# HG changeset patch
# User iuc
# Date 1670607627 0
# Node ID 7c6c282ecf5a52bb01c4fff74f06522abe89ed2b

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri commit f9348123725f421ddbdbd8d372d038da4880dbac

diff -r 000000000000 -r 7c6c282ecf5a all_fasta.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/all_fasta.loc.sample	Fri Dec 09 17:40:27 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.
+#
diff -r 000000000000 -r 7c6c282ecf5a cherri_eval.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cherri_eval.xml	Fri Dec 09 17:40:27 2022 +0000
@@ -0,0 +1,87 @@
+<tool id="cherri_eval" name="Evaluation of RRIs using CheRRI" version="@VERSION@" profile="@PROFILE@">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        export PYTHONHASHSEED=31337 &&
+        ln -s '$ref_source.genome_fasta' genome.fa &&
+        mkdir model_dir &&
+        tar -C model_dir -xvf '$model_tar' > /dev/null &&
+        cherri eval 
+        -i1 '$rris_table'
+        -g genome.fa
+        -l '$chrom_len_file'
+        -o . 
+        -on cherri_eval
+        -c '$context'
+        -st $use_structure
+        -hf $hand_feat
+        -m 'model_dir/final_full.model'
+        -mp 'model_dir/features.npz'
+        #if $occupied_regions:
+            -i2 '$occupied_regions'
+        #end if
+        #if $intarna_param_file:
+            -p '$intarna_param_file'
+        #end if
+    ]]></command>
+    <inputs>
+        <param name="rris_table" type="data" format="csv" label="CSV file containing all RRIs that should be evaluated" />
+        <expand macro="reference_source_conditional"/>
+        <param name="model_tar" type="data" format="tgz" label="Model and feature files in a tar" />
+        <param name="context" type="integer" value="150" label="How much context should be added at up- and downstream of each sequence" />
+        <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="hand_feat" type="boolean" truevalue="on" falsevalue="off" checked="false" label="If you want to start from hand-curated feature files, use this for evaluating test set performance. Default: 'off'" />
+        <param name="occupied_regions" optional="True" type="data" format="binary" label="Occupied regions python object file containing a dictionary" />
+        <param name="intarna_param_file" optional="True" type="data" format="txt" label="IntaRNA parameters file" />
+    </inputs>
+    <outputs>
+        <data name="eval_out" format="csv" from_work_dir="cherri_eval/evaluation/evaluation_results_eval_rri.csv" label="Evaluation results on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="rris_table" value="test_evaluate_rris.csv"/>
+            <conditional name="ref_source">
+                <param name="ref_source_selector" value="history"/>
+                <param name="genome_fasta" value="genome.fa"/>
+            </conditional>  
+            <param name="chrom_len_file" value="genome.sizes" />
+            <param name="model_tar" value="context_150_model.tgz" />
+            <output name="eval_out" file="evaluation_results_st_on.csv"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**What it does**
+
+CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm, by removing false positive interactions.
+
+**Inputs**
+        
+CheRRI takes a table of RNA-RNA interactions. It supports output of ChiRA or a csv files of interactions in the following format. The table needs the following header line:
+        
+    `chrom1,start1,stop1,strand1,chrom2,start2,stop2,strand2`
+        
+Following the header line, each subsequent line represents an RRI, with chromosome ID (format: 1,2,3 ...), interaction start, interaction end, and strand ("+" or "-") of the two interacting partners. For example, you might want to evaluate the following three RRI sites::
+        
+    19,18307518,18307539,-,14,90454500,90454521,+
+    X,109054541,109054590,+,9,89178539,89178562,-
+    10,123136102,123136122,+,5,1245880,1245902,+
+
+The tool also additionally takes a genome FASTA file and a chromosome lengths file. User can select an in-built FASTA or a FASTA file from history.
+A chromosome legths file is tabular file where each line contains a tab separated chromosome name and its length. Followin is an example:
+
+    chr1    23200231
+    chr2    12497572
+    chr3    8387920
+
+CheRRI also needs a model file (in binary format). It can be generated by using CheRRI train tool.
+
+**Outputs**
+
+This tool outputs a tabular file containing predictions for each input interaction.
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff -r 000000000000 -r 7c6c282ecf5a macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Dec 09 17:40:27 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>
diff -r 000000000000 -r 7c6c282ecf5a test-data/context_150_model.tgz
Binary file test-data/context_150_model.tgz has changed
diff -r 000000000000 -r 7c6c282ecf5a test-data/context_150_st_off.npz
Binary file test-data/context_150_st_off.npz has changed
diff -r 000000000000 -r 7c6c282ecf5a 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 17:40:27 2022 +0000
@@ -0,0 +1,6 @@
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diff -r 000000000000 -r 7c6c282ecf5a test-data/genome.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome.fa	Fri Dec 09 17:40:27 2022 +0000
@@ -0,0 +1,4 @@
+>chr1
+GGCUCAGGGAAGGACGACAGCUCCCGGCUCAGUCCUCAGCCUCCAACCCCCACUCUUCAAUCUCCUUCCCAGACCAAUGACCCCCUCUGCGGGAGAACCUGCGGCGAAAGGCAGAGCCCCAGAGCAGGGUCUGGAGUGGCAGGACCGGCAGCCAAUGAAGGUGAAGGCCGAGCAUUACAUCAUCACCