# HG changeset patch # User iuc # Date 1670607640 0 # Node ID f28df61581f49adccc39a48d5ee6e5aaaeffc8aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac diff -r 000000000000 -r f28df61581f4 all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all_fasta.loc.sample Fri Dec 09 17:40:40 2022 +0000 @@ -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 f28df61581f4 cherri_train.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cherri_train.xml Fri Dec 09 17:40:40 2022 +0000 @@ -0,0 +1,231 @@ + + + macros.xml + + + 1: + ln -s '../$experiment.exp_name' 'mixed_model/$experiment.exp_name' && + #else: + ln -s $experiment.exp_name/model/optimized/${experiment.exp_name}_context_${context}.model final_full.model && + #if $use_structure == 'off': + ln -s $experiment.exp_name/model/features/${experiment.exp_name}_context_${context}.npz features.npz && + #else: + ln -s $experiment.exp_name/feature_files/training_data_${experiment.exp_name}_context_${context}.npz features.npz && + #end if + #end if + #end for + #if len($rep_experiment) > 1: + cherri train + -mi on + -i1 mixed_model + -r #echo ' '.join($experiments) + -g /not/needed/ + -l /not/needed/ + -n mixed + -o . + -on mixed_model + @COMMONPARAMS@ && + ln -s mixed_model/mixed/model/optimized/full_mixed_context_${context}.model final_full.model && + #if $use_structure == 'off': + ln -s mixed_model/mixed/model/features/mixed_context_${context}.npz features.npz && + #else: + ln -s mixed_model/mixed/feature_files/training_data_mixed_context_${context}.npz features.npz && + #end if + #end if + tar -zhcvf model.tgz final_full.model features.npz + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r f28df61581f4 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Dec 09 17:40:40 2022 +0000 @@ -0,0 +1,65 @@ + + 0.7 + 21.05 + + + cherri + + + + + + + + + + + + + + + + + + + + + + + + + + topic_0080 + topic_0081 + topic_0160 + + + operation_2995 + + + + + cherri + + + + + cherri + + + + + + + + + diff -r 000000000000 -r f28df61581f4 test-data/context_150_model.tgz Binary file test-data/context_150_model.tgz has changed diff -r 000000000000 -r f28df61581f4 test-data/context_150_st_off.npz Binary file test-data/context_150_st_off.npz has changed diff -r 000000000000 -r f28df61581f4 test-data/evaluation_results_st_on.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/evaluation_results_st_on.csv Fri Dec 09 17:40:40 2022 +0000 @@ -0,0 +1,6 @@ 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diff -r 000000000000 -r f28df61581f4 test-data/genome.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome.fa Fri Dec 09 17:40:40 2022 +0000 @@ -0,0 +1,4 @@ +>chr1 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+>chr2 +CAGUCACCACCUCACACAUGAGGAAGCUGAGGCUGGAGACUUAGGUGACCUGGCCUAGAGUUUCAGGGCGCCGGGAUCCUGUCGAAGGUCCCACCCACCUGGCUCUGCUGCAGCGCCCUCUCUCUGUCCUCUAGGUGUGUUUGGUGGCCGGGGCCGAGGUGGGAUCCCGGGCACAGGCAGAGGCCAGCCAGAGAAGAAGCCUGGCAGACAGGCGGGCAAACAGUGAGCGCCCACCCAGACCGGCUGCUGCGCCCCCUCCUGCCAGGGUGGCGAUUCCGCUCCACAGUCUCGGACGGAUCUGCUCAGAAAGGAAGAGGCAGGUCUGGCACGGUGAAGAGACGUGAGAGGUGUAGAAUAAGUGGGAGGCCCCCGGCGCCCCCCGGUGUCCCCGCGAGGGGUCCAGGGCGGGGUCUGCCGGCCCUGCGGGCCGCCGGUGAAAUACCACUACUCUGAUCGUUUUUUCACUGACCCGGUGAGGCGGGGGGGCGAGCCCUGAGGGGCUCUCGCUUCUGGCGCCAAGCGCCCGGCCGCACGCAAAAGAGCUCCUGAAGGAAGCGCUAAACAUGGAAAGGAACAACGGGUACCAGCCGCUGCAAAAUCAUGCCAAAAUGUAAAGACCAUCGAGACUAGGAAGAAACUGCAUCAACUAACGAGCAAAAUCACCAGCUAAAGUUCCGUUUAUGGUCUGAUUUCCGGCCUCUCGCCUGCUCGCCCCGCCGCCCGCCUGUCCCGCUCCCUCCCUCCCGGGGACCCGGAGGAGAGGGGACCAUGCCGGAACCCGGGCCGGACGCUGCCGGCACCGCCAGCGCACAGCCCCAACCGCCGCCGCCCCCCCCACCCGCUCCCAAGGAGUCCCCGUUCUCCAUCAAGAACCUGCUCAACGGAGACCACCACCGGCCGCCCCCUAAGCCUCAGCCGCCCCCACGGACGCUCUUCGCGCCAGCCUCGGCUGCCGCCGCCGCCGCCGCUGCCGCUGCCGCGGCGGCCAAGCAGGCAUGCGCUGCCUAGCCCCGUGUGGUUAACAUGUCCGUAUUUAAAGAACACACAAUUAAUUGCCUAAAAGCAUUAUCCUUCUCAGCACUCUCCUAUCCUUCAGAUCUAACCUUUAGGCACUGCCGGCUGCCGGCGGGGUCCAGGACCCAGCGGGGCUGGGCGCGCGGAGCAGCGCUGGGUGCAGCGCCUGCGCCGGCAGCUGCAAGGGCCGCAGAAAUUAAACGCGAGUGUCCAGAAUCGGGCAUUGUGGGUUUAAAUCCUGAAUCCACUGGUCACUAUCUGAGACUUUCCCCUGUCACAAAUUAGUUACCUUCUUACUUUUGCAAAGCAAACGUGCAACCCCAAGCAGCGGUCUCCCGGGCCGGGGCUGCGCGGCCGCCGCUGUGCUGGCUUUUAACGGUGGGAGGGCACCAUCCUCUUGCUCUGCUCUCGUUCUCCAGAAGGCUGUCCCGGGGCCCCCACUCUCCGUCCCGCUCCGGGGACAGUGGCUCGCCUGCUAUGCGCGGCAGCCCGCGCCGGGGCCGGCACCAGCAGCGCCCGGGCGGAUGCAGCGAGCCCACGGAGGGGCAUGCUUCCACGCACCAAGUAUAACCGCUUCAGGAAUGACUCGGUGACAUCGGUCGAUGACCUUCUCCACAGGCCUUGGCCCCGCCCCCGCCGCCGCGCAGGCGCUGACGCAAGCGCAGCAGGCGCGCGCUGUUUCCGGAAGUCGCGGCCGGCGUCACCGCUGCGGCUGCCUCAGCUACUGCCGCAGUCGCCGCGGAAUUCGGCGAGUAGAACCGCUGAGGCGGGCGCGGGCCCGGGUGGGGCCAAGGUUCCGGCCACUCUGCAGAAUGGAGAUAAUCAGGAGCAGUGCGUGUCCGCCGUACACCUCCCCGCCUCCCCACACCCGGCUGCCCCUGGCCUGCUAGGCCGAGACCAUGGCCGGCGUGUUUGGCUGGGCCUGGGGCUGAGGCAGCCCUGUUGUGUAUCACUCACUGAGGCUGGACAAGAGGGAAGGCGGAGAAGCCUGGCCACAUGUCUCCUGAGGGCUCCAGGCAGGGCCCUCUCACCUGCUGCCAGGGUCCCAGCCCGCAGGAGCUUCCCGUCCACCUCUGAACUCACGGUCCACAUGGCGCUGGAGCGUCGGGCACCAUCUACAGGGCUUGAGGCCAGCAGCCUAGCCUCUGGGUCCACUGGGGCAGGCAAGGUGAGUCCUGCUGUCUGUGGAGCCAGCGUGCUGGGCCGGGCAGGGGGCCUCGUUGGCUGGGGUGGCUGCAGCUCCGCCCUGCCUGGGGCAUU diff -r 000000000000 -r f28df61581f4 test-data/genome.fa.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome.fa.fai Fri Dec 09 17:40:40 2022 +0000 @@ -0,0 +1,2 @@ +chr1 2290 6 2290 2291 +chr2 2274 2303 2274 2275 diff -r 000000000000 -r f28df61581f4 test-data/genome.sizes --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome.sizes Fri Dec 09 17:40:40 2022 +0000 @@ -0,0 +1,2 @@ +chr1 2292 +chr2 2276 diff -r 000000000000 -r f28df61581f4 test-data/mixed_context_150_st_off.npz Binary file test-data/mixed_context_150_st_off.npz has changed diff -r 000000000000 -r f28df61581f4 test-data/test_evaluate_rris.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_evaluate_rris.csv Fri Dec 09 17:40:40 2022 +0000 @@ -0,0 +1,8 @@ +chrom1,start1,stop1,strand1,chrom2,start2,stop2,strand2 +chr2,150,171,+,chr1,150,171,+ +chr2,471,520,+,chr1,471,494,+ +chr2,820,840,+,chr1,794,816,+ +chr2,1140,1159,+,chr1,1116,1136,+ +chr2,1459,1482,+,chr1,1436,1496,+ +chr2,1782,1804,+,chr1,1796,1816,+ +chr2,2104,2124,+,chr1,2116,2140,+ diff -r 000000000000 -r f28df61581f4 test-data/train_1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/train_1.fa Fri Dec 09 17:40:40 2022 +0000 @@ -0,0 +1,4 @@ +>chr1 +CCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCCGUGGCGGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCGGUGCCGCGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCCGUGGCGGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCGGUGCCGGGUGAGGCGGGGGGGCGAGCCCUGAGGGGCUCUCGCUUCUGGCGCCAAGCCCAGCGGGGCUGGGCGCGCGGAGUAGGGGGCGGGCUCCGGCGCUGCCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACGCGCGUGCGCCCGAGCGCGGCCCGGUGGUCCCUCCCGGACAGGCGUUCGUGCGACGUGUGCGCGCGUGCGCCCGAGCGCGGCCCGGUGGUCCCUCCCGGACAGGCGUUCGUGCGACGUGUGCCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGANANANANACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGAAGGGAGAAGGGUCGGGGCAGGGCCCCGGGGAGCCCGGCGGCCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGAGUAGGGGGCGGGCUCCGGCGCUGCCCAGCGGGGCUGGGCGCGCGGAGUAGGGGGCGGGCUCCGGCGCUGCCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGANACCCCGGGGAGCCCGGCGGGUAGGGGGCGGGCUCCGGCGCUGCCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGAGGUGAGGCGGGGGGGCGAGCCCUGAGGGGCUCUCGCUUCUGGCGCCAAGGGUGAGGCGGGGGGGCGAGCCCUGAGGGGCUCUCGCUUCUGGCGCCAAGAGGGAGAAGGGUCGGGGCAGGGGUAGGGGGCGGGCUCCGGCGCUGCCCAGCGGGGCUGGGCGCGCGGACCCCGGGGAGCCCGGCGGCCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGAGUAGGGGGCGGGCUCCGGCGCUGCGGAUCCGAGUCACGGCACCAAACCCAGCGGGGCUGGGCGCGCGGAGUAGGGGGCGGGCUCCGGCGCUGGUAGGGGGCGGGCUCCGGCGCUGGUAGGGGGCGGGCUCCGGCGCUGGUAGGGGGCGGGCUCCGGCGCUGCCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCA +>chr2 +GUUGCGGCUGGACGAGGCGCAGUGGCCGCGGCGCGAGCCGGGGGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCGGUGCCGCGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCCGUGGCGGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCGGUGCCGCGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCCGUGGCACUGGUGAAGAGACAUGAGAGGAUGGGCGCGCGCCGGGCCCGUGCCGUUCCCUCCUCCUCCUCCCCUGCCGCGGCGAGCCGGGCCCUGGGGGCCCUUCCCGUGCGCGGGCGAGCCGGGCCCGAUGCCUUCCCCGUCCGUCCGUCCGUCCGUCCAUCCGUCCACCCCCGGGCCGGGCACCGCCCCCGGGCCGGGCACCGCGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAGAAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCGGGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAGAAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCGGGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAGAAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCGGGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAGAAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCGGGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGNANANANAGGACGGGCCCUUCCCGUGGCGCUGCGCGAGCCGGGCGCUGCGGCUGGAUGAGGCGCUCGCCCUCUCUCUCUCUCUCUCUGUCUCUCUCUCUCUCUGGAGCCGGGGGGGGGGGGGGGGGGGGGGGGGGGCAGGCGGCGCCGCCGCCCUCUCCCACCCCAGAAAAGGUGUUGGUUGAUAUAGACAGCAGGACGGUGGCCAUGGAAGUCAGAAUCCACUAAGGAGUGUGUAACAACUCACCUGCCGAAUCAACUAGCCCUGAAAAUGGAUGGCACUGGAGCAUCAGGCCCAUACCCGGCCAUCGCCAGCAGUCCGGCCGCCGCGGCGCGCGCCCGGGUCCCCCGCCGCCCCUCCGGUGCUCCCUCCCCACCCCGCAGUGAUGCCUUCCCCGUCCGUCCGUCCGUCCGUCCAUCCGUCCACGCCUCCCUCCCCACCCCGCGAGCCUCCCUCCCCACCCCGCGAGCCUCCCUCCCCACCCCGCGAGCCUCCCUCCCCACCCCGCGAGCCUCCCUCCCCACCCCGCGAAUACUUACCUGGCAGGGGAGAUACCAUGAUCACGAAGGUGGUUUUCCCAGGGCGAGGCUUAUCCAUUGCACUC diff -r 000000000000 -r f28df61581f4 test-data/train_1_len.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/train_1_len.tabular Fri Dec 09 17:40:40 2022 +0000 @@ -0,0 +1,2 @@ +chr1 1888 +chr2 1652 diff -r 000000000000 -r f28df61581f4 test-data/train_1_pos.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/train_1_pos.tabular Fri Dec 09 17:40:40 2022 +0000 @@ -0,0 +1,25 @@ +383 chr1 0 23 + chr2 1 24 - GUUGCGGCUGGACGAGGCGCAGU CCCAGCGGGGCUGGGCGCGCGGA .((((((((.(.(....(((...&....)))..).).))).))))). -14.5 UUGCGGCUGGACGAGGCGC GCGGGGCUGGGCGCGCGG 2&5 chr1 1 19 + chr2 5 19 - 489.80 3308.00 3797.8 1.0 1.0 1.0 CDS miRNA ENST00000624358;ENST00000651965 ENST00000584178 +164 chr1 23 42 - chr2 24 47 - GGCCGCGGCGCGAGCCGGG CCCAGCGGGGCUGGGCGCGCGGA ..(((((((.(.(((((((&))).....)))).))).))))). -23.9 CCGCGGCGCGAGCCGGG CCCAGCGGGGCUGGGCGCGCGG 3&1 chr1 25 40 - chr2 24 46 - 219.80 3308.00 3527.8 1.0 1.0 1.0 protein_coding miRNA ENST00000257765;ENST00000423730;ENST00000433730;ENST00000610435 ENST00000584178 +141 chr1 42 90 + chr2 47 97 + GGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCGGUGCCG CGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCCGUGGC (((((((.(((((.((.((((((((((.((((((((((((((......&)))))).))).)))))..)))))))))))).)))).).)))))))..... -74.1 GGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCG CGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCC 1&1 chr1 42 84 + chr2 47 92 + 84.07 73.88 157.95 1.0 1.0 1.0 miRNA miRNA ENST00000615959 ENST00000581792 +141 chr1 90 140 + chr2 97 145 + CGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCCGUGGC GGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCGGUGCCG ((((((.(((.(((((..((((((((((((.((((.(.(((((((.....&))))))).))))).)).)))))))))).))))))))))))))...... -74.1 CGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCC GGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCG 1&1 chr1 90 135 + chr2 97 139 + 73.88 84.07 157.95 1.0 1.0 1.0 miRNA miRNA ENST00000615959 ENST00000615959 +141 chr1 140 188 + chr2 145 195 + GGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCGGUGCCG CGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCCGUGGC (((((((.(((((.((.((((((((((.((((((((((((((......&)))))).))).)))))..)))))))))))).)))).).)))))))..... -74.1 GGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCG CGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCC 1&1 chr1 140 182 + chr2 145 190 + 84.07 73.88 157.95 1.0 1.0 1.0 miRNA miRNA ENST00000581792 ENST00000615959 +141 chr1 188 238 + chr2 195 243 + CGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCCGUGGC GGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCGGUGCCG ((((((.(((.(((((..((((((((((((.((((.(.(((((((.....&))))))).))))).)).)))))))))).))))))))))))))...... -74.1 CGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCC GGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCG 1&1 chr1 188 233 + chr2 195 237 + 73.88 84.07 157.95 1.0 1.0 1.0 miRNA miRNA ENST00000581792 ENST00000581792 +134 chr1 238 263 - chr2 243 292 + ACUGGUGAAGAGACAUGAGAGGAUG GGUGAGGCGGGGGGGCGAGCCCUGAGGGGCUCUCGCUUCUGGCGCCAAG ..(((((.((((...((((((....&.............................)))))).))))..))))).. -17 UGGUGAAGAGACAUGAGAG CUCUCGCUUCUGGCGCCA 3&30 chr1 240 257 - chr2 272 261 + 2216.00 1579.00 3795.0 1.0 1.0 1.0 lncRNA miRNA ENST00000667915 ENST00000611066 +131 chr1 263 285 + chr2 292 315 - GGCGCGCGCCGGGCCCGUGCCG CCCAGCGGGGCUGGGCGCGCGGA ..((((((((.(((((.(((..&....)))))))).)))))))).. -35.6 CGCGCGCCGGGCCCGUGC GCGGGGCUGGGCGCGCG 3&5 chr1 265 281 + chr2 296 309 - 161.60 3308.00 3469.6 1.0 0.84 0.84 CDS miRNA ENST00000369800;ENST00000522853 ENST00000584178 +92 chr1 285 305 - chr2 315 338 + UUCCCUCCUCCUCCUCCCCU GUAGGGGGCGGGCUCCGGCGCUG ..(((.((((((.(......&).)))))).)))........... -15.3 CCCUCCUCCUCC GUAGGGGGCGGG 3&1 chr1 287 297 - chr2 315 327 + 124.00 5122.00 5246.0 1.0 1.0 1.0 lncRNA miRNA ENST00000607278 ENST00000577388 +75 chr1 305 323 - chr2 338 361 - GCCGCGGCGAGCCGGGCC CCCAGCGGGGCUGGGCGCGCGGA .(((((.(..(((.((((&........)))).))))))))). -22.4 CCGCGGCGAGCCGGGCC GGCUGGGCGCGCGG 2&9 chr1 306 322 - chr2 346 352 - 104.40 3308.00 3412.4 1.0 1.0 1.0 protein_coding miRNA ENST00000371984 ENST00000584178 +72 chr1 323 341 + chr2 361 384 - CUGGGGGCCCUUCCCGUG CCCAGCGGGGCUGGGCGCGCGGA (((.(.((((.((((((.&....))))))..)))).).))). -25.7 CUGGGGGCCCUUCCCGU GCGGGGCUGGGCGCGCGG 1&5 chr1 323 340 + chr2 365 379 - 99.15 3308.00 3407.15 1.0 0.84 0.84 lncRNA miRNA ENST00000609544 ENST00000584178 +66 chr1 341 359 + chr2 384 407 - CGCGGGCGAGCCGGGCCC CCCAGCGGGGCUGGGCGCGCGGA .....(((.(((.(((((&.......))))).))).)))... -23.6 GCGAGCCGGGCCC GGGCUGGGCGCGC 6&8 chr1 346 354 + chr2 391 397 - 99.15 3308.00 3407.15 1.0 0.84 0.84 CDS miRNA ENST00000270458 ENST00000584178 +64 chr1 359 401 - chr2 407 430 - GAUGCCUUCCCCGUCCGUCCGUCCGUCCGUCCAUCCGUCCAC CCCAGCGGGGCUGGGCGCGCGGA .................(((((.((((((.((..((((....&....)))))).)))))).))))) -23.8 UCCGUCCGUCCGUCCAUCCGU GCGGGGCUGGGCGCGCGGA 18&5 chr1 376 380 - chr2 411 426 - 19720.00 3308.00 23028.0 1.0 0.84 0.84 protein_coding miRNA ENST00000356861;ENST00000425528;ENST00000450764;ENST00000589149 ENST00000584178 +51 chr1 401 419 + chr2 430 491 + CCCCGGGCCGGGCACCGC CGCGCGUGCGCCCGAGCGCGGCCCGGUGGUCCCUCCCGGACAGGCGUUCGUGCGACGUGUG (((((((((((((.((((&...))).).))))......))))))).))................................ -29.9 CCCCGGGCCGGGCACCGC GCGUGCGCCCGAGCGCGGCCCGGUGG 1&4 chr1 401 419 + chr2 433 456 + 88.57 68.87 157.44 1.0 1.0 1.0 protein_coding miRNA ENST00000343605 ENST00000614492 +51 chr1 419 437 + chr2 491 552 + CCCCGGGCCGGGCACCGC CGCGCGUGCGCCCGAGCGCGGCCCGGUGGUCCCUCCCGGACAGGCGUUCGUGCGACGUGUG (((((((((((((.((((&...))).).))))......))))))).))................................ -29.9 CCCCGGGCCGGGCACCGC GCGUGCGCCCGAGCGCGGCCCGGUGG 1&4 chr1 419 437 + chr2 494 517 + 88.57 68.87 157.44 1.0 1.0 1.0 protein_coding miRNA ENST00000343605 ENST00000577708 +37 chr1 437 590 + chr2 552 575 - GACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAGAAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCGGGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCG CCCAGCGGGGCUGGGCGCGCGGA .......................................................................................................(((.(.(.((((((((..........(((.....................&)))..)))))))).).).))).. -26.5 CGCACUUGCGGCCCCGGGUUCCUCCCGGG CCCAGCGGGGCUGGGCGCGCG 104&1 chr1 540 466 + chr2 552 573 - 10440.00 3308.00 13748.0 1.0 0.84 0.84 rRNA miRNA ENST00000612463 ENST00000584178 +37 chr1 590 743 + chr2 575 598 - GACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAGAAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCGGGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCG CCCAGCGGGGCUGGGCGCGCGGA .......................................................................................................(((.