# HG changeset patch # User iuc # Date 1579469432 18000 # Node ID 6c398f64ad6aa6749bc7362d147c86a4d1815c2f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2" diff -r 000000000000 -r 6c398f64ad6a all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all_fasta.loc.sample Sun Jan 19 16:30:32 2020 -0500 @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +# +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# diff -r 000000000000 -r 6c398f64ad6a chira_map.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chira_map.xml Sun Jan 19 16:30:32 2020 -0500 @@ -0,0 +1,148 @@ + + map reads to trascriptome + + macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + alignment['aligner'] == "bwa" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. class:: infomark + +**What it does** + +This tool handles the mapping of the reads to reference transcriptome. User can choose between the bwa-mem and CLAN alignment tools. + +**Inputs** + +* A fasta file containing reads +* A reference fasta file containing transcript sequences +* An optional second reference fasta file, incase if you split your reference into two + +**Output** + +* BED file containing the alignments +* Optional unmapped FASTA file + + + + diff -r 000000000000 -r 6c398f64ad6a macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sun Jan 19 16:30:32 2020 -0500 @@ -0,0 +1,15 @@ + + @TOOL_VERSION@+galaxy + 1.0.2 + + + chira + + + + + + + + + diff -r 000000000000 -r 6c398f64ad6a test-data/alignments.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignments.bed Sun Jan 19 16:30:32 2020 -0500 @@ -0,0 +1,337 @@ +mmu-miR-124-3p 0 20 3|2,mmu-miR-124-3p,0,20,+,5S20M30S 0 + +ENSMUST00000182884 6023 6051 28|3,ENSMUST00000182884,6023,6051,+,27S28M 0 + +ENSMUST00000182010 428 477 36|10,ENSMUST00000182010,428,477,+,5S49M1S 0 + +ENSMUST00000113560 1969 1992 38|2,ENSMUST00000113560,1969,1992,+,32S23M 0 + +mmu-miR-9-5p 0 23 11|1,mmu-miR-9-5p,0,23,+,5S23M27S 0 + +mmu-miR-9-5p 0 23 38|2,mmu-miR-9-5p,0,23,+,5S23M27S 0 + +ENSMUST00000138581 1621 1644 38|2,ENSMUST00000138581,1621,1644,+,32S23M 0 + +ENSMUST00000182010 419 468 34|1,ENSMUST00000182010,419,468,+,5S49M1S 0 + +ENSMUST00000047061 2204 2232 28|3,ENSMUST00000047061,2204,2232,+,27S28M 0 + +ENSMUST00000100207 1580 1603 38|2,ENSMUST00000100207,1580,1603,+,32S23M 0 + +ENSMUST00000172109 1499 1514 11|1,ENSMUST00000172109,1499,1514,+,35S15M5S 0 + +ENSMUST00000182795 2429 2457 28|3,ENSMUST00000182795,2429,2457,+,27S28M 0 + +ENSMUST00000075326 1661 1684 38|2,ENSMUST00000075326,1661,1684,+,32S23M 0 + +ENSMUST00000106215 953 1003 21|3,ENSMUST00000106215,953,1003,+,5S50M 0 + +ENSMUST00000182439 2218 2246 28|3,ENSMUST00000182439,2218,2246,+,27S28M 0 + +ENSMUST00000185502 4240 4290 7|1,ENSMUST00000185502,4240,4290,+,5S50M 0 + +ENSMUST00000166060 435 467 19|2,ENSMUST00000166060,435,467,+,26S12M3D17M 0 + +ENSMUST00000107857 399 431 19|2,ENSMUST00000107857,399,431,+,26S12M3D17M 0 + +ENSMUST00000155835 2617 2667 4|2,ENSMUST00000155835,2617,2667,+,5S50M 0 + +ENSMUST00000071555 1077 1127 21|3,ENSMUST00000071555,1077,1127,+,5S50M 0 + +ENSMUST00000181221 1499 1514 11|1,ENSMUST00000181221,1499,1514,+,35S15M5S 0 + +ENSMUST00000182010 424 474 35|9,ENSMUST00000182010,424,474,+,5S50M 0 + +ENSMUST00000100208 1748 1771 38|2,ENSMUST00000100208,1748,1771,+,32S23M 0 + +ENSMUST00000113562 1759 1782 38|2,ENSMUST00000113562,1759,1782,+,32S23M 0 + +ENSMUST00000128302 226 257 6|4,ENSMUST00000128302,226,257,+,24S31M 0 + +ENSMUST00000148758 777 805 27|1,ENSMUST00000148758,777,805,+,27S28M 0 + +ENSMUST00000111596 608 626 19|2,ENSMUST00000111596,608,626,+,30S18M7S 0 + +ENSMUST00000106992 3071 3121 16|3,ENSMUST00000106992,3071,3121,+,5S50M 0 + +mmu-miR-9-5p 0 23 32|1,mmu-miR-9-5p,0,23,+,5S23M27S 0 + +ENSMUST00000182972 3233 3261 28|3,ENSMUST00000182972,3233,3261,+,27S28M 0 + +ENSMUST00000064989 2466 2516 29|1,ENSMUST00000064989,2466,2516,+,5S50M 0 + +ENSMUST00000182029 3343 3371 28|3,ENSMUST00000182029,3343,3371,+,27S28M 0 + +ENSMUST00000182010 426 476 15|2,ENSMUST00000182010,426,476,+,5S50M 0 + +ENSMUST00000187980 1254 1305 24|1,ENSMUST00000187980,1254,1305,+,4S51M 0 + +ENSMUST00000182692 3374 3402 28|3,ENSMUST00000182692,3374,3402,+,27S28M 0 + +ENSMUST00000167541 285 336 1|3,ENSMUST00000167541,285,336,+,4S51M 0 + +ENSMUST00000113564 1723 1746 38|2,ENSMUST00000113564,1723,1746,+,32S23M 0 + +ENSMUST00000128500 1065 1088 38|2,ENSMUST00000128500,1065,1088,+,32S23M 0 + +ENSMUST00000045218 5944 5972 3|2,ENSMUST00000045218,5944,5972,+,27S28M 0 + +ENSMUST00000111134 233 264 6|4,ENSMUST00000111134,233,264,+,24S31M 0 + +ENSMUST00000182010 9 59 8|4,ENSMUST00000182010,9,59,+,5S50M 0 + +ENSMUST00000167930 463 495 19|2,ENSMUST00000167930,463,495,+,26S12M3D17M 0 + +ENSMUST00000075012 856 906 14|1,ENSMUST00000075012,856,906,+,5S50M 0 + +ENSMUST00000041591 326 377 1|3,ENSMUST00000041591,326,377,+,4S51M 0 + +ENSMUST00000106746 905 955 14|1,ENSMUST00000106746,905,955,+,5S50M 0 + +ENSMUST00000182437 2388 2416 28|3,ENSMUST00000182437,2388,2416,+,27S28M 0 + +ENSMUST00000171545 470 521 1|3,ENSMUST00000171545,470,521,+,4S51M 0 + +ENSMUST00000181455 1765 1780 11|1,ENSMUST00000181455,1765,1780,+,35S15M5S 0 + +ENSMUST00000032571 4128 4178 20|1,ENSMUST00000032571,4128,4178,+,5S15M1D34M 0 + +ENSMUST00000092432 5519 5547 28|3,ENSMUST00000092432,5519,5547,+,27S28M 0 + +ENSMUST00000182010 0 47 31|10,ENSMUST00000182010,0,47,+,8S47M 0 + +mmu-miR-124-3p 0 20 19|2,mmu-miR-124-3p,0,20,+,6S20M29S 0 + +ENSMUST00000182010 0 44 5|12,ENSMUST00000182010,0,44,+,9S44M2S 0 + +ENSMUST00000062147 344 394 21|3,ENSMUST00000062147,344,394,+,5S50M 0 + +ENSMUST00000166972 469 501 19|2,ENSMUST00000166972,469,501,+,26S12M3D17M 0 + +ENSMUST00000085399 463 495 19|2,ENSMUST00000085399,463,495,+,26S12M3D17M 0 + +ENSMUST00000027103 804 832 27|1,ENSMUST00000027103,804,832,+,27S28M 0 + +mmu-miR-124-3p 0 20 27|1,mmu-miR-124-3p,0,20,+,6S20M29S 0 + +ENSMUST00000183169 5204 5232 28|3,ENSMUST00000183169,5204,5232,+,27S28M 0 + +ENSMUST00000182010 0 46 13|8,ENSMUST00000182010,0,46,+,9S46M 0 + +mmu-miR-9-5p 0 22 28|3,mmu-miR-9-5p,0,22,+,5S22M28S 0 + +ENSMUST00000130489 1065 1115 18|2,ENSMUST00000130489,1065,1115,+,5S50M 0 + +ENSMUST00000182010 0 46 17|4,ENSMUST00000182010,0,46,+,9S46M 0 + +ENSMUST00000118936 1387 1402 11|1,ENSMUST00000118936,1387,1402,+,33S15M7S 0 + +ENSMUST00000183148 5792 5820 28|3,ENSMUST00000183148,5792,5820,+,27S28M 0 + +ENSMUST00000092434 5573 5601 28|3,ENSMUST00000092434,5573,5601,+,27S28M 0 + +ENSMUST00000182010 9 34 37|2,ENSMUST00000182010,9,34,+,30S25M 0 + +ENSMUST00000183023 1361 1389 28|3,ENSMUST00000183023,1361,1389,+,27S28M 0 + +ENSMUST00000100301 1765 1780 11|1,ENSMUST00000100301,1765,1780,+,35S15M5S 0 + +ENSMUST00000113559 1621 1644 38|2,ENSMUST00000113559,1621,1644,+,32S23M 0 + +ENSMUST00000173516 342 393 1|3,ENSMUST00000173516,342,393,+,4S51M 0 + +ENSMUST00000113555 1676 1699 38|2,ENSMUST00000113555,1676,1699,+,32S23M 0 + +ENSMUST00000182010 408 458 22|1,ENSMUST00000182010,408,458,+,5S50M 0 + +ENSMUST00000128621 775 803 27|1,ENSMUST00000128621,775,803,+,27S28M 0 + +ENSMUST00000182207 1067 1095 28|3,ENSMUST00000182207,1067,1095,+,27S28M 0 + +ENSMUST00000182010 9 59 33|2,ENSMUST00000182010,9,59,+,5S50M 0 + +ENSMUST00000100305 917 967 14|1,ENSMUST00000100305,917,967,+,5S50M 0 + +ENSMUST00000107586 2666 2716 4|2,ENSMUST00000107586,2666,2716,+,5S50M 0 + +mmu-miR-124-3p 0 20 25|1,mmu-miR-124-3p,0,20,+,5S20M30S 0 + +ENSMUST00000181974 2606 2634 28|3,ENSMUST00000181974,2606,2634,+,27S28M 0 + +ENSMUST00000039796 1502 1517 11|1,ENSMUST00000039796,1502,1517,+,33S15M7S 0 + +ENSMUST00000068237 606 624 19|2,ENSMUST00000068237,606,624,+,30S18M7S 0 + +ENSMUST00000149559 180 198 37|2,ENSMUST00000149559,180,198,+,20S18M17S 0 + +ENSMUST00000092433 3616 3644 28|3,ENSMUST00000092433,3616,3644,+,27S28M 0 + +ENSMUST00000182010 430 477 30|4,ENSMUST00000182010,430,477,+,5S47M3S 0 + +ENSMUST00000044730 2734 2784 4|2,ENSMUST00000044730,2734,2784,+,5S50M 0 + +ENSMUST00000092431 5510 5538 28|3,ENSMUST00000092431,5510,5538,+,27S28M 0 + +ENSMUST00000139950 1170 1220 18|2,ENSMUST00000139950,1170,1220,+,5S50M 0 + +ENSMUST00000182010 409 459 12|3,ENSMUST00000182010,409,459,+,5S50M 0 + +ENSMUST00000172835 4128 4178 20|1,ENSMUST00000172835,4128,4178,+,5S15M1D34M 0 + +ENSMUST00000182155 5247 5275 28|3,ENSMUST00000182155,5247,5275,+,27S28M 0 + +ENSMUST00000028829 496 511 11|1,ENSMUST00000028829,496,511,+,29S15M11S 0 + +ENSMUST00000182269 2748 2776 28|3,ENSMUST00000182269,2748,2776,+,27S28M 0 + +ENSMUST00000094844 1360 1410 18|2,ENSMUST00000094844,1360,1410,+,5S50M 0 + +ENSMUST00000183074 3336 3364 28|3,ENSMUST00000183074,3336,3364,+,27S28M 0 + +ENSMUST00000182992 7998 8026 28|3,ENSMUST00000182992,7998,8026,+,27S28M 0 + +ENSMUST00000054167 5456 5484 28|3,ENSMUST00000054167,5456,5484,+,27S28M 0 + +ENSMUST00000073879 1565 1588 38|2,ENSMUST00000073879,1565,1588,+,32S23M 0 + +ENSMUST00000183261 3336 3364 28|3,ENSMUST00000183261,3336,3364,+,27S28M 0 + +ENSMUST00000110901 232 247 11|1,ENSMUST00000110901,232,247,+,29S15M11S 0 + +mmu-miR-124-3p 0 20 6|4,mmu-miR-124-3p,0,20,+,5S20M30S 0 + +mmu-miR-124-3p 8 19 14|1,mmu-miR-124-3p,8,19,+,2S11M42S 0 + +mmu-miR-127-3p 12 22 29|1,mmu-miR-127-3p,12,22,+,17S10M28S 0 + +mmu-miR-188-3p 1 11 10|2,mmu-miR-188-3p,1,11,+,22S10M23S 0 + +mmu-miR-344d-1-5p 8 17 9|1,mmu-miR-344d-1-5p,8,17,+,3S9M43S 0 + +mmu-miR-344c-5p 8 17 9|1,mmu-miR-344c-5p,8,17,+,3S9M43S 0 + +mmu-miR-344d-2-5p 8 17 9|1,mmu-miR-344d-2-5p,8,17,+,3S9M43S 0 + +mmu-miR-196a-2-3p 6 16 25|1,mmu-miR-196a-2-3p,6,16,+,29S10M16S 0 + +mmu-miR-208a-5p 0 10 26|1,mmu-miR-208a-5p,0,10,+,10M45S 0 + +mmu-miR-22-3p 8 18 12|3,mmu-miR-22-3p,8,18,+,10M45S 0 + +mmu-miR-33-3p 1 11 29|1,mmu-miR-33-3p,1,11,+,1S10M44S 0 + +mmu-miR-181c-5p 8 18 14|1,mmu-miR-181c-5p,8,18,+,44S10M1S 0 + +mmu-miR-3109-3p 3 13 2|1,mmu-miR-3109-3p,3,13,+,41S10M3S 0 + +mmu-miR-6407 7 17 2|1,mmu-miR-6407,7,17,+,33S10M11S 0 + +mmu-miR-3076-5p 13 22 18|2,mmu-miR-3076-5p,13,22,+,9M46S 0 + +mmu-miR-106a-3p 4 13 18|2,mmu-miR-106a-3p,4,13,+,9M46S 0 + +mmu-miR-871-5p 10 19 18|2,mmu-miR-871-5p,10,19,+,1S9M45S 0 + +mmu-miR-25-3p 0 10 32|1,mmu-miR-25-3p,0,10,+,44S10M1S 0 + +mmu-miR-497a-3p 3 13 7|1,mmu-miR-497a-3p,3,13,+,42S10M3S 0 + +mmu-miR-190b-5p 6 17 18|2,mmu-miR-190b-5p,6,17,+,32S11M12S 0 + +mmu-miR-3098-3p 3 14 16|3,mmu-miR-3098-3p,3,14,+,39S11M5S 0 + +mmu-miR-6900-5p 0 10 18|2,mmu-miR-6900-5p,0,10,+,45S10M 0 + +mmu-miR-3104-3p 10 20 21|3,mmu-miR-3104-3p,10,20,+,40S10M5S 0 + +mmu-miR-7651-3p 6 16 24|1,mmu-miR-7651-3p,6,16,+,6S10M39S 0 + +mmu-miR-742-3p 7 16 16|3,mmu-miR-742-3p,7,16,+,35S9M11S 0 + +mmu-miR-6936-3p 2 11 20|1,mmu-miR-6936-3p,2,11,+,31S9M14S 0 + +mmu-miR-6936-3p 2 11 20|1,mmu-miR-6936-3p,2,11,+,33S9M12S 0 + +mmu-miR-6992-5p 0 10 6|4,mmu-miR-6992-5p,0,10,+,21S10M24S 0 + +mmu-miR-7016-3p 10 20 23|1,mmu-miR-7016-3p,10,20,+,34S10M11S 0 + +mmu-miR-7019-5p 6 16 4|2,mmu-miR-7019-5p,6,16,+,30S10M15S 0 + +mmu-miR-7046-5p 13 22 2|1,mmu-miR-7046-5p,13,22,+,24S9M21S 0 + +mmu-miR-7046-5p 8 19 1|3,mmu-miR-7046-5p,8,19,+,11S11M33S 0 + +mmu-miR-7046-5p 9 22 9|1,mmu-miR-7046-5p,9,22,+,12S13M30S 0 + +mmu-miR-7046-5p 9 20 29|1,mmu-miR-7046-5p,9,20,+,10S11M34S 0 + +mmu-miR-7046-5p 10 22 4|2,mmu-miR-7046-5p,10,22,+,7S12M36S 0 + +mmu-miR-7046-5p 12 21 21|3,mmu-miR-7046-5p,12,21,+,9M46S 0 + +mmu-miR-7077-5p 6 16 16|3,mmu-miR-7077-5p,6,16,+,23S10M22S 0 + +mmu-miR-7092-3p 5 17 24|1,mmu-miR-7092-3p,5,17,+,19S12M24S 0 + +mmu-miR-7092-3p 5 17 24|1,mmu-miR-7092-3p,5,17,+,43S12M 0 + +mmu-miR-7092-3p 5 17 24|1,mmu-miR-7092-3p,5,17,+,38S12M5S 0 + +mmu-miR-7222-5p 6 16 18|2,mmu-miR-7222-5p,6,16,+,15S10M30S 0 + +mmu-miR-7651-3p 3 14 7|1,mmu-miR-7651-3p,3,14,+,25S11M19S 0 + +mmu-miR-7651-3p 8 18 16|3,mmu-miR-7651-3p,8,18,+,10S10M35S 0 + +mmu-miR-7116-3p 0 10 16|3,mmu-miR-7116-3p,0,10,+,11S10M34S 0 + +mmu-miR-7651-3p 9 19 10|2,mmu-miR-7651-3p,9,19,+,16S10M29S 0 + +mmu-miR-7651-3p 10 20 23|1,mmu-miR-7651-3p,10,20,+,10S10M35S 0 + +mmu-miR-7003-3p 7 17 23|1,mmu-miR-7003-3p,7,17,+,12S10M33S 0 + +mmu-miR-7651-3p 10 20 26|1,mmu-miR-7651-3p,10,20,+,39S10M6S 0 + +mmu-miR-7677-5p 14 25 37|2,mmu-miR-7677-5p,14,25,+,38S11M6S 0 + +mmu-miR-7677-5p 14 25 5|12,mmu-miR-7677-5p,14,25,+,26S11M18S 0 + +mmu-miR-7677-5p 14 25 13|8,mmu-miR-7677-5p,14,25,+,26S11M18S 0 + +mmu-miR-7677-5p 14 25 17|4,mmu-miR-7677-5p,14,25,+,26S11M18S 0 + +mmu-miR-7677-5p 14 25 31|10,mmu-miR-7677-5p,14,25,+,25S11M19S 0 + +mmu-miR-7677-5p 14 25 8|4,mmu-miR-7677-5p,14,25,+,13S11M31S 0 + +mmu-miR-7677-5p 14 25 33|2,mmu-miR-7677-5p,14,25,+,13S11M31S 0 + +mmu-miR-1931 7 16 37|2,mmu-miR-1931,7,16,+,28S9M18S 0 + +mmu-miR-106a-3p 6 15 37|2,mmu-miR-106a-3p,6,15,+,33S9M13S 0 + +mmu-miR-1943-3p 2 11 37|2,mmu-miR-1943-3p,2,11,+,32S9M14S 0 + +mmu-miR-1943-3p 2 11 5|12,mmu-miR-1943-3p,2,11,+,20S9M26S 0 + +mmu-miR-106a-3p 6 15 5|12,mmu-miR-106a-3p,6,15,+,21S9M25S 0 + +mmu-miR-1943-3p 2 11 13|8,mmu-miR-1943-3p,2,11,+,20S9M26S 0 + +mmu-miR-106a-3p 6 15 13|8,mmu-miR-106a-3p,6,15,+,21S9M25S 0 + +mmu-miR-1943-3p 2 11 17|4,mmu-miR-1943-3p,2,11,+,20S9M26S 0 + +mmu-miR-106a-3p 6 15 17|4,mmu-miR-106a-3p,6,15,+,21S9M25S 0 + +mmu-miR-106a-3p 6 15 31|10,mmu-miR-106a-3p,6,15,+,20S9M26S 0 + +mmu-miR-1943-3p 2 11 31|10,mmu-miR-1943-3p,2,11,+,19S9M27S 0 + +mmu-miR-106a-3p 6 15 8|4,mmu-miR-106a-3p,6,15,+,8S9M38S 0 + +mmu-miR-1943-3p 2 11 8|4,mmu-miR-1943-3p,2,11,+,7S9M39S 0 + +mmu-miR-106a-3p 6 15 33|2,mmu-miR-106a-3p,6,15,+,8S9M38S 0 + +mmu-miR-1943-3p 2 11 33|2,mmu-miR-1943-3p,2,11,+,7S9M39S 0 + +mmu-miR-335-3p 1 10 22|1,mmu-miR-335-3p,1,10,+,13S9M33S 0 + +mmu-miR-335-3p 1 10 12|3,mmu-miR-335-3p,1,10,+,12S9M34S 0 + +mmu-miR-708-5p 12 22 20|1,mmu-miR-708-5p,12,22,+,7S10M37S 0 + +mmu-miR-9-5p 8 18 20|1,mmu-miR-9-5p,8,18,+,6S10M38S 0 + +ENSMUST00000147700 79 92 26|1,ENSMUST00000147700,79,92,+,13M42S 0 + +ENSMUST00000114036 1867 1880 26|1,ENSMUST00000114036,1867,1880,+,13M42S 0 + +ENSMUST00000119368 1868 1881 26|1,ENSMUST00000119368,1868,1881,+,13M42S 0 + +ENSMUST00000117633 2241 2254 26|1,ENSMUST00000117633,2241,2254,+,13M42S 0 + +ENSMUST00000063481 941 954 26|1,ENSMUST00000063481,941,954,+,13M42S 0 + +ENSMUST00000114037 1868 1881 26|1,ENSMUST00000114037,1868,1881,+,13M42S 0 + +ENSMUST00000030643 328 341 26|1,ENSMUST00000030643,328,341,+,13M42S 0 + +ENSMUST00000147482 15 28 26|1,ENSMUST00000147482,15,28,+,13M42S 0 + +ENSMUST00000190294 194 207 26|1,ENSMUST00000190294,194,207,+,1S13M41S 0 + +ENSMUST00000145732 41 54 18|2,ENSMUST00000145732,41,54,+,1S13M41S 0 + +ENSMUST00000112588 5877 5890 18|2,ENSMUST00000112588,5877,5890,+,13M42S 0 + +ENSMUST00000138549 606 621 32|1,ENSMUST00000138549,606,621,+,36S15M4S 0 + +ENSMUST00000135330 1390 1405 32|1,ENSMUST00000135330,1390,1405,+,38S15M2S 0 + +ENSMUST00000049453 998 1013 32|1,ENSMUST00000049453,998,1013,+,39S15M1S 0 + +ENSMUST00000069557 6226 6240 9|1,ENSMUST00000069557,6226,6240,+,4S14M37S 0 + +ENSMUST00000030212 2661 2674 32|1,ENSMUST00000030212,2661,2674,+,12S13M30S 0 + +ENSMUST00000160533 69 82 34|1,ENSMUST00000160533,69,82,+,42S13M 0 + +ENSMUST00000041226 629 642 34|1,ENSMUST00000041226,629,642,+,42S13M 0 + +ENSMUST00000167262 4234 4245 35|9,ENSMUST00000167262,4234,4245,+,44S11M 0 + +ENSMUST00000059279 10635 10646 35|9,ENSMUST00000059279,10635,10646,+,44S11M 0 + +ENSMUST00000026084 264 275 35|9,ENSMUST00000026084,264,275,+,44S11M 0 + +ENSMUST00000094844 1366 1410 18|2,ENSMUST00000094844,1366,1410,+,11S44M 0 + +ENSMUST00000130489 1071 1115 18|2,ENSMUST00000130489,1071,1115,+,11S44M 0 + +ENSMUST00000139950 1176 1220 18|2,ENSMUST00000139950,1176,1220,+,11S44M 0 + +ENSMUST00000163279 1561 1575 9|1,ENSMUST00000163279,1561,1575,+,40S14M1S 0 + +ENSMUST00000133696 4650 4667 6|4,ENSMUST00000133696,4650,4667,+,15S17M23S 0 + +ENSMUST00000025897 4205 4222 6|4,ENSMUST00000025897,4205,4222,+,15S17M23S 0 + +ENSMUST00000155655 2001 2018 6|4,ENSMUST00000155655,2001,2018,+,15S17M23S 0 + +ENSMUST00000099265 1630 1645 10|2,ENSMUST00000099265,1630,1645,+,10S15M30S 0 + +ENSMUST00000026084 264 277 15|2,ENSMUST00000026084,264,277,+,42S13M 0 + +ENSMUST00000026084 264 278 36|10,ENSMUST00000026084,264,278,+,40S14M1S 0 + +ENSMUST00000026084 264 278 30|4,ENSMUST00000026084,264,278,+,38S14M3S 0 + +ENSMUST00000036618 6627 6641 25|1,ENSMUST00000036618,6627,6641,+,16S14M25S 0 + +ENSMUST00000160720 1759 1773 25|1,ENSMUST00000160720,1759,1773,+,16S14M25S 0 + +ENSMUST00000162169 734 748 25|1,ENSMUST00000162169,734,748,+,16S14M25S 0 + +ENSMUST00000161129 1633 1647 25|1,ENSMUST00000161129,1633,1647,+,16S14M25S 0 + +ENSMUST00000195700 463 477 2|1,ENSMUST00000195700,463,477,+,1S14M39S 0 + +ENSMUST00000166678 2882 2896 2|1,ENSMUST00000166678,2882,2896,+,5S14M35S 0 + +ENSMUST00000176204 2884 2898 2|1,ENSMUST00000176204,2884,2898,+,5S14M35S 0 + +ENSMUST00000102654 3943 3957 2|1,ENSMUST00000102654,3943,3957,+,7S14M33S 0 + +ENSMUST00000176250 3988 4002 2|1,ENSMUST00000176250,3988,4002,+,7S14M33S 0 + +ENSMUST00000144534 2090 2104 2|1,ENSMUST00000144534,2090,2104,+,4S14M36S 0 + +ENSMUST00000031680 1723 1737 2|1,ENSMUST00000031680,1723,1737,+,4S14M36S 0 + +ENSMUST00000102655 4078 4092 2|1,ENSMUST00000102655,4078,4092,+,7S14M33S 0 + +ENSMUST00000181694 1051 1065 2|1,ENSMUST00000181694,1051,1065,+,14M40S 0 + +ENSMUST00000115389 1604 1618 2|1,ENSMUST00000115389,1604,1618,+,4S14M36S 0 + +ENSMUST00000187359 1416 1430 2|1,ENSMUST00000187359,1416,1430,+,10S14M30S 0 + +ENSMUST00000176551 1408 1422 2|1,ENSMUST00000176551,1408,1422,+,5S14M35S 0 + +ENSMUST00000180471 583 598 32|1,ENSMUST00000180471,583,598,+,28S15M12S 0 + +ENSMUST00000170280 878 893 26|1,ENSMUST00000170280,878,893,+,10S15M30S 0 + +ENSMUST00000175724 1136 1151 26|1,ENSMUST00000175724,1136,1151,+,10S15M30S 0 + +ENSMUST00000032571 4128 4154 20|1,ENSMUST00000032571,4128,4154,+,5S26M23S 0 + +ENSMUST00000172835 4128 4154 20|1,ENSMUST00000172835,4128,4154,+,5S26M23S 0 + +ENSMUST00000032571 4144 4170 20|1,ENSMUST00000032571,4144,4170,+,20S26M8S 0 + +ENSMUST00000172835 4144 4170 20|1,ENSMUST00000172835,4144,4170,+,20S26M8S 0 + +ENSMUST00000085585 1714 1729 26|1,ENSMUST00000085585,1714,1729,+,18S15M22S 0 + +ENSMUST00000136501 1647 1661 17|4,ENSMUST00000136501,1647,1661,+,14M41S 0 + +ENSMUST00000145323 2397 2411 17|4,ENSMUST00000145323,2397,2411,+,1S14M40S 0 + +ENSMUST00000011934 20143 20158 2|1,ENSMUST00000011934,20143,20158,+,20S15M19S 0 + +ENSMUST00000127723 637 652 2|1,ENSMUST00000127723,637,652,+,14S15M25S 0 + +ENSMUST00000128756 653 668 2|1,ENSMUST00000128756,653,668,+,14S15M25S 0 + +ENSMUST00000111882 39978 39993 2|1,ENSMUST00000111882,39978,39993,+,20S15M19S 0 + +ENSMUST00000099981 45124 45139 2|1,ENSMUST00000099981,45124,45139,+,20S15M19S 0 + +ENSMUST00000072868 1467 1482 2|1,ENSMUST00000072868,1467,1482,+,24S15M15S 0 + +ENSMUST00000121270 659 674 2|1,ENSMUST00000121270,659,674,+,14S15M25S 0 + +ENSMUST00000018610 2341 2356 2|1,ENSMUST00000018610,2341,2356,+,19S15M20S 0 + +ENSMUST00000144248 458 473 2|1,ENSMUST00000144248,458,473,+,14S15M25S 0 + +ENSMUST00000111846 39755 39770 2|1,ENSMUST00000111846,39755,39770,+,20S15M19S 0 + +ENSMUST00000037472 672 687 2|1,ENSMUST00000037472,672,687,+,14S15M25S 0 + +ENSMUST00000073364 2988 3003 37|2,ENSMUST00000073364,2988,3003,+,7S15M33S 0 + +ENSMUST00000125924 2988 3003 37|2,ENSMUST00000125924,2988,3003,+,7S15M33S 0 + +ENSMUST00000021443 766 779 25|1,ENSMUST00000021443,766,779,+,6S13M36S 0 + +ENSMUST00000069259 1162 1175 25|1,ENSMUST00000069259,1162,1175,+,6S13M36S 0 + +ENSMUST00000094391 1254 1267 25|1,ENSMUST00000094391,1254,1267,+,6S13M36S 0 + +ENSMUST00000145226 237 249 37|2,ENSMUST00000145226,237,249,+,12M43S 0 + +ENSMUST00000025052 248 260 37|2,ENSMUST00000025052,248,260,+,12M43S 0 + +ENSMUST00000152982 712 724 37|2,ENSMUST00000152982,712,724,+,12M43S 0 + +ENSMUST00000114881 276 288 37|2,ENSMUST00000114881,276,288,+,12M43S 0 + +ENSMUST00000155071 284 296 37|2,ENSMUST00000155071,284,296,+,12M43S 0 + +ENSMUST00000114882 284 296 