "TCONS_00000045"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.89.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS92"; +chr1 Cufflinks exon 3379889 3379915 . . . gene_id "XLOC_000081"; transcript_id "TCONS_00000099"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.97.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS93"; +chr1 Cufflinks exon 3386740 3386836 . . . gene_id "XLOC_000082"; transcript_id "TCONS_00000100"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.99.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS94"; +chr1 Cufflinks exon 3391326 3391352 . . . gene_id "XLOC_000083"; transcript_id "TCONS_00000046"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.91.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS95"; +chr1 Cufflinks exon 3435842 3435880 . . . gene_id "XLOC_000084"; transcript_id "TCONS_00000047"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.93.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS96"; +chr1 Cufflinks exon 3447762 3447788 . . . gene_id "XLOC_000085"; transcript_id "TCONS_00000048"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.95.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS97"; +chr1 Cufflinks exon 3450907 3450965 . . . gene_id "XLOC_000086"; transcript_id "TCONS_00000049"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.97.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS98"; +chr1 Cufflinks exon 3451052 3451109 . . . gene_id "XLOC_000087"; transcript_id "TCONS_00000050"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.99.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS99"; diff -r bde09cbd60865053ffd0ab05138d6fa3e594d399 -r 277403d31907d71e5e77694c0c97c16772f23e27 test-data/cuffcompare_out6.tracking --- a/test-data/cuffcompare_out6.tracking +++ b/test-data/cuffcompare_out6.tracking @@ -1,100 +1,100 @@ -TCONS_00000001 XLOC_000001 - u q1:CUFF.1|CUFF.1.1|100|0.000000|0.000000|0.000000|0.000000|- - -TCONS_00000002 XLOC_000002 - u q1:CUFF.3|CUFF.3.1|100|0.000000|0.000000|0.000000|0.000000|- - -TCONS_00000003 XLOC_000006 - u q1:CUFF.29|CUFF.29.1|100|0.000000|0.000000|0.000000|0.000000|- - -TCONS_00000004 XLOC_000006 - u q1:CUFF.31|CUFF.31.1|100|0.000000|0.000000|0.000000|0.000000|- - -TCONS_00000005 XLOC_000006 - u q1:CUFF.33|CUFF.33.1|100|0.000000|0.000000|0.000000|0.000000|- - -TCONS_00000006 XLOC_000008 - u q1:CUFF.35|CUFF.35.1|100|0.000000|0.000000|0.000000|0.000000|- - -TCONS_00000007 XLOC_000008 - u q1:CUFF.37|CUFF.37.1|100|0.000000|0.000000|0.000000|0.000000|- - -TCONS_00000008 XLOC_000010 - u q1:CUFF.39|CUFF.39.1|100|0.000000|0.000000|0.000000|0.000000|- - -TCONS_00000009 XLOC_000011 - u q1:CUFF.41|CUFF.41.1|100|0.000000|0.000000|0.000000|0.000000|- - -TCONS_00000010 XLOC_000013 - u q1:CUFF.43|CUFF.43.1|100|0.000000|0.000000|0.000000|0.000000|- - -TCONS_00000011 XLOC_000014 - u q1:CUFF.45|CUFF.45.1|100|0.000000|0.000000|0.000000|0.000000|- - -TCONS_00000012 XLOC_000015 - u