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changeset 0:f28df61581f4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac
author iuc
date Fri, 09 Dec 2022 17:40:40 +0000
parents
children 2f7daa5d2d82
files all_fasta.loc.sample cherri_train.xml macros.xml test-data/context_150_model.tgz test-data/context_150_st_off.npz test-data/evaluation_results_st_on.csv test-data/genome.fa test-data/genome.fa.fai test-data/genome.sizes test-data/mixed_context_150_st_off.npz test-data/test_evaluate_rris.csv test-data/train_1.fa test-data/train_1_len.tabular test-data/train_1_pos.tabular test-data/train_2.fa test-data/train_2_len.tabular test-data/train_2_pos.tabular test-data/training_data_context_150_st_on.npz test-data/training_data_mixed_context_100_st_on.npz
diffstat 19 files changed, 398 insertions(+), 0 deletions(-) [+]
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--- /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):
+#
+#<unique_build_id>	<dbkey>	<display_name>	<file_path>
+#
+#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.
+#
--- /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 @@
+<tool id="cherri_train" name="Train a CheRRI model using RRIs" version="@VERSION@" profile="@PROFILE@">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        export PYTHONHASHSEED=31337 &&
+        mkdir mixed_model &&
+        #set experiments = []
+        #for $experiment in $rep_experiment:
+            mkdir $experiment.exp_name &&
+            ln -s '$experiment.ref_source.genome_fasta' '$experiment.exp_name/genome.fa' &&
+            $experiments.append(str($experiment.exp_name))
+            #set replicates = []
+            #for $i, $sample in enumerate($experiment.rep_samples):
+                ln -s '$sample.file' '$experiment.exp_name/${i}.tabular' &&
+                $replicates.append(str($i) + ".tabular")
+            #end for
+            cherri train
+            -i1 '$experiment.exp_name'
+            -r #echo ' '.join($replicates)
+            -g '$experiment.exp_name/genome.fa'
+            -l '$experiment.chrom_len_file'
+            -n '$experiment.exp_name'
+            #if $experiment.occupied_regions:
+                -i2 '$experiment.occupied_regions'
+            #end if
+            -o .
+            -on '$experiment.exp_name' 
+            @COMMONPARAMS@ &&
+            #if len($rep_experiment) > 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
+    ]]></command>
+    <inputs>
+        <repeat name="rep_experiment" title="Experiment" min="1" default="1">
+            <param name="exp_name" type="text" value="myExperiment" label="Name of the experiment" help="Only letters, numbers and underscores will be retained in this field. If more than one experiment is provided, then the tool generates a mixed model by combining datasets.">
+                <sanitizer>
+                    <valid initial="string.letters,string.digits"><add value="_" /></valid>
+                </sanitizer>
+            </param>
+            <expand macro="reference_source_conditional"/>
+            <repeat name="rep_samples" title="Interaction summary file" min="1" default="1">
+                <param name="file" type="data" format="tabular" multiple="false" label="Interaction summary file of a replicate" />
+            </repeat>
+            <param name="occupied_regions" optional="True" type="data" format="bed" label="Path to the genomic RBP crosslink or binding site locations (in BED format)" />
+        </repeat>
+        <param name="context" type="integer" value="150" label="How much context should be added at up- and downstream of each sequence" />
+        <param name="intarna_param_file" optional="True" type="data" format="txt" label="IntaRNA parameters file" />
+        <param name="use_structure" type="boolean" truevalue="on" falsevalue="off" checked="true" label="Set 'off' if you want to disable structure, default 'on'" />
+        <param name="run_time" type="integer" value="43200" label="Time used for the optimization in seconds, default: 43200 (12h)" />
+        <param name="filter_hybrid" type="boolean" truevalue="on" falsevalue="off" checked="false" label="Filter the data for hybrids already detected by ChiRA" />
+    </inputs>
+    <outputs>
+        <data name="out_model" format="tgz" from_work_dir="model.tgz" label="Trained model and features file on ${on_string}"/>
+    </outputs>
+    <tests>
+        <!-- Single experiment -st on -->
+        <test>
+            <repeat name="rep_experiment">
+                <param name="exp_name" value="myExperiment1"/>
+                <conditional name="ref_source">
+                    <param name="ref_source_selector" value="history"/>
+                    <param name="genome_fasta" value="train_1.fa"/>
+                </conditional>
+                <param name="chrom_len_file" value="train_2_len.tabular" />
+                <repeat name="rep_samples">
+                    <param name="file" value="train_1_pos.tabular" />
+                </repeat>
+                <repeat name="rep_samples">
+                    <param name="file" value="train_1_pos.tabular" />
+                </repeat>
+                <repeat name="rep_samples">
+                    <param name="file" value="train_1_pos.tabular" />
+                </repeat>
+            </repeat>
+            <param name="run_time" value="60" />
+            <output name="out_model">
+                <assert_contents>