37|2,ENSMUST00000114882,284,296,+,12M43S 0 + +ENSMUST00000178774 211 223 37|2,ENSMUST00000178774,211,223,+,12M43S 0 + +ENSMUST00000150763 72 84 37|2,ENSMUST00000150763,72,84,+,12M43S 0 + +ENSMUST00000074353 211 223 37|2,ENSMUST00000074353,211,223,+,12M43S 0 + +ENSMUST00000153125 886 901 32|1,ENSMUST00000153125,886,901,+,31S15M9S 0 + +ENSMUST00000146006 6703 6718 10|2,ENSMUST00000146006,6703,6718,+,24S15M16S 0 + +ENSMUST00000105902 8013 8028 10|2,ENSMUST00000105902,8013,8028,+,24S15M16S 0 + +ENSMUST00000105900 7194 7209 10|2,ENSMUST00000105900,7194,7209,+,24S15M16S 0 + +ENSMUST00000122432 681 696 2|1,ENSMUST00000122432,681,696,+,36S15M3S 0 + +ENSMUST00000002336 841 856 2|1,ENSMUST00000002336,841,856,+,36S15M3S 0 + +ENSMUST00000018966 430 445 9|1,ENSMUST00000018966,430,445,+,29S15M11S 0 + +ENSMUST00000105818 2592 2606 25|1,ENSMUST00000105818,2592,2606,+,30S14M11S 0 + +ENSMUST00000017783 1483 1496 9|1,ENSMUST00000017783,1483,1496,+,32S13M10S 0 + +ENSMUST00000049393 5443 5458 10|2,ENSMUST00000049393,5443,5458,+,16S15M24S 0 + +ENSMUST00000165055 615 630 10|2,ENSMUST00000165055,615,630,+,12S15M28S 0 + +ENSMUST00000140487 2875 2890 10|2,ENSMUST00000140487,2875,2890,+,23S15M17S 0 + +ENSMUST00000168430 291 306 10|2,ENSMUST00000168430,291,306,+,12S15M28S 0 + +ENSMUST00000089011 2222 2235 25|1,ENSMUST00000089011,2222,2235,+,42S13M 0 + +ENSMUST00000003981 1574 1590 23|1,ENSMUST00000003981,1574,1590,+,32S16M7S 0 + +ENSMUST00000070720 1638 1649 25|1,ENSMUST00000070720,1638,1649,+,11M44S 0 + +ENSMUST00000162505 10763 10774 25|1,ENSMUST00000162505,10763,10774,+,11M44S 0 + +ENSMUST00000130911 1259 1272 23|1,ENSMUST00000130911,1259,1272,+,13M42S 0 + +ENSMUST00000143749 3013 3026 23|1,ENSMUST00000143749,3013,3026,+,13M42S 0 + +ENSMUST00000126936 37 52 32|1,ENSMUST00000126936,37,52,+,7S15M33S 0 + +ENSMUST00000143959 937 953 9|1,ENSMUST00000143959,937,953,+,12S16M27S 0 + +ENSMUST00000085116 2528 2542 2|1,ENSMUST00000085116,2528,2542,+,38S14M2S 0 + +ENSMUST00000111272 2082 2096 2|1,ENSMUST00000111272,2082,2096,+,39S14M1S 0 + +ENSMUST00000155324 1114 1128 2|1,ENSMUST00000155324,1114,1128,+,39S14M1S 0 + +ENSMUST00000097442 476 490 2|1,ENSMUST00000097442,476,490,+,40S14M 0 + +ENSMUST00000027898 43 57 2|1,ENSMUST00000027898,43,57,+,40S14M 0 + +ENSMUST00000170188 2393 2407 2|1,ENSMUST00000170188,2393,2407,+,38S14M2S 0 + +ENSMUST00000128275 79 93 2|1,ENSMUST00000128275,79,93,+,40S14M 0 + +ENSMUST00000194127 469 483 2|1,ENSMUST00000194127,469,483,+,40S14M 0 + +ENSMUST00000111813 56 73 10|2,ENSMUST00000111813,56,73,+,38S17M 0 + +ENSMUST00000151752 1887 1902 26|1,ENSMUST00000151752,1887,1902,+,39S15M1S 0 + +ENSMUST00000137408 2183 2198 26|1,ENSMUST00000137408,2183,2198,+,39S15M1S 0 + +ENSMUST00000189036 14 25 20|1,ENSMUST00000189036,14,25,+,41S11M2S 0 + +ENSMUST00000000254 463 474 20|1,ENSMUST00000000254,463,474,+,41S11M2S 0 + +ENSMUST00000138762 6784 6795 20|1,ENSMUST00000138762,6784,6795,+,43S11M 0 + +ENSMUST00000129785 2240 2251 20|1,ENSMUST00000129785,2240,2251,+,42S11M1S 0 + +ENSMUST00000166429 2767 2778 20|1,ENSMUST00000166429,2767,2778,+,41S11M2S 0 + +ENSMUST00000136610 265 276 20|1,ENSMUST00000136610,265,276,+,42S11M1S 0 + +ENSMUST00000131422 2324 2335 20|1,ENSMUST00000131422,2324,2335,+,42S11M1S 0 + +ENSMUST00000142388 401 412 20|1,ENSMUST00000142388,401,412,+,41S11M2S 0 + +ENSMUST00000075789 241 252 20|1,ENSMUST00000075789,241,252,+,41S11M2S 0 + +ENSMUST00000053969 2571 2582 20|1,ENSMUST00000053969,2571,2582,+,41S11M2S 0 + +ENSMUST00000030826 1172 1183 20|1,ENSMUST00000030826,1172,1183,+,42S11M1S 0 + +ENSMUST00000113169 7470 7481 20|1,ENSMUST00000113169,7470,7481,+,43S11M 0 + +ENSMUST00000149694 433 444 20|1,ENSMUST00000149694,433,444,+,43S11M 0 + +ENSMUST00000081569 891 902 20|1,ENSMUST00000081569,891,902,+,43S11M 0 + +ENSMUST00000073639 2840 2851 20|1,ENSMUST00000073639,2840,2851,+,43S11M 0 + +ENSMUST00000127216 2946 2957 20|1,ENSMUST00000127216,2946,2957,+,42S11M1S 0 + +ENSMUST00000087085 1296 1307 20|1,ENSMUST00000087085,1296,1307,+,43S11M 0 + +ENSMUST00000088373 8054 8065 20|1,ENSMUST00000088373,8054,8065,+,43S11M 0 + +ENSMUST00000129865 905 916 20|1,ENSMUST00000129865,905,916,+,43S11M 0 + +ENSMUST00000147228 572 585 13|8,ENSMUST00000147228,572,585,+,13M42S 0 + +ENSMUST00000106220 383 396 13|8,ENSMUST00000106220,383,396,+,13M42S 0 + +ENSMUST00000006311 2407 2420 13|8,ENSMUST00000006311,2407,2420,+,13M42S 0 + +ENSMUST00000099628 995 1008 13|8,ENSMUST00000099628,995,1008,+,13M42S 0 + +ENSMUST00000114132 3670 3682 23|1,ENSMUST00000114132,3670,3682,+,43S12M 0 + +ENSMUST00000028761 3500 3512 23|1,ENSMUST00000028761,3500,3512,+,43S12M 0 + +ENSMUST00000029025 3154 3166 23|1,ENSMUST00000029025,3154,3166,+,43S12M 0 + +ENSMUST00000055032 3310 3323 31|10,ENSMUST00000055032,3310,3323,+,13M42S 0 + +ENSMUST00000168713 538 551 31|10,ENSMUST00000168713,538,551,+,1S13M41S 0 + +ENSMUST00000187296 2127 2140 31|10,ENSMUST00000187296,2127,2140,+,13M42S 0 + +ENSMUST00000167448 329 342 31|10,ENSMUST00000167448,329,342,+,1S13M41S 0 + +ENSMUST00000043169 442 455 31|10,ENSMUST00000043169,442,455,+,1S13M41S 0 + +ENSMUST00000045562 3691 3703 5|12,ENSMUST00000045562,3691,3703,+,2S12M41S 0 + +ENSMUST00000179869 1671 1683 5|12,ENSMUST00000179869,1671,1683,+,12M43S 0 + +ENSMUST00000182010 408 445 22|1,ENSMUST00000182010,408,445,+,5S37M13S 0 + +ENSMUST00000182010 409 445 12|3,ENSMUST00000182010,409,445,+,5S36M14S 0 + +ENSMUST00000182010 419 445 34|1,ENSMUST00000182010,419,445,+,5S26M24S 0 + +ENSMUST00000182010 424 445 35|9,ENSMUST00000182010,424,445,+,5S21M29S 0 + +ENSMUST00000182010 426 445 15|2,ENSMUST00000182010,426,445,+,5S19M31S 0 + +ENSMUST00000182010 428 445 36|10,ENSMUST00000182010,428,445,+,5S17M33S 0 + +ENSMUST00000182010 430 445 30|4,ENSMUST00000182010,430,445,+,5S15M35S 0 + +ENSMUST00000182010 446 458 22|1,ENSMUST00000182010,446,458,+,43S12M 0 + +ENSMUST00000182010 446 459 12|3,ENSMUST00000182010,446,459,+,42S13M 0 + +ENSMUST00000182010 446 458 34|1,ENSMUST00000182010,446,458,+,32S12M11S 0 + +ENSMUST00000182010 446 468 35|9,ENSMUST00000182010,446,468,+,27S22M6S 0 + +ENSMUST00000182010 446 468 15|2,ENSMUST00000182010,446,468,+,25S22M8S 0 + +ENSMUST00000182010 446 468 36|10,ENSMUST00000182010,446,468,+,23S22M10S 0 + +ENSMUST00000182010 446 468 30|4,ENSMUST00000182010,446,468,+,21S22M12S 0 + +ENSMUST00000064314 967 982 23|1,ENSMUST00000064314,967,982,+,18S15M22S 0 + diff -r 000000000000 -r 6c398f64ad6a test-data/annotation.