q1:CUFF.47|CUFF.47.1|100|0.000000|0.000000|0.000000|0.000000|- - -TCONS_00000013 XLOC_000016 - u q1:CUFF.49|CUFF.49.1|100|0.000000|0.000000|0.000000|0.000000|- - -TCONS_00000014 XLOC_000018 - u q1:CUFF.51|CUFF.51.1|100|0.000000|0.000000|0.000000|0.000000|- - -TCONS_00000015 XLOC_000019 - u q1:CUFF.53|CUFF.53.1|100|0.000000|0.000000|0.000000|0.000000|- - -TCONS_00000016 XLOC_000020 - u q1:CUFF.55|CUFF.55.1|100|0.000000|0.000000|0.000000|0.000000|- - -TCONS_00000017 XLOC_000021 - u q1:CUFF.57|CUFF.57.1|100|0.000000|0.000000|0.000000|0.000000|- - -TCONS_00000018 XLOC_000022 - u q1:CUFF.59|CUFF.59.1|100|0.000000|0.000000|0.000000|0.000000|- - -TCONS_00000019 XLOC_000024 - u q1:CUFF.7|CUFF.7.1|100|0.000000|0.000000|0.000000|0.000000|- - -TCONS_00000020 XLOC_000025 - u q1:CUFF.5|CUFF.5.1|100|0.000000|0.000000|0.000000|0.000000|- - -TCONS_00000021 XLOC_000028 - u q1:CUFF.9|CUFF.9.1|100|0.000000|0.000000|0.000000|0.000000|- - -TCONS_00000022 XLOC_000030 - u 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q1:CUFF.79|CUFF.79.1|100|31.293533|0.000000|75.549272|2.000000|- - +TCONS_00000041 XLOC_000071 Xkr4|Xkr4 i q1:CUFF.81|CUFF.81.1|100|13.201959|0.000000|31.872349|0.843750|- - +TCONS_00000042 XLOC_000073 Xkr4|Xkr4 i q1:CUFF.83|CUFF.83.1|100|13.201959|0.000000|28.446269|0.843750|- - +TCONS_00000043 XLOC_000075 Xkr4|Xkr4 i q1:CUFF.85|CUFF.85.1|100|31.293533|0.000000|75.549272|2.000000|- - +TCONS_00000044 XLOC_000077 Xkr4|Xkr4 i q1:CUFF.87|CUFF.87.1|100|17.243375|0.000000|41.629191|1.102041|- - +TCONS_00000045 XLOC_000080 Xkr4|Xkr4 i q1:CUFF.89|CUFF.89.1|100|16.567165|0.000000|39.996674|1.058824|- - +TCONS_00000046 XLOC_000083 Xkr4|Xkr4 i q1:CUFF.91|CUFF.91.1|100|31.293533|0.000000|75.549272|2.000000|- - +TCONS_00000047 XLOC_000084 Xkr4|Xkr4 i q1:CUFF.93|CUFF.93.1|100|21.664754|0.000000|52.303342|1.384615|- - +TCONS_00000048 XLOC_000085 Xkr4|Xkr4 i q1:CUFF.95|CUFF.95.1|100|46.940300|0.000000|101.142289|3.000000|- - +TCONS_00000049 XLOC_000086 Xkr4|Xkr4 i q1:CUFF.97|CUFF.97.1|100|21.481154|0.000000|46.285454|1.372881|- - +TCONS_00000050 XLOC_000087 Xkr4|Xkr4 i q1:CUFF.99|CUFF.99.1|100|14.567679|0.000000|35.169489|0.931034|- - +TCONS_00000051 XLOC_000004 - u - q2:CUFF.1|CUFF.1.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000052 XLOC_000005 - u - q2:CUFF.3|CUFF.3.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000053 XLOC_000006 - u - q2:CUFF.5|CUFF.5.1|100|21.226627|0.000000|59.889707|1.205672|- +TCONS_00000054 XLOC_000007 - u - q2:CUFF.11|CUFF.11.1|100|32.531777|24.582998|40.480555|1.847804|- +TCONS_00000055 XLOC_000008 - u - q2:CUFF.7|CUFF.7.1|100|29.709524|19.806349|39.612698|1.687500|- +TCONS_00000056 XLOC_000009 - u - q2:CUFF.9|CUFF.9.1|100|34.072933|23.364686|44.781179|1.935341|- +TCONS_00000057 XLOC_000010 - u - q2:CUFF.13|CUFF.13.1|100|16.582060|0.000000|35.729373|0.941860|- +TCONS_00000058 XLOC_000013 - u - q2:CUFF.15|CUFF.15.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000059 XLOC_000018 - u - q2:CUFF.17|CUFF.17.