+                    <has_size min="100000"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Single experiment -st off -->
+        <test>
+            <repeat name="rep_experiment">
+                <param name="exp_name" value="myExperiment1"/>
+                <conditional name="ref_source">
+                    <param name="ref_source_selector" value="history"/>
+                    <param name="genome_fasta" value="train_1.fa"/>
+                </conditional>
+                <param name="chrom_len_file" value="train_2_len.tabular" />
+                <repeat name="rep_samples">
+                    <param name="file" value="train_1_pos.tabular" />
+                </repeat>
+                <repeat name="rep_samples">
+                    <param name="file" value="train_1_pos.tabular" />
+                </repeat>
+                <repeat name="rep_samples">
+                    <param name="file" value="train_1_pos.tabular" />
+                </repeat>
+            </repeat>
+            <param name="run_time" value="60" />
+            <param name="use_structure" value="off" />
+            <output name="out_model">
+                <assert_contents>
+                    <has_size min="100000"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Mixed model -st on -->
+        <test>
+            <repeat name="rep_experiment">
+                <param name="exp_name" value="myExperiment1"/>
+                <conditional name="ref_source">
+                    <param name="ref_source_selector" value="history"/>
+                    <param name="genome_fasta" value="train_1.fa"/>
+                </conditional>
+                <param name="chrom_len_file" value="train_2_len.tabular" />
+                <repeat name="rep_samples">
+                    <param name="file" value="train_1_pos.tabular" />
+                </repeat>
+                <repeat name="rep_samples">
+                    <param name="file" value="train_1_pos.tabular" />
+                </repeat>
+                <repeat name="rep_samples">
+                    <param name="file" value="train_1_pos.tabular" />
+                </repeat>
+            </repeat>
+            <repeat name="rep_experiment">
+                <param name="exp_name" value="myExperiment2"/>
+                <conditional name="ref_source">
+                    <param name="ref_source_selector" value="history"/>
+                    <param name="genome_fasta" value="train_2.fa"/>
+                </conditional>
+                <param name="chrom_len_file" value="train_2_len.tabular" />
+                <repeat name="rep_samples">
+                    <param name="file" value="train_2_pos.tabular" />
+                </repeat>
+                <repeat name="rep_samples">
+                    <param name="file" value="train_2_pos.tabular" />
+                </repeat>
+                <repeat name="rep_samples">
+                    <param name="file" value="train_2_pos.tabular" />
+                </repeat>
+            </repeat>
+            <param name="run_time" value="60" />
+            <param name="context" value="100" />
+            <output name="out_model">
+                <assert_contents>
+                    <has_size min="100000"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Mixed model -st off -->
+        <test>
+            <repeat name="rep_experiment">
+                <param name="exp_name" value="myExperiment1"/>
+                <conditional name="ref_source">
+                    <param name="ref_source_selector" value="history"/>
+                    <param name="genome_fasta" value="train_1.fa"/>
+                </conditional>
+                <param name="chrom_len_file" value="train_2_len.tabular" />
+                <repeat name="rep_samples">
+                    <param name="file" value="train_1_pos.tabular" />
+                </repeat>
+                <repeat name="rep_samples">
+                    <param name="file" value="train_1_pos.tabular" />
+                </repeat>
+                <repeat name="rep_samples">
+                    <param name="file" value="train_1_pos.tabular" />
+                </repeat>
+            </repeat>
+            <repeat name="rep_experiment">
+                <param name="exp_name" value="myExperiment2"/>
+                <conditional name="ref_source">
+                    <param name="ref_source_selector" value="history"/>
+                    <param name="genome_fasta" value="train_2.fa"/>
+                </conditional>
+                <param name="chrom_len_file" value="train_2_len.tabular" />
+                <repeat name="rep_samples">
+                    <param name="file" value="train_2_pos.tabular" />
+                </repeat>
+                <repeat name="rep_samples">
+                    <param name="file" value="train_2_pos.tabular" />
+                </repeat>
+                <repeat name="rep_samples">
+                    <param name="file" value="train_2_pos.tabular" />
+                </repeat>
+            </repeat>
+            <param name="run_time" value="60" />
+            <param name="use_structure" value="off" />
+            <output name="out_model">
+                <assert_contents>
+                    <has_size min="100000"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        CheRRI in train mode to build a predictive model. Takes interactions summary files from ChiRA tool as input. Generates a model file and a features file that can be used in CheRRI eval mode.