(.(.((((((((..........(((.....................&)))..)))))))).).).))).. -26.5 CGCACUUGCGGCCCCGGGUUCCUCCCGGG CCCAGCGGGGCUGGGCGCGCG 104&1 chr1 693 619 + chr2 575 596 - 10440.00 3308.00 13748.0 1.0 0.84 0.84 rRNA miRNA ENST00000610460 ENST00000584178 +37 chr1 743 896 + chr2 598 621 - GACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAGAAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCGGGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCG CCCAGCGGGGCUGGGCGCGCGGA .......................................................................................................(((.(.(.((((((((..........(((.....................&)))..)))))))).).).))).. -26.5 CGCACUUGCGGCCCCGGGUUCCUCCCGGG CCCAGCGGGGCUGGGCGCGCG 104&1 chr1 846 772 + chr2 598 619 - 10440.00 3308.00 13748.0 1.0 0.84 0.84 rRNA miRNA ENST00000613359 ENST00000584178 +37 chr1 896 1049 + chr2 621 644 - GACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAGAAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCGGGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCG CCCAGCGGGGCUGGGCGCGCGGA .......................................................................................................(((.(.(.((((((((..........(((.....................&)))..)))))))).).).))).. -26.5 CGCACUUGCGGCCCCGGGUUCCUCCCGGG CCCAGCGGGGCUGGGCGCGCG 104&1 chr1 999 925 + chr2 621 642 - 10440.00 3308.00 13748.0 1.0 0.84 0.84 rRNA miRNA ENST00000619471 ENST00000584178 +37 chr1 1049 1202 + chr2 644 667 - NA NA NA NA NA NA NA chr1 1049 1202 + chr2 644 667 - 10440.00 3308.00 13748.0 1.0 0.84 0.84 rRNA miRNA ENST00000611446 ENST00000584178 +37 chr1 1202 1355 + chr2 667 690 - NA NA NA NA NA NA NA chr1 1202 1355 + chr2 667 690 - 10440.00 3308.00 13748.0 1.0 0.84 0.84 rRNA miRNA ENST00000619779 ENST00000584178 +37 chr1 1355 1508 + chr2 690 713 - NA NA NA NA NA NA NA chr1 1355 1508 + chr2 690 713 - 10440.00 3308.00 13748.0 1.0 0.84 0.84 rRNA miRNA ENST00000616292 ENST00000584178 +37 chr1 1508 1661 + chr2 713 736 - NA NA NA NA NA NA NA chr1 1508 1661 + chr2 713 736 - 10440.00 3308.00 13748.0 1.0 0.84 0.84 rRNA miRNA ENST00000618998 ENST00000584178 +36 chr1 1661 1679 + chr2 736 759 - GGACGGGCCCUUCCCGUG CCCAGCGGGGCUGGGCGCGCGGA .(.((.((((.((((((.&....))))))..)))).)))... -22.5 GACGGGCCCUUCCCGU GCGGGGCUGGGCGCGC 2&5 chr1 1662 1677 + chr2 740 752 - 50.24 3308.00 3358.24 1.0 0.84 0.84 CDS miRNA ENST00000305943 ENST00000584178 +32 chr1 1679 1697 - chr2 759 782 - GCGCUGCGCGAGCCGGGC CCCAGCGGGGCUGGGCGCGCGGA ...((((((..(((.(((&.........))).))))))))). -20.7 CUGCGCGAGCCGGGC GCUGGGCGCGCGG 4&10 chr1 1682 1694 - chr2 768 772 - 43.63 3308.00 3351.63 1.0 1.0 1.0 CDS miRNA ENST00000269503;ENST00000585159 ENST00000584178 diff -r 000000000000 -r f28df61581f4 test-data/train_2.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/train_2.fa Fri Dec 09 17:40:40 2022 +0000 @@ -0,0 +1,4 @@ +>chr1 +CCCAGCGGGGCUGGGCGCGCGGAGGUGAGGCGGGGGGGCGAGCCCUGAGGGGCUCUCGCUUCUGGCGCCAAGAGGCCCCGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCCGUGGCGGCCGCGGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCGGUGAGGCCCCGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCCGUGGCGGCCGCGGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCGGUGCCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGAGUAGGGGGCGGGCUCCGGCGCCCCAGCGGGGCUGGGCGCGCGGACGCGCGUGCGCCCGAGCGCGGCCCGGUGGUCCCUCCCGGACAGGCGUUCGUGCGACGCGCGUGCGCCCGAGCGCGGCCCGGUGGUCCCUCCCGGACAGGCGUUCGUGCGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGAGUAGGGGGCGGGCUCCGGCGCUGGCGUCCCCUUCCCCGCCGGCCGCCUUUCUCGCGCGCGACUGCGGCGGCGGUGGUGGGGGGAGCCGCGGGGAUCCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGAUGGCGUCCCCUUCCCCGCCGGCCGCCUUUCUCGCGCGCGACUGCGGCGGCGGUGGUGGGGGGAGCCGCGGGGAUNANANANACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGAGUAGGGGGCGGGCUCCGGCGCGGUGAGGCGGGGGGGCGAGCCCUGAGGGGCUCUCGCUUCUGGCGCCAAGCCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGAAGGGAGAAGGGUCGGGGCAGNANACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGAGGUGAGGCGGGGGGGCGAGCCCUGAGGGGCUCUCGCUUCUGGCGCCAAGGGUGAGGCGGGGGGGCGAGCCCUGAGGGGCUCUCGCUUCUGGCGCCAAGGGUGAGGCGGGGGGGCGAGCCCUGAGGGGCUCUCGCUUCUGGCGCCAAGCCCCGGGGAGCCCGGCGGNANANANAGUAGGGGGCGGGCUCCGGCGCCCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGAGGUGAGGCGGGGGGGCGAGCCCUGAGGGGCUCUCGCUUCUGGCGCCAAGCCCAGCGGGGCUGGGCGCGCGGACC +>chr2 +GUUGCGGCUGGACGAGGCGCAGCUGGUGAAGAGACAUGAGAGGAUGCCGCGGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCGGUGAGGCCCCGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCCGUGGCGGCCGCGGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCGGUGAGGCCCCGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCCGUGGCGGCUGCGGCUGGAUGAGGCGGGGCCGCGGCGCGAGCCGGGCUGGGGGCCCUUCCCGUGGUUCCCUCCUCCUCCUCCCCUGGCGCGCGCCGGGCCCGUGCCGCCCCGGGCCGGGCACCGCCCCCGGGCCGGGCACCGCGCCGCGGCGAGCCGGGCCGGACGGGCCCUUCCCGUGUGCCUUCCCCGUCCGUCCGUCCGUCCGUCCAUCCGUCCACCGCGACUGCGGCGGCGGUGGUGGGGGGAGCCGCGGGGAUUGGCGUCCCCUUCCCCGCCGGCCGCCUUUCUCGCGGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAGAAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCGGGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAGAAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCGGGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAGAAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCGGGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAGAAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCGGGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGCGCGACUGCGGCGGCGGUGGUGG diff -r 000000000000 -r f28df61581f4 test-data/train_2_len.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/train_2_len.tabular Fri Dec 09 17:40:40 2022 +0000 @@ -0,0 +1,2 @@ +chr1 1416 +chr2 1180 diff -r 000000000000 -r f28df61581f4 test-data/train_2_pos.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/train_2_pos.tabular Fri Dec 09 17:40:40 2022 +0000 @@ -0,0 +1,25 @@ +386 chr1 0 22 + chr2 1 24 - GUUGCGGCUGGACGAGGCGCAG CCCAGCGGGGCUGGGCGCGCGGA .((((((((.(.(....(((..&....)))..).).))).))))). -14.5 UUGCGGCUGGACGAGGCGC GCGGGGCUGGGCGCGCGG 2&5 chr1 1 19 + chr2 5 19 - 527.40 2400.00 2927.4 1.0 1.0 1.0 CDS miRNA ENST00000624358;ENST00000651965 ENST00000584178 +156 chr1 22 45 - chr2 24 73 + CUGGUGAAGAGACAUGAGAGGAU GGUGAGGCGGGGGGGCGAGCCCUGAGGGGCUCUCGCUUCUGGCGCCAAG .(((((.((((...((((((...&.............................)))))).))))..))))).. -17 UGGUGAAGAGACAUGAGAG CUCUCGCUUCUGGCGCCA 2&30 chr1 23 41 - chr2 53 42 + 2419.00 1304.00 3723.0 1.0 1.0 1.0 lncRNA miRNA ENST00000667915 ENST00000611066 +102 chr1 45 95 + chr2 73 130 + GCCGCGGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCGGUG AGGCCCCGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCCGUGGCG ((((((((((((.(((((.((.((((((((((.(((((((((((((((..&.....))))))).))).)))))..)))))))))))).)))).).)))))))))))). -90.1 GCCGCGGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCGG CCGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCCGUGGC 1&6 chr1 45 93 + chr2 78 124 + 54.44 50.81 105.25 1.0 1.0 1.0 miRNA miRNA ENST00000615959 ENST00000581792 +102 chr1 95 152 + chr2 130 180 + AGGCCCCGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCCGUGGCG GCCGCGGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCGGUG .....(((((((.(((.(((((..((((((((((((.((((.(.((((((((((((.&)))))))))))).))))).)).)))))))))).))))))))))))))).. -90.1 CCGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCCGUGGC GCCGCGGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCGG 6&1 chr1 100 146 + chr2 130 178 + 50.81 54.44 105.25 1.0 1.0 1.0 miRNA miRNA ENST00000615959 ENST00000615959 +102 chr1 152 202 + chr2 180 237 + GCCGCGGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCGGUG AGGCCCCGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCCGUGGCG ((((((((((((.(((((.((.((((((((((.(((((((((((((((..&.....))))))).))).)))))..)))))))))))).)))).).)))))))))))). -90.1 GCCGCGGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCGG CCGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCCGUGGC 1&6 chr1 152 200 + chr2 185 231 + 54.44 50.81 105.25 1.0 1.0 1.0 miRNA miRNA ENST00000581792 ENST00000615959 +102 chr1 202 259 + chr2 237 287 + AGGCCCCGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCCGUGGCG GCCGCGGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCGGUG .....(((((((.(((.(((((..((((((((((((.((((.(.((((((((((((.&)))))))))))).))))).)).)))))))))).))))))))))))))).. -90.1 CCGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCCGUGGC GCCGCGGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCGG 6&1 chr1 207 253 + chr2 237 285 + 50.81 54.44 105.25 1.0 1.0 1.0 miRNA miRNA ENST00000581792 ENST00000581792 +86 chr1 259 280 - chr2 287 310 - GCUGCGGCUGGAUGAGGCGGG CCCAGCGGGGCUGGGCGCGCGGA .((((((((.(.....(((((&))).)).....).))).))))). -18.6 CUGCGGCUGGAUGAGGCGGG CCCAGCGGGGCUGGGCGCGCGG 2&1 chr1 260 279 - chr2 287 309 - 124.00 2400.00 2524.0 1.0 1.0 1.0 CDS miRNA ENST00000338754;ENST00000398110;ENST00000403880;ENST00000442495 ENST00000584178 +65 chr1 280 298 - chr2 310 333 - GCCGCGGCGCGAGCCGGG CCCAGCGGGGCUGGGCGCGCGGA .(((((((.(.(((((((&))).....)))).))).))))). -23.9 CCGCGGCGCGAGCCGGG CCCAGCGGGGCUGGGCGCGCGG 2&1 chr1 281 297 - chr2 310 332 - 89.73 2400.00 2489.73 1.0 1.0 1.0 protein_coding miRNA ENST00000257765;ENST00000423730;ENST00000433730;ENST00000610435 ENST00000584178 +45 chr1 298 316 + chr2 333 356 - CUGGGGGCCCUUCCCGUG CCCAGCGGGGCUGGGCGCGCGGA (((.(.((((.((((((.&....))))))..)))).).))). -25.7 CUGGGGGCCCUUCCCGU GCGGGGCUGGGCGCGCGG 1&5 chr1 298 315 + chr2 337 351 - 67.94 2400.00 2467.94 1.0 0.83 0.83 lncRNA miRNA ENST00000609544 ENST00000584178 +42 chr1 316 337 - chr2 356 377 + GUUCCCUCCUCCUCCUCCCCU GUAGGGGGCGGGCUCCGGCGC ((((((.((((((.(......&).)))))).)))....))).. -15.4 GUUCCCUCCUCCUCC GUAGGGGGCGGGCUCCGGC 1&1 chr1 316 331 - chr2 356 375 + 53.16 5016.00 5069.16 1.0 1.0 1.0 lncRNA miRNA ENST00000607278 ENST00000577388 +40 chr1 337 359 + chr2 377 400 - GGCGCGCGCCGGGCCCGUGCCG CCCAGCGGGGCUGGGCGCGCGGA ..((((((((.(((((.(((..&....)))))))).)))))))).. -35.6 CGCGCGCCGGGCCCGUGC GCGGGGCUGGGCGCGCG 3&5 chr1 339 355 + chr2 381 394 - 54.01 2400.00 2454.01 1.0 0.83 0.83 CDS miRNA ENST00000369800;ENST00000522853 ENST00000584178 +35 chr1 359 377 + chr2 400 455 + CCCCGGGCCGGGCACCGC CGCGCGUGCGCCCGAGCGCGGCCCGGUGGUCCCUCCCGGACAGGCGUUCGUGCGA (((((((((((((.((((&...))).).))))......))))))).)).......................... -29.9 CCCCGGGCCGGGCACCGC GCGUGCGCCCGAGCGCGGCCCGGUGG 1&4 chr1 359 377 + chr2 403 426 + 80.76 74.37 155.13 1.0 1.0 1.0 protein_coding miRNA ENST00000343605 ENST00000614492 +35 chr1 377 395 + chr2 455 510 + CCCCGGGCCGGGCACCGC CGCGCGUGCGCCCGAGCGCGGCCCGGUGGUCCCUCCCGGACAGGCGUUCGUGCGA (((((((((((((.((((&...))).).))))......))))))).)).......................... -29.9 CCCCGGGCCGGGCACCGC GCGUGCGCCCGAGCGCGGCCCGGUGG 1&4 chr1 377 395 + chr2 458 481 + 80.76 74.37 155.13 1.0 1.0 1.0 protein_coding miRNA ENST00000343605 ENST00000577708 +34 chr1 395 413 - chr2 510 533 - GCCGCGGCGAGCCGGGCC CCCAGCGGGGCUGGGCGCGCGGA .(((((.(..(((.((((&........)))).))))))))). -22.4 CCGCGGCGAGCCGGGCC GGCUGGGCGCGCGG 2&9 chr1 396 412 - chr2 518 524 - 47.43 2400.00 2447.43 1.0 1.0 1.0 protein_coding miRNA ENST00000371984 ENST00000584178 +23 chr1 413 431 + chr2 533 556 - GGACGGGCCCUUCCCGUG CCCAGCGGGGCUGGGCGCGCGGA .(.((.((((.((((((.&....))))))..)))).)))... -22.5 GACGGGCCCUUCCCGU GCGGGGCUGGGCGCGC 2&5 chr1 414 429 + chr2 537 549 - 35.89 2400.00 2435.89 1.0 0.83 0.83 CDS miRNA ENST00000305943 ENST00000584178 +22 chr1 431 471 - chr2 556 577 + UGCCUUCCCCGUCCGUCCGUCCGUCCGUCCAUCCGUCCAC GUAGGGGGCGGGCUCCGGCGC .........((.(((...((((((((..((..........&...))))))))))..))))). -20.7 CGUCCGUCCGUCCGUCCGUCC GGGGGCGGGCUCCGGCG 10&4 chr1 440 452 - chr2 559 573 + 14510.00 5016.00 19526.0 1.0 1.0 1.0 protein_coding miRNA ENST00000356861;ENST00000425528;ENST00000450764;ENST00000589149 ENST00000577388 +20 chr1 471 510 + chr2 577 612 + CGCGACUGCGGCGGCGGUGGUGGGGGGAGCCGCGGGGAU UGGCGUCCCCUUCCCCGCCGGCCGCCUUUCUCGCG (((((..((((((((((.((.((((((.(((........&.))).)))))).)))))))).)))).....))))) -49.4 CGCGACUGCGGCGGCGGUGGUGGGGGGAGCC GGCGUCCCCUUCCCCGCCGGCCGCCUUUCUCGCG 1&2 chr1 471 502 + chr2 578 611 + 42.67 25.71 68.38 1.0 1.0 1.0 miRNA miRNA ENST00000615959 ENST00000581792 +20 chr1 510 545 + chr2 612 651 + UGGCGUCCCCUUCCCCGCCGGCCGCCUUUCUCGCG CGCGACUGCGGCGGCGGUGGUGGGGGGAGCCGCGGGGAU .