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000060 XLOC_000024 - u - q2:CUFF.19|CUFF.19.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000061 XLOC_000025 - u - q2:CUFF.23|CUFF.23.1|100|16.205195|0.000000|34.917342|0.920455|- +TCONS_00000062 XLOC_000027 - u - q2:CUFF.21|CUFF.21.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000063 XLOC_000028 - u - q2:CUFF.26|CUFF.26.1|100|29.709524|0.000000|71.725135|1.687500|- +TCONS_00000064 XLOC_000029 - u - q2:CUFF.25|CUFF.25.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000065 XLOC_000030 - u - q2:CUFF.29|CUFF.29.1|100|13.581496|0.000000|32.788633|0.771429|- +TCONS_00000066 XLOC_000032 - u - q2:CUFF.31|CUFF.31.1|100|22.635827|0.000000|45.271655|1.285714|- +TCONS_00000067 XLOC_000033 Xkr4|Xkr4 i - q2:CUFF.33|CUFF.33.1|100|23.767619|0.000000|57.380108|1.350000|- +TCONS_00000068 XLOC_000036 Xkr4|Xkr4 i - q2:CUFF.35|CUFF.35.1|100|11.317914|0.000000|27.323861|0.642857|- +TCONS_00000069 XLOC_000037 Xkr4|Xkr4 i - q2:CUFF.37|CUFF.37.1|100|11.500461|0.000000|24.780049|0.653226|- +TCONS_00000070 XLOC_000038 Xkr4|Xkr4 i - q2:CUFF.39|CUFF.39.1|100|52.816931|0.000000|113.804669|3.000000|- +TCONS_00000071 XLOC_000039 Xkr4|Xkr4 i - q2:CUFF.41|CUFF.41.1|100|43.213852|0.000000|93.112911|2.454545|- +TCONS_00000072 XLOC_000041 Xkr4|Xkr4 i - q2:CUFF.43|CUFF.43.1|100|23.474191|0.000000|46.948383|1.333333|- +TCONS_00000073 XLOC_000043 Xkr4|Xkr4 i - q2:CUFF.45|CUFF.45.1|100|20.667495|0.000000|49.895746|1.173913|- +TCONS_00000074 XLOC_000045 Xkr4|Xkr4 i - q2:CUFF.47|CUFF.47.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000075 XLOC_000047 Xkr4|Xkr4 i - q2:CUFF.49|CUFF.49.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000076 XLOC_000049 Xkr4|Xkr4 i - q2:CUFF.51|CUFF.51.1|100|14.948188|7.228977|22.667399|0.849057|- +TCONS_00000077 XLOC_000050 Xkr4|Xkr4 i - q2:CUFF.53|CUFF.53.1|100|52.816931|0.000000|113.804669|3.000000|- +TCONS_00000078 XLOC_000051 Xkr4|Xkr4 i - q2:CUFF.55|CUFF.55.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000079 XLOC_000053 Xkr4|Xkr4 i - q2:CUFF.57|CUFF.57.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000080 XLOC_000054 Xkr4|Xkr4 i - q2:CUFF.59|CUFF.59.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000081 XLOC_000055 Xkr4|Xkr4 i - q2:CUFF.61|CUFF.61.1|100|13.204233|0.000000|31.877838|0.750000|- +TCONS_00000082 XLOC_000056 Xkr4|Xkr4 i - q2:CUFF.63|CUFF.63.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000083 XLOC_000058 Xkr4|Xkr4 i - q2:CUFF.65|CUFF.65.1|100|31.170648|0.000000|62.341295|1.770492|- +TCONS_00000084 XLOC_000059 Xkr4|Xkr4 i - q2:CUFF.69|CUFF.69.1|100|18.799247|8.750627|28.847866|1.067797|- +TCONS_00000085 XLOC_000060 Xkr4|Xkr4 i - q2:CUFF.67|CUFF.67.1|100|15.681351|3.378764|27.983938|0.890700|- +TCONS_00000086 XLOC_000061 Xkr4|Xkr4 i - q2:CUFF.71|CUFF.71.1|100|22.635827|0.000000|54.647722|1.285714|- +TCONS_00000087 XLOC_000063 Xkr4|Xkr4 i - q2:CUFF.73|CUFF.73.