+    ]]></help>
+    <expand macro="citations" />
+</tool>
--- /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 @@
+<macros>
+    <token name="@VERSION@">0.7</token>
+    <token name="@PROFILE@">21.05</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">cherri</requirement>
+        </requirements>
+    </xml>
+    <macro name="reference_source_conditional">
+        <conditional name="ref_source">
+            <param name="ref_source_selector" type="select" label="Reference genome in FASTA format">
+                <option value="cached">locally cached</option>
+                <option value="history">in your history</option>
+            </param>
+            <when value="cached">
+                <param name="genome_fasta" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
+                    <options from_data_table="all_fasta">
+                        <filter type="sort_by" column="2" />
+                        <validator type="no_options" message="No indices are available." />
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="genome_fasta" type="data" format="fasta" label="Select a reference dataset in FASTA format" />
+            </when>
+        </conditional>
+        <param name="chrom_len_file" type="data" format="tabular" label="Two column tabular file containing chromosome lengths" help="Format: 'chrom name' \t 'chrom length'" />        
+    </macro>
+    <token name="@COMMONPARAMS@" ><![CDATA[
+            #if $intarna_param_file: 
+                -p '$intarna_param_file'
+            #end if
+            -c '$context'
+            -st $use_structure
+            -t '$run_time'
+            -me "\${GALAXY_MEMORY_MB_PER_SLOT:-8000}"
+            -j "\${GALAXY_SLOTS:-1}"
+        ]]></token>
+    <xml name="edam_ontology">
+        <edam_topics>
+            <edam_topic>topic_0080</edam_topic>
+            <edam_topic>topic_0081</edam_topic>
+            <edam_topic>topic_0160</edam_topic>
+        </edam_topics>
+        <edam_operations>
+            <edam_operation>operation_2995</edam_operation>
+        </edam_operations>
+    </xml>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">cherri</xref>
+        </xrefs>
+    </xml>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">cherri</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <yield />
+        </citations>
+    </xml>
+</macros>
Binary file test-data/context_150_model.tgz has changed
Binary file test-data/context_150_st_off.npz has changed
--- /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 @@