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotation.gtf Sun Jan 19 16:30:32 2020 -0500 @@ -0,0 +1,58 @@ +14 . miRNA 115044183 115044205 . + . ID=MIMAT0000529;Alias=MIMAT0000529;Name=mmu-miR-20a-5p;Derives_from=MI0000568 +16 . miRNA 93369775 93369796 . + . ID=MIMAT0017240;Alias=MIMAT0017240;Name=mmu-miR-802-3p;Derives_from=MI0004249 +1 . miRNA 36348732 36348753 . - . ID=MIMAT0027696;Alias=MIMAT0027696;Name=mmu-miR-6898-5p;Derives_from=MI0022745 +18 . miRNA 37854605 37854625 . - . ID=MIMAT0027861;Alias=MIMAT0027861;Name=mmu-miR-6979-3p;Derives_from=MI0022827 +11 havana transcript 116338339 116347444 . - . gene_id "ENSMUSG00000052949"; gene_version "10"; transcript_id "ENSMUST00000137264"; transcript_version "1"; gene_name "Rnf157"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rnf157-011"; transcript_source "havana"; transcript_biotype "processed_transcript"; transcript_support_level "3"; +11 havana exon 116347342 116347444 . - . gene_id "ENSMUSG00000052949"; gene_version "10"; transcript_id "ENSMUST00000137264"; transcript_version "1"; exon_number "1"; gene_name "Rnf157"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rnf157-011"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSMUSE00000834936"; exon_version "1"; transcript_support_level "3"; +11 havana exon 116347033 116347098 . - . gene_id "ENSMUSG00000052949"; gene_version "10"; transcript_id "ENSMUST00000137264"; transcript_version "1"; exon_number "2"; gene_name "Rnf157"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rnf157-011"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSMUSE00001212609"; exon_version "1"; transcript_support_level "3"; +11 havana exon 116345907 116345955 . - . gene_id "ENSMUSG00000052949"; gene_version "10"; transcript_id "ENSMUST00000137264"; transcript_version "1"; exon_number "3"; gene_name "Rnf157"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rnf157-011"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSMUSE00001217820"; exon_version "1"; transcript_support_level "3"; +11 havana exon 116340338 116340378 . - . gene_id "ENSMUSG00000052949"; gene_version "10"; transcript_id "ENSMUST00000137264"; transcript_version "1"; exon_number "4"; gene_name "Rnf157"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rnf157-011"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSMUSE00001233021"; exon_version "1"; transcript_support_level "3"; +11 havana exon 116338339 116338830 . - . gene_id "ENSMUSG00000052949"; gene_version "10"; transcript_id "ENSMUST00000137264"; transcript_version "1"; exon_number "5"; gene_name "Rnf157"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rnf157-011"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSMUSE00000796470"; exon_version "1"; transcript_support_level "3"; +2 havana transcript 128237693 128239643 . - . gene_id "ENSMUSG00000086879"; gene_version "1"; transcript_id "ENSMUST00000136025"; transcript_version "1"; gene_name "Gm14012"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "Gm14012-001"; transcript_source "havana"; transcript_biotype "lincRNA"; tag "basic"; transcript_support_level "1"; +2 havana exon 128239424 128239643 . - . gene_id "ENSMUSG00000086879"; gene_version "1"; transcript_id "ENSMUST00000136025"; transcript_version "1"; exon_number "1"; gene_name "Gm14012"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "Gm14012-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSMUSE00000756585"; exon_version "1"; tag "basic"; transcript_support_level "1"; +2 havana exon 128238858 128239058 . - . gene_id "ENSMUSG00000086879"; gene_version "1"; transcript_id "ENSMUST00000136025"; transcript_version "1"; exon_number "2"; gene_name "Gm14012"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "Gm14012-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSMUSE00000805740"; exon_version "1"; tag "basic"; transcript_support_level "1"; +2 havana exon 128238028 128238200 . - . gene_id "ENSMUSG00000086879"; gene_version "1"; transcript_id "ENSMUST00000136025"; transcript_version "1"; exon_number "3"; gene_name "Gm14012"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "Gm14012-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSMUSE00000818254"; exon_version "1"; tag "basic"; transcript_support_level "1"; +2 havana exon 128237693 128237775 . - . gene_id "ENSMUSG00000086879"; gene_version "1"; transcript_id "ENSMUST00000136025"; transcript_version "1"; exon_number "4"; gene_name "Gm14012"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "Gm14012-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSMUSE00000741865"; exon_version "1"; tag "basic"; transcript_support_level "1"; +17 havana transcript 39846958 39848788 . + . gene_id "ENSMUSG00000098178"; gene_version "1"; transcript_id "ENSMUST00000182010"; transcript_version "1"; gene_name "Yam1"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "Yam1-001"; transcript_source "havana"; transcript_biotype "lincRNA"; tag "basic"; transcript_support_level "NA"; +17 havana exon 39846958 39848788 . + . gene_id "ENSMUSG00000098178"; gene_version "1"; transcript_id "ENSMUST00000182010"; transcript_version "1"; exon_number "1"; gene_name "Yam1"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "Yam1-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSMUSE00001231387"; exon_version "1"; tag "basic"; transcript_support_level "NA"; +5 havana transcript 137134924 137142413 . - . gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)"; +5 havana exon 137142259 137142413 . - . gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; exon_number "1"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; exon_id "ENSMUSE00000310616"; exon_version "4"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)"; +5 havana CDS 137142259 137142413 . - 1 gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; exon_number "1"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; protein_id "ENSMUSP00000123755"; protein_version "1"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)"; +5 havana exon 137141137 137141205 . - . gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; exon_number "2"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; exon_id "ENSMUSE00000487002"; exon_version "2"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)"; +5 havana CDS 137141137 137141205 . - 2 gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; exon_number "2"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; protein_id "ENSMUSP00000123755"; protein_version "1"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)"; +5 havana exon 137140691 137140853 . - . gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; exon_number "3"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; exon_id "ENSMUSE00000488051"; exon_version "2"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)"; +5 havana CDS 137140691 137140853 . - 2 gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; exon_number "3"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; protein_id "ENSMUSP00000123755"; protein_version "1"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)"; +5 havana exon 137138188 137138349 . - . gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; exon_number "4"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; exon_id "ENSMUSE00001307390"; exon_version "1"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)"; +5 havana CDS 137138188 137138349 . - 1 gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; exon_number "4"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; protein_id "ENSMUSP00000123755"; protein_version "1"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)"; +5 havana exon 137137925 137138022 . - . gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; exon_number "5"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; exon_id "ENSMUSE00001251017"; exon_version "1"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)"; +5 havana CDS 137137925 137138022 . - 1 gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; exon_number "5"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; protein_id "ENSMUSP00000123755"; protein_version "1"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)"; +5 havana exon 137137057 137137136 . - . gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; exon_number "6"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; exon_id "ENSMUSE00001259522"; exon_version "1"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)"; +5 havana CDS 137137057 137137136 . - 2 gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; exon_number "6"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; protein_id "ENSMUSP00000123755"; protein_version "1"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)"; +5 havana exon 137134924 137135485 . - . gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; exon_number "7"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; exon_id "ENSMUSE00000869736"; exon_version "1"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)"; +5 havana CDS 137135444 137135485 . - 0 gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; exon_number "7"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; protein_id "ENSMUSP00000123755"; protein_version "1"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)"; +5 havana UTR 137134924 137135443 . - . gene_id "ENSMUSG00000037390"; gene_version "11"; transcript_id "ENSMUST00000160533"; transcript_version "3"; gene_name "Muc3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Muc3-001"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "cds_start_NF"; tag "mRNA_start_NF"; transcript_support_level "5 (assigned to previous version 2)"; +17 ensembl_havana transcript 27655588 27711106 . + . gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)"; +17 ensembl_havana exon 27655588 27655759 . + . gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "1"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; exon_id "ENSMUSE00000460067"; exon_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)"; +17 ensembl_havana exon 27701767 27701941 . + . gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "2"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; exon_id "ENSMUSE00000460051"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)"; +17 ensembl_havana CDS 27701888 27701941 . + 0 gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "2"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; protein_id "ENSMUSP00000044168"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)"; +17 ensembl_havana start_codon 27701888 27701890 . + 0 gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "2"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)"; +17 ensembl_havana exon 27702700 27702856 . + . gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "3"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; exon_id "ENSMUSE00000460033"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)"; +17 ensembl_havana CDS 27702700 27702856 . + 0 gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "3"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; protein_id "ENSMUSP00000044168"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)"; +17 ensembl_havana exon 27704845 27705080 . + . gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "4"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; exon_id "ENSMUSE00000460027"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)"; +17 ensembl_havana CDS 27704845 27705080 . + 2 gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "4"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; protein_id "ENSMUSP00000044168"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)"; +17 ensembl_havana exon 27705625 27705780 . + . gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "5"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; exon_id "ENSMUSE00000460023"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)"; +17 ensembl_havana CDS 27705625 27705780 . + 0 gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "5"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; protein_id "ENSMUSP00000044168"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)"; +17 ensembl_havana exon 27705917 27706092 . + . gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "6"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; exon_id "ENSMUSE00000460015"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)"; +17 ensembl_havana CDS 27705917 27706092 . + 0 gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "6"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; protein_id "ENSMUSP00000044168"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)"; +17 ensembl_havana exon 27706994 27707114 . + . gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "7"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; exon_id "ENSMUSE00000245756"; exon_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)"; +17 ensembl_havana CDS 27706994 27707114 . + 1 gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "7"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; protein_id "ENSMUSP00000044168"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)"; +17 ensembl_havana exon 27707219 27707346 . + . gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "8"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; exon_id "ENSMUSE00000245736"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)"; +17 