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000088 XLOC_000064 Xkr4|Xkr4 i - q2:CUFF.75|CUFF.75.1|100|52.816931|0.000000|113.804669|3.000000|- +TCONS_00000089 XLOC_000066 Xkr4|Xkr4 i - q2:CUFF.77|CUFF.77.1|100|17.605644|0.000000|52.816931|1.000000|- +TCONS_00000090 XLOC_000067 Xkr4|Xkr4 i - q2:CUFF.79|CUFF.79.1|100|13.390208|0.000000|32.326821|0.760563|- +TCONS_00000091 XLOC_000068 Xkr4|Xkr4 i - q2:CUFF.81|CUFF.81.1|100|11.211141|1.183592|21.238690|0.636792|- +TCONS_00000092 XLOC_000069 Xkr4|Xkr4 i - q2:CUFF.83|CUFF.83.1|100|21.126772|0.000000|51.004540|1.200000|- +TCONS_00000093 XLOC_000070 Xkr4|Xkr4 i - q2:CUFF.85|CUFF.85.1|100|19.014095|0.000000|38.028190|1.080000|- +TCONS_00000094 XLOC_000072 Xkr4|Xkr4 i - q2:CUFF.87|CUFF.87.1|100|24.170460|0.000000|52.080103|1.372881|- +TCONS_00000095 XLOC_000074 Xkr4|Xkr4 i - q2:CUFF.89|CUFF.89.1|100|29.709524|0.000000|64.015126|1.687500|- +TCONS_00000096 XLOC_000076 Xkr4|Xkr4 i - q2:CUFF.91|CUFF.91.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000097 XLOC_000078 Xkr4|Xkr4 i - q2:CUFF.93|CUFF.93.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000098 XLOC_000079 Xkr4|Xkr4 i - q2:CUFF.95|CUFF.95.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000099 XLOC_000081 Xkr4|Xkr4 i - q2:CUFF.97|CUFF.97.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000100 XLOC_000082 Xkr4|Xkr4 i - q2:CUFF.99|CUFF.99.1|100|19.602160|0.000000|39.204320|1.113402|- diff -r bde09cbd60865053ffd0ab05138d6fa3e594d399 -r 277403d31907d71e5e77694c0c97c16772f23e27 test-data/cuffcompare_out7.txt --- a/test-data/cuffcompare_out7.txt +++ b/test-data/cuffcompare_out7.txt @@ -1,13 +1,26 @@ -# Cuffcompare v1.0.3 | Command line was: -#cuffcompare -o cc_output -r cuffcompare_in3.gtf -R cuffcompare_in1.gtf cuffcompare_in2.gtf +# Cuffcompare v1.1.0 | Command line was: +#cuffcompare -o cc_output -r /Users/jeremy/projects/galaxy-central/database/files/010/dataset_10115.dat -R ./input1 ./input2 # -#= Summary for dataset: cuffcompare_in1.gtf : +#= Summary for dataset: ./input1 : # Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) # (0 multi-transcript loci, ~1.0 transcripts per locus) -# Reference mRNAs : 0 in 0 loci (0 multi-exon) +# Reference mRNAs : 1 in 1 loci (1 multi-exon) +# Corresponding super-loci: 1 +#--------------------| Sn | Sp | fSn | fSp + Base level: 2.2 2.3 - - + Exon level: 0.0 0.0 0.0 0.0 + Intron level: 0.0 nan 0.0 nan +Intron chain level: 0.0 nan 0.0 nan + Transcript level: 0.0 0.0 0.0 0.0 + Locus level: 0.0 0.0 0.0 0.0 + Missed exons: 2/3 ( 66.7%) + Wrong exons: 49/50 ( 98.0%) + Missed introns: 2/2 (100.0%) + Missed loci: 0/1 ( 0.0%) + Wrong loci: 49/50 ( 98.0%) -#= Summary for dataset: cuffcompare_in2.gtf : +#= Summary for dataset: ./input2 : # Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) # (0 multi-transcript loci, ~1.0 transcripts per locus) # Reference mRNAs : 0 in 0 loci (0 multi-exon) Repository URL: 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