+target_ID,query_ID,instance_score,predicted_label,E_hybrid,ED1,ED2,len_interaction_target,len_interaction_query,no_bps,max_inter_len,inter_len_normby_bp,bp_normby_inter_len,sum_ED,mfe_normby_GC,max_ED_normby_GC,mfe_normby_len,max_ED_normby_len,max_ED_normby_GC_len,complex_target_site,complex_query_site,103,218,3965,4390,4479,5431,5795,6434,6626,6635,7552,7808,8077,8174,11632,14000,15997,18340,19158,20963,21262,21694,27390,29287,29554,32863,33178,33547,34282,34422,34488,37176,37477,37532,38032,38039,38210,38612,38772,39174,40128,40201,40431,40441,41157,41484,42542,42839,43658,44532,45157,46069,46829,47317,49554,49956,52245,52435,53754,54604,56416,56450,56861,57646,59007,59023,59235,60144,60775,61153,61593,62084,62119,62321,63264,63533,63886,64400,66975,68842,69673,70066,70539,70993,71500,72034,72770,72893,76620,77916,79250,81006,83486,83553,84211,84686,85177,88601,88775,89371,89540,89800,91132,96396,96533,99879,100150,100319,101025,102113,102117,102491,104186,104635,105777,106659,107362,107877,110927,111135,111913,112240,113099,113123,115953,116421,116995,117587,118534,118785,119888,119955,120357,121948,123283,123341,125626,125838,126094,126867,128188,128428,130250,130651,131729,131834,133411,133417,134749,135445,135610,136332,136664,137596,139199,140424,141658,143218,143223,144347,144588,146175,146217,148182,148717,148840,148968,150801,150956,151321,152152,152399,152543,153917,154459,154546,154657,155274,156328,156681,157727,158027,158053,158868,159127,159265,162328,162485,163775,165891,166307,166970,167231,167372,167583,167628,167961,167971,168188,168851,169312,170207,170500,170699,172282,172357,173965,174219,174727,174947,179377,181689,181814,182942,183668,184345,184806,185260,185297,185808,186013,186285,186857,186871,187824,187840,189082,192986,193099,193860,194876,195156,195170,195325,195449,196564,197600,197675,199001,199931,200065,200863,201409,203349,204997,206423,206678,207027,207715,210220,210871,212552,212616,214127,214790,215521,215789,216063,217850,217874,218567,219482,220128,220256,220427,221245,222067,222931,223613,223729,224656,225488,226419,227603,229088,229857,230101,231806,231841,231882,232458,233010,234231,234297,234449,234564,235569,237392,239574,241915,242858,246680,247158,247200,248248,249295,250145,251764,251957,252112,252166,252543,252640,254243,255793,257183,257455,258465,258994,259160,259568,259702,261161
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--- /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