(((.((((((.(((((((.(((((.....(((((&)))))..)))))))))).)).)))))).)))........ -49.4 GGCGUCCCCUUCCCCGCCGGCCGCCUUUCUCGCG CGCGACUGCGGCGGCGGUGGUGGGGGGAGCC 2&1 chr1 511 544 + chr2 612 643 + 25.71 42.67 68.38 1.0 1.0 1.0 miRNA miRNA ENST00000615959 ENST00000615959 +20 chr1 545 698 + chr2 651 674 - GACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAGAAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCGGGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCG CCCAGCGGGGCUGGGCGCGCGGA .......................................................................................................(((.(.(.((((((((..........(((.....................&)))..)))))))).).).))).. -26.5 CGCACUUGCGGCCCCGGGUUCCUCCCGGG CCCAGCGGGGCUGGGCGCGCG 104&1 chr1 648 574 + chr2 651 672 - 10610.00 2400.00 13010.0 1.0 0.83 0.83 rRNA miRNA ENST00000612463 ENST00000584178 +20 chr1 698 851 + chr2 674 697 - GACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAGAAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCGGGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCG CCCAGCGGGGCUGGGCGCGCGGA .......................................................................................................(((.(.(.((((((((..........(((.....................&)))..)))))))).).).))).. -26.5 CGCACUUGCGGCCCCGGGUUCCUCCCGGG CCCAGCGGGGCUGGGCGCGCG 104&1 chr1 801 727 + chr2 674 695 - 10610.00 2400.00 13010.0 1.0 0.83 0.83 rRNA miRNA ENST00000610460 ENST00000584178 +20 chr1 851 1004 + chr2 697 720 - GACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAGAAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCGGGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCG CCCAGCGGGGCUGGGCGCGCGGA .......................................................................................................(((.(.(.((((((((..........(((.....................&)))..)))))))).).).))).. -26.5 CGCACUUGCGGCCCCGGGUUCCUCCCGGG CCCAGCGGGGCUGGGCGCGCG 104&1 chr1 954 880 + chr2 697 718 - 10610.00 2400.00 13010.0 1.0 0.83 0.83 rRNA miRNA ENST00000613359 ENST00000584178 +20 chr1 1004 1157 + chr2 720 743 - GACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAGAAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCGGGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCG CCCAGCGGGGCUGGGCGCGCGGA .......................................................................................................(((.(.(.((((((((..........(((.....................&)))..)))))))).).).))).. -26.5 CGCACUUGCGGCCCCGGGUUCCUCCCGGG CCCAGCGGGGCUGGGCGCGCG 104&1 chr1 1107 1033 + chr2 720 741 - 10610.00 2400.00 13010.0 1.0 0.83 0.83 rRNA miRNA ENST00000619471 ENST00000584178 +20 chr1 1157 1196 + chr2 743 778 + CGCGACUGCGGCGGCGGUGGUGGGGGGAGCCGCGGGGAU UGGCGUCCCCUUCCCCGCCGGCCGCCUUUCUCGCG (((((..((((((((((.((.((((((.(((........&.))).)))))).)))))))).)))).....))))) -49.4 CGCGACUGCGGCGGCGGUGGUGGGGGGAGCC GGCGUCCCCUUCCCCGCCGGCCGCCUUUCUCGCG 1&2 chr1 1157 1188 + chr2 744 777 + 42.67 25.71 68.38 1.0 1.0 1.0 miRNA miRNA ENST00000581792 ENST00000615959 +20 chr1 1196 1231 + chr2 778 817 + UGGCGUCCCCUUCCCCGCCGGCCGCCUUUCUCGCG CGCGACUGCGGCGGCGGUGGUGGGGGGAGCCGCGGGGAU .(((.((((((.(((((((.(((((.....(((((&)))))..)))))))))).)).)))))).)))........ -49.4 GGCGUCCCCUUCCCCGCCGGCCGCCUUUCUCGCG CGCGACUGCGGCGGCGGUGGUGGGGGGAGCC 2&1 chr1 1197 1230 + chr2 778 809 + 25.71 42.67 68.38 1.0 1.0 1.0 miRNA miRNA ENST00000581792 ENST00000581792 +20 chr1 1231 1384 + chr2 817 840 - NA NA NA NA NA NA NA chr1 1231 1384 + chr2 817 840 - 10610.00 2400.00 13010.0 1.0 0.83 0.83 rRNA miRNA ENST00000611446 ENST00000584178 diff -r 000000000000 -r f28df61581f4 test-data/training_data_context_150_st_on.npz Binary file test-data/training_data_context_150_st_on.npz has changed diff -r 000000000000 -r f28df61581f4 test-data/training_data_mixed_context_100_st_on.npz Binary file test-data/training_data_mixed_context_100_st_on.npz has changed