ensembl_havana CDS 27707219 27707346 . + 0 gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "8"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; protein_id "ENSMUSP00000044168"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)"; +17 ensembl_havana exon 27707880 27708067 . + . gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "9"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; exon_id "ENSMUSE00000459997"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)"; +17 ensembl_havana CDS 27707880 27708067 . + 1 gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "9"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; protein_id "ENSMUSP00000044168"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)"; +17 ensembl_havana exon 27708426 27711106 . + . gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "10"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; exon_id "ENSMUSE00000348638"; exon_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)"; +17 ensembl_havana CDS 27708426 27708532 . + 2 gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "10"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; protein_id "ENSMUSP00000044168"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)"; +17 ensembl_havana stop_codon 27708533 27708535 . + 0 gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "10"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)"; +17 ensembl_havana UTR 27655588 27655759 . + . gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)"; +17 ensembl_havana UTR 27701767 27701887 . + . gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)"; +17 ensembl_havana UTR 27708536 27711106 . + . gene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)"; diff -r 000000000000 -r 6c398f64ad6a test-data/chimeras --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chimeras Sun Jan 19 16:30:32 2020 -0500 @@ -0,0 +1,3 @@ +tagid txid1 txid2 geneid1 geneid2 symbol1 symbol2 region1 region2 tx_pos_start1 tx_pos_end1 tx_pos_strand1 length1 tx_pos_start2 tx_pos_end2 tx_pos_strand2 length2 read_info genomic_pos1 genomic_pos2 locus1 locus2 groupid1 groupid2 tpm1 tpm2 score1 score2 score sequences hybrid hybrid_pos mfe +4|1 ENSMUST00000136025 mmu-miR-6979-3p NA NA NA NA NA NA 32 46 + NA 2 12 + NA 2,15,30,39,54 ENSMUST00000136025:32:46:+ mmu-miR-6979-3p:2:12:+ ENSMUST00000136025:32:46:+ mmu-miR-6979-3p:2:12:+ 1 7 121100.0 165100.0 1.0 1.0 2.0 CAGGACUCUUGGCU&GUGUCUGUCU NA NA NA +3|2 mmu-miR-20a-5p ENSMUST00000136025 NA NA NA NA NA NA 0 23 + NA 132 142 + NA 6,28,35,44,55 mmu-miR-20a-5p:0:23:+ ENSMUST00000136025:132:142:+ mmu-miR-20a-5p:0:23:+ ENSMUST00000136025:132:142:+ 5 2 75660.0 165100.0 1.0 1.0 2.0 UAAAGUGCUUAUAGUGCAGGUAG&CUGCCUGCCU ((.((((((((&)))))))))) 13&1 -10.88 diff -r 000000000000 -r 6c398f64ad6a test-data/loci.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/loci.counts Sun Jan 19 16:30:32 2020 -0500 @@ -0,0 +1,9 @@ +6|1|1 ENSMUST00000182010 4 0 19 68 + 5S49M1S ENSMUST00000182010:19:68:+ ENSMUST00000182010:19:74:+ 1 1 6.485e+04 +7|9|1 ENSMUST00000182010 4 0 24 74 + 5S50M ENSMUST00000182010:24:74:+ ENSMUST00000182010:19:74:+ 1 1 6.485e+04 +4|1|2 ENSMUST00000136025 0 1 32 46 + 1S14M39S ENSMUST00000136025:32:46:+ ENSMUST00000136025:32:46:+ 1 1 1.211e+05 +3|2|2 ENSMUST00000136025 1 2 132 142 + 34S10M11S ENSMUST00000136025:132:142:+ ENSMUST00000136025:132:142:+ 1 1 1.651e+05 +2|2|2 ENSMUST00000137264 2 3 12 27 + 4S15M30S ENSMUST00000137264:12:27:+ ENSMUST00000137264:12:27:+ 1 1 1.135e+05 +6|1|4 ENSMUST00000160533 3 4 69 82 + 42S13M ENSMUST00000160533:69:82:+ ENSMUST00000160533:69:82:+ 1 1 1.297e+05 +3|2|1 mmu-miR-20a-5p 5 5 0 23 + 5S23M27S mmu-miR-20a-5p:0:23:+ mmu-miR-20a-5p:0:23:+ 1 1 7.566e+04 +2|2|1 mmu-miR-6898-5p 6 6 11 21 + 10M39S mmu-miR-6898-5p:11:21:+ mmu-miR-6898-5p:11:21:+ 1 1 1.651e+05 +4|1|1 mmu-miR-6979-3p 7 7 2 12 + 29S10M15S mmu-miR-6979-3p:2:12:+ mmu-miR-6979-3p:2:12:+ 1 1 1.651e+05 diff -r 000000000000 -r 6c398f64ad6a test-data/merged.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/merged.bed Sun Jan 19 16:30:32 2020 -0500 @@ -0,0 +1,8 @@ +ENSMUST00000136025 32 46 + 4|1|2,ENSMUST00000136025,32,46,+,1S14M39S +ENSMUST00000136025 132 142 + 3|2|2,ENSMUST00000136025,132,142,+,34S10M11S +ENSMUST00000137264 12 27 + 2|2|2,ENSMUST00000137264,12,27,+,4S15M30S +ENSMUST00000160533 69 82 + 6|1|4,ENSMUST00000160533,69,82,+,42S13M +ENSMUST00000182010 19 74 + 6|1|1,ENSMUST00000182010,19,68,+,5S49M1S;7|9|1,ENSMUST00000182010,24,74,+,5S50M +mmu-miR-20a-5p 0 23 + 3|2|1,mmu-miR-20a-5p,0,23,+,5S23M27S +mmu-miR-6898-5p 11 21 + 2|2|1,mmu-miR-6898-5p,11,21,+,10M39S +mmu-miR-6979-3p 2 12 + 4|1|1,mmu-miR-6979-3p,2,12,+,29S10M15S diff -r 000000000000 -r 6c398f64ad6a test-data/reads.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads.fasta Sun Jan 19 16:30:32 2020 -0500 @@ -0,0 +1,14 @@ +>1|1 +AAAAGACTCTGTAGACATGGCTGGTCTTGAACTCACAGAGATTTGTCTGCCTTTC +>2|2 +ATGCAGGGAGGACGATGCGAATGGGGAATCAGGCTAAACAGTTTGAATA +>3|2 +CGCGGTAAAGTGCTTATAGTGCAGGTAGACAGTACTGCCTGCCTTAATGAATGAA +>4|1 +TCAGGACTCTTGGCTGTATCCTTTCCTAAGTGTCTGTCTTCCTTACCACTAACA +>5|8 +TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA +>6|1 +TGTGGTCATTAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATTAGATACCGTC +>7|9 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT diff -r 000000000000 -r 6c398f64ad6a test-data/reads.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads.fastq Sun Jan 19 16:30:32 2020 -0500 @@ -0,0 +1,96 @@ +@183438/1 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT ++ +GGGGHHHHHHHHHHHGGGGGHHGGGGGGHHGHHGGHGGGHGHHHHHHGGGGGHGG +@397634/1 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT ++ +GGGGHHGHHHHHHHHGGGGGHHGGGGGGHHGHHGGHGGGHGHHHHHHGGGGGHGG +@701890/1 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT ++ +EEGGHGHHHHHHHHHGGGGGGHGGCGGFGHGHHGGHGGGHGHHHHHHGGGGGGFG +@745414/1 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT ++ +GGGGHHHHHHHHHHHGGGGGHHGGGGGGHHGHHGGHGGGHGHHHHHHGGGGGHGF +@753363/1 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT ++ +EEEGHHHFHHHHHHHGGFEEFGGGGGGGHHGHHGGHGGFHGHHHHHHGFGGGGGG +@881071/1 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT ++ +GGGGHHHHHHHHHHHGGGGGHHGGFGGGHHGHHGGHGGGHGHHHHHHGFGGFHGG +@1059959/1 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT ++ +GGGGHHHHHHHHHHHGGGGGHHGGGGGEHHGHHGGHGGGHGHHHHHHGGGGGHGG +@1157152/1 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT ++ +GGGGHHHHHHHHHHHGGGGGHHGGGGGEHHGHHGGHGGGHGHHHHHHGGGGGHGG +@1295751/1 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT ++ +GGGGHHHHHHHHHHHGGGGGHHGGGGGGHHGHHGGHGGGHGHHHHHHGGGGGHGG +@585749/1 +TGTGGTCATTAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATTAGATACCGTC ++ +GGEGGHHHHHHHHHHHFHHHG?FGEHHGGGFEEHHGHHGGFF?FHGHHHHHGEGG +@1209323/1 +ATGCAGGGAGGACGATGCGAATGGGGAATCAGGCTAAACAGTTTGAATA ++ +3AAABFFBBBBBGGEFGGG2AAGHHGGAGHHHHHHHHCHGHHHHHH5GF +@1248864/1 +ATGCAGGGAGGACGATGCGAATGGGGAATCAGGCTAAACAGTTTGAATA ++ +ABBBAF4DAB?BGGEFEFG2AAF3CEGGHHGGFCG33FHFHFHHHHHHH +@475998/1 +CGCGGTAAAGTGCTTATAGTGCAGGTAGACAGTACTGCCTGCCTTAATGAATGAA ++ +GGEEGB1FFFDGGGFHHHDDFGGHFHEFHHHHFDGGGE?GHFHHHHFHHHDEDHD +@478112/1 +CGCGGTAAAGTGCTTATAGTGCAGGTAGACAGTACTGCCTGCCTTAATGAATGAA ++ +EEFGGFGEHHFGHBBFHHHFGHHHHAGHHHFHFFGEF@BFGGAEHFFHHHGHGHF +@74093/1 +TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA ++ +G?FHHFFHFEFHH3FBAGGC2AAFEEGHFGFDEGGGFEAGFGE5AFF5@@BE5G +@448633/1 +TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA ++ +EFGGFHH5BAFA23AAFFHHDGGHHFGHHHEGHCFGFAFGH3FGGBBG@E@FGF +@849624/1 +TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA ++ +AABFBFFFF2CGDBADEFB2FAFFFHBGHFHDFGHAEGCFFEFDD5GGG@BBFE +@1076923/1 +TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA ++ +GCEFGHHHFEFH23DB553A2BGFFDBBA35FGFFGGGEECGH5DD@@@EBEGF +@1278542/1 +TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA ++ +EGGFHGHHHHGHGEGFHHHHHHFHHHFHGFGHHHHHGGEE3GHGGHGFDBGHHE +@1290525/1 +TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA ++ +CEFFDHH5B2AE2F555532AGF3EGH3AFAEHHFHGD133335DFGH5D@3FF +@1379287/1 +TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA ++ +AEEF1FGHHHGHHFGHHHGG/E1EHHHHGHHFDGGEG?CFGBGEGHHGHHHHHH +@1490590/1 +TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA ++ +GEA3BD5DF2EGCGEDF5EGH3AGHHHFHGFBFHBGGGGH33BFFD555D53FG +@854752/1 +AAAAGACTCTGTAGACATGGCTGGTCTTGAACTCACAGAGATTTGTCTGCCTTTC ++ +G?EFFAF5335DD5B5553222B1A55AFAGHHE33BAF325555A5DF5B3F3B +@1180232/1 +TCAGGACTCTTGGCTGTATCCTTTCCTAAGTGTCTGTCTTCCTTACCACTAACA ++ +EGE0F10B01DDBGC/0BFFGGHHHFE21BA2D221DGHH2DBAGHBDFBG1GF diff -r 000000000000 -r 6c398f64ad6a test-data/ref.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ref.fasta Sun Jan 19 16:30:32 2020 -0500 @@ -0,0 +1,18 @@ +>mmu-miR-20a-5p +TAAAGTGCTTATAGTGCAGGTAG +>mmu-miR-802-3p +ACGGAGAGTCTTTGTCACTCAG +>mmu-miR-6898-5p +TGTAAGGGGAGATGCAGGGAGC +>mmu-miR-6979-3p +TTGTGTCTGTCTGGCTCCCAG +>ENSMUST00000137264 +CTACTCACATGAAGGGAGGACGATGCGCAACCCTCCACCCACCTGCCTCATCGCCTGTAACCGCGATTCTTACCCTCTCAGAAAGAACCAGAAGCCTTCCCTCTGTGGGCTAATACGTGCCAGCCAAACCTGTGGGCCAGCTGAGCTGAGGGTCAGGGCTGGTTGTTTCTGTAGGCTTTCTCTTCTGAGTGGAGACCAAGAAGACTGAAGAGTTTGGCAGCCTTGTTAGACGCCCATGGACAGGTTTTGGTCTCTGGCACTC +>ENSMUST00000136025 +GATCTGATTGAGTCACAGCTGAGATGTGGCACCAGGACTCTTGGCTACACTCAGTTCTCTCAGTTTGACTGAGTACTCTGGGATCACAGAAGTGACTACATGATGCAGCCCAGAGGTCTGAACTCAAAGCTTCTGCCTGCCTACCTTATCTCACTGCTGGCAAATGCATCCCCTCTGCTCCACCCATC +>ENSMUST00000182010 +GCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCGGAGTTTCGAAGACGATCAGATACCGTTGTAGTTCCAACCATAAACGATGCCGACTGGC +>ENSMUST00000160533 +CAAAGGCAGTATCGTGGTGGATTATGATGTCATCCTGAAGGCCAAGTACACCCCAGGATTTGAAAACACATTAGATACCGTCGTCAAAAACCTGGAGACA +>ENSMUST00000045896 +GAGGCCAATGGTGGCGCCAACCCCTTCGAGGATGATGCCAAGGGAGTTCGTGTACGGGCACTCTATGACTACGACGGTCAGGAGCAGGATGAGCTCAGCT diff -r 000000000000 -r 6c398f64ad6a test-data/ref1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ref1.fasta Sun Jan 19 16:30:32 2020 -0500 @@ -0,0 +1,8 @@ +>mmu-miR-20a-5p +TAAAGTGCTTATAGTGCAGGTAG +>mmu-miR-802-3p +ACGGAGAGTCTTTGTCACTCAG +>mmu-miR-6898-5p +TGTAAGGGGAGATGCAGGGAGC +>mmu-miR-6979-3p +TTGTGTCTGTCTGGCTCCCAG diff -r 000000000000 -r 6c398f64ad6a test-data/ref2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ref2.fasta Sun Jan 19 16:30:32 2020 -0500 @@ -0,0 +1,10 @@ +>ENSMUST00000137264 +CTACTCACATGAAGGGAGGACGATGCGCAACCCTCCACCCACCTGCCTCATCGCCTGTAACCGCGATTCTTACCCTCTCAGAAAGAACCAGAAGCCTTCCCTCTGTGGGCTAATACGTGCCAGCCAAACCTGTGGGCCAGCTGAGCTGAGGGTCAGGGCTGGTTGTTTCTGTAGGCTTTCTCTTCTGAGTGGAGACCAAGAAGACTGAAGAGTTTGGCAGCCTTGTTAGACGCCCATGGACAGGTTTTGGTCTCTGGCACTC +>ENSMUST00000136025 +GATCTGATTGAGTCACAGCTGAGATGTGGCACCAGGACTCTTGGCTACACTCAGTTCTCTCAGTTTGACTGAGTACTCTGGGATCACAGAAGTGACTACATGATGCAGCCCAGAGGTCTGAACTCAAAGCTTCTGCCTGCCTACCTTATCTCACTGCTGGCAAATGCATCCCCTCTGCTCCACCCATC +>ENSMUST00000182010 +GCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCGGAGTTTCGAAGACGATCAGATACCGTTGTAGTTCCAACCATAAACGATGCCGACTGGC +>ENSMUST00000160533 +CAAAGGCAGTATCGTGGTGGATTATGATGTCATCCTGAAGGCCAAGTACACCCCAGGATTTGAAAACACATTAGATACCGTCGTCAAAAACCTGGAGACA +>ENSMUST00000045896 +GAGGCCAATGGTGGCGCCAACCCCTTCGAGGATGATGCCAAGGGAGTTCGTGTACGGGCACTCTATGACTACGACGGTCAGGAGCAGGATGAGCTCAGCT diff -r 000000000000 -r 6c398f64ad6a test-data/segments.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/segments.bed Sun Jan 19 16:30:32 2020 -0500 @@ -0,0 +1,13 @@ +ENSMUST00000182010 19 68 6|1|1,ENSMUST00000182010,19,68,+,5S49M1S 0 + +ENSMUST00000182010 24 74 7|9|1,ENSMUST00000182010,24,74,+,5S50M 0 + +mmu-miR-20a-5p 0 23 3|2|1,mmu-miR-20a-5p,0,23,+,5S23M27S 0 + +mmu-miR-6898-5p 11 21 2|2|1,mmu-miR-6898-5p,11,21,+,10M39S 0 + +mmu-miR-6979-3p 2 12 4|1|1,mmu-miR-6979-3p,2,12,+,29S10M15S 0 + +ENSMUST00000137264 12 27 2|2|2,ENSMUST00000137264,12,27,+,4S15M30S 0 + +ENSMUST00000136025 32 46 4|1|2,ENSMUST00000136025,32,46,+,1S14M39S 0 + +ENSMUST00000136025 132 142 3|2|2,ENSMUST00000136025,132,142,+,34S10M11S 0 + +ENSMUST00000182010 19 45 6|1|2,ENSMUST00000182010,19,45,+,5S26M24S 0 + +ENSMUST00000182010 24 45 7|9|2,ENSMUST00000182010,24,45,+,5S21M29S 0 + +ENSMUST00000182010 46 58 6|1|3,ENSMUST00000182010,46,58,+,32S12M11S 0 + +ENSMUST00000182010 46 68 7|9|3,ENSMUST00000182010,46,68,+,27S22M6S 0 + +ENSMUST00000160533 69 82 6|1|4,ENSMUST00000160533,69,82,+,42S13M 0 + diff -r 000000000000 -r 6c398f64ad6a test-data/singletons --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/singletons Sun Jan 19 16:30:32 2020 -0500 @@ -0,0 +1,4 @@ +tagid txid geneid symbol region tx_pos_start tx_pos_end tx_pos_strand length read_info genomic_pos locus groupid tpm score score sequences +6|1 ENSMUST00000182010 NA NA NA 19 68 + NA 6,54,55 ENSMUST00000182010:19:68:+ ENSMUST00000182010:19:74:+ 0 64850.0 1.0 1.0 UCAUUAAUCAAGAACGAAAGUCGGAGUUUCGAAGACGAUCAGAUACCGUUGUAGU +7|9 ENSMUST00000182010 NA NA NA 24 74 + NA 6,55,55 ENSMUST00000182010:24:74:+ ENSMUST00000182010:19:74:+ 0 64850.0 1.0 1.0 UCAUUAAUCAAGAACGAAAGUCGGAGUUUCGAAGACGAUCAGAUACCGUUGUAGU +2|2 ENSMUST00000137264 NA NA NA 12 27 + NA 5,19,49 ENSMUST00000137264:12:27:+ ENSMUST00000137264:12:27:+ 3 113500.0 1.0 1.0 AGGGAGGACGAUGCG diff -r 000000000000 -r 6c398f64ad6a tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Sun Jan 19 16:30:32 2020 -0500 @@ -0,0 +1,7 @@ + + + + value, dbkey, name, path + +
+