+GGCUCAGGGAAGGACGACAGCUCCCGGCUCAGUCCUCAGCCUCCAACCCCCACUCUUCAAUCUCCUUCCCAGACCAAUGACCCCCUCUGCGGGAGAACCUGCGGCGAAAGGCAGAGCCCCAGAGCAGGGUCUGGAGUGGCAGGACCGGCAGCCAAUGAAGGUGAAGGCCGAGCAUUACAUCAUCACCGUGGUCUCCCAUUGGUUUACAUCCUGGGCUUCCUGACUCCGCCUCCCAGCCUUAACAAUGGGCCUCUCUGCUCCCCAGGCUUCUGACCCUGGUGCCAGCUUUGCCCAGAAGGCCACAGUCGGGCAGAGUCCUGGACUUUUGCAAAGCAAACGUGCAACCCCAAGCAGCGGUCUCCCGGGCCGGGGCUGCGCGGCCGCCGCUGUGCUGGCUUUUAACGGUGGGAGGGCACCAUCCUCUUGCUCUGCUCUCGUUCUCCAGAAGGCUGUCCCGGGGCCCCCACUCUCCGUCCCGCUCCGGGGACAGUGGCUCGCCUGCUAUGCGCGGCAGCCCGCGCCGGGGCCGGCACCAGCAGCGCCCGGGCGGAUGCAGCGAGCCCACGGAGGGGCAUGCUUCCACGCACCAAGUAUAACCGCUUCAGGAAUGACUCGGUGACAUCGGUCGAUGACCUUCUCCACAGCAUUCCCAUCCAAGUCCGGGUGGGCAGGUGGCUCUUGCCCCUUGGAUUGAGGAGCACGGGGGUCAGCCUCACGGCCCAGGGUGGCCGGCGCCAGCUAAUGAGGCUGUGGUCCCGCAGGAGCUGUUCCCCUCGCGUCAGGAGAAGCUCUACCCGGGCUGGGCGCGCGCCGCCUGUGUGCUGCUGUCCUUGCUGCCCGUGCUGUGGGUCCCGGUGGCCGCGCUUGCUCAGCUGCUCACCCGGCGGAGGCGGACGUGGAGGGACAGGGACGCGCGCCCAGACACGGACAUGCGCCCGGACACGGACACGCGCCCAGACACGGACAAGUUCCGUUUAUGGUCUGAUUUCCGGCCUCUCGCCUGCUCGCCCCGCCGCCCGCCUGUCCCGCUCCCUCCCUCCCGGGGACCCGGAGGAGAGGGGACCAUGCCGGAACCCGGGCCGGACGCUGCCGGCACCGCCAGCGCACAGCCCCAACCGCCGCCGCCCCCCCCACCCGCUCCCAAGGAGUCCCCGUUCUCCAUCAAGAACCUGCUCAACGGAGACCACCACCGGCCGCCCCCUAAGCCUCAGCCGCCCCCACGGACGCUCUUCGCGCCAGCCUCGGCUGCCGCCGCCGCCGCCGCUGCCGCUGCCGCGGCGGCCAAGCAGGGCCUGGUGGCGAGAGCGCGGCUGUCACUGCGCCCGAGCAUCCCAGAGCUUUCCGAGCGGACGAGCCGGCCGUGCCGGGCAUCCCCAGCCUCGCUACCCUCGCAGCACACGUCGAGCCCCGCACAGGCGAGGGUCCGGAACUUAGCCCAAAGCACGUUUCCCCUGGCAGCGCAGGAAACGCCCGGCCGCGCGCCGGCGCACGCCCCCCUCUCCUCCUUUGUUCCGGGGGUCGGCGGCCGCUCUCCUGCCAGCGUCGGGAUCUCGGCCCCGGGAGGCGGGCCGUCGGGCGCAGCCGCGAAGAUGCCGUUGGAACUGACGCAGAGCCGAGUGCAGAAGAUCUGGGUGCCCGUGGACCACGGACUACACUUCCCAGGAUGCGUCGGGGGAAGAGGCCACAGGGACAGGCAGAGGGAGGGGGCGGCCCCAGUCCUCCGGGGCGUCGCUGUUUCCAAGCGGCGAGAUCUCGCCUAGUAACCGGCAGCUGAGGUUCACUAGCGCGGCGUUGUGGCCCCGCCCCCGGAGCCCCGGCUGGAGGAAGAACCUGUCUCCCGCGGCGCCCCAGUGACGAAGUCCAUCCCCGGGUGCGGGAGGCGGGGAGGGGAGGGCAGGCAGAGGAUUUCGCUCGCUCGCCCGCGCGGGAUCCGGGACGCGCCGGUGGCGUCCGCUGGCAGCAGAGGCUCAGCCCCGACAAGGCGGCCGAGGUGCUGAGCCAGGGCGCUCACCUGGCGGCCGGGCCCGACGGCCGGACCAUCGACCGUUUCUCUCCCACCUAGAGCGCCCCUCGCCAGCCCGCUCUGUCGCUGCUGCGCGGCCCUGGCCCGCACCCCAGGGAGCGGCGGGGGCGGCGCGCAGGGCCCACUGUGCCCGGGACAACCGCAGCGUCGCCACAGUGGCGGCUCCACCUCUCGGCGGCCUCACCUGGCCUCACUGCUUCGUGCCUUAGCUCGGGGGUCGGGGGAGAACCCCGGGACGGGGGUGGGAUGGGGUAAGGGAAAUUUAUA
+>chr2
+CAGUCACCACCUCACACAUGAGGAAGCUGAGGCUGGAGACUUAGGUGACCUGGCCUAGAGUUUCAGGGCGCCGGGAUCCUGUCGAAGGUCCCACCCACCUGGCUCUGCUGCAGCGCCCUCUCUCUGUCCUCUAGGUGUGUUUGGUGGCCGGGGCCGAGGUGGGAUCCCGGGCACAGGCAGAGGCCAGCCAGAGAAGAAGCCUGGCAGACAGGCGGGCAAACAGUGAGCGCCCACCCAGACCGGCUGCUGCGCCCCCUCCUGCCAGGGUGGCGAUUCCGCUCCACAGUCUCGGACGGAUCUGCUCAGAAAGGAAGAGGCAGGUCUGGCACGGUGAAGAGACGUGAGAGGUGUAGAAUAAGUGGGAGGCCCCCGGCGCCCCCCGGUGUCCCCGCGAGGGGUCCAGGGCGGGGUCUGCCGGCCCUGCGGGCCGCCGGUGAAAUACCACUACUCUGAUCGUUUUUUCACUGACCCGGUGAGGCGGGGGGGCGAGCCCUGAGGGGCUCUCGCUUCUGGCGCCAAGCGCCCGGCCGCACGCAAAAGAGCUCCUGAAGGAAGCGCUAAACAUGGAAAGGAACAACGGGUACCAGCCGCUGCAAAAUCAUGCCAAAAUGUAAAGACCAUCGAGACUAGGAAGAAACUGCAUCAACUAACGAGCAAAAUCACCAGCUAAAGUUCCGUUUAUGGUCUGAUUUCCGGCCUCUCGCCUGCUCGCCCCGCCGCCCGCCUGUCCCGCUCCCUCCCUCCCGGGGACCCGGAGGAGAGGGGACCAUGCCGGAACCCGGGCCGGACGCUGCCGGCACCGCCAGCGCACAGCCCCAACCGCCGCCGCCCCCCCCACCCGCUCCCAAGGAGUCCCCGUUCUCCAUCAAGAACCUGCUCAACGGAGACCACCACCGGCCGCCCCCUAAGCCUCAGCCGCCCCCACGGACGCUCUUCGCGCCAGCCUCGGCUGCCGCCGCCGCCGCCGCUGCCGCUGCCGCGGCGGCCAAGCAGGCAUGCGCUGCCUAGCCCCGUGUGGUUAACAUGUCCGUAUUUAAAGAACACACAAUUAAUUGCCUAAAAGCAUUAUCCUUCUCAGCACUCUCCUAUCCUUCAGAUCUAACCUUUAGGCACUGCCGGCUGCCGGCGGGGUCCAGGACCCAGCGGGGCUGGGCGCGCGGAGCAGCGCUGGGUGCAGCGCCUGCGCCGGCAGCUGCAAGGGCCGCAGAAAUUAAACGCGAGUGUCCAGAAUCGGGCAUUGUGGGUUUAAAUCCUGAAUCCACUGGUCACUAUCUGAGACUUUCCCCUGUCACAAAUUAGUUACCUUCUUACUUUUGCAAAGCAAACGUGCAACCCCAAGCAGCGGUCUCCCGGGCCGGGGCUGCGCGGCCGCCGCUGUGCUGGCUUUUAACGGUGGGAGGGCACCAUCCUCUUGCUCUGCUCUCGUUCUCCAGAAGGCUGUCCCGGGGCCCCCACUCUCCGUCCCGCUCCGGGGACAGUGGCUCGCCUGCUAUGCGCGGCAGCCCGCGCCGGGGCCGGCACCAGCAGCGCCCGGGCGGAUGCAGCGAGCCCACGGAGGGGCAUGCUUCCACGCACCAAGUAUAACCGCUUCAGGAAUGACUCGGUGACAUCGGUCGAUGACCUUCUCCACAGGCCUUGGCCCCGCCCCCGCCGCCGCGCAGGCGCUGACGCAAGCGCAGCAGGCGCGCGCUGUUUCCGGAAGUCGCGGCCGGCGUCACCGCUGCGGCUGCCUCAGCUACUGCCGCAGUCGCCGCGGAAUUCGGCGAGUAGAACCGCUGAGGCGGGCGCGGGCCCGGGUGGGGCCAAGGUUCCGGCCACUCUGCAGAAUGGAGAUAAUCAGGAGCAGUGCGUGUCCGCCGUACACCUCCCCGCCUCCCCACACCCGGCUGCCCCUGGCCUGCUAGGCCGAGACCAUGGCCGGCGUGUUUGGCUGGGCCUGGGGCUGAGGCAGCCCUGUUGUGUAUCACUCACUGAGGCUGGACAAGAGGGAAGGCGGAGAAGCCUGGCCACAUGUCUCCUGAGGGCUCCAGGCAGGGCCCUCUCACCUGCUGCCAGGGUCCCAGCCCGCAGGAGCUUCCCGUCCACCUCUGAACUCACGGUCCACAUGGCGCUGGAGCGUCGGGCACCAUCUACAGGGCUUGAGGCCAGCAGCCUAGCCUCUGGGUCCACUGGGGCAGGCAAGGUGAGUCCUGCUGUCUGUGGAGCCAGCGUGCUGGGCCGGGCAGGGGGCCUCGUUGGCUGGGGUGGCUGCAGCUCCGCCCUGCCUGGGGCAUU
--- /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
--- /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
Binary file test-data/mixed_context_150_st_off.npz has changed
--- /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,+
--- /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
--- /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
--- /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
--- /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
--- /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
--- /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
Binary file test-data/training_data_context_150_st_on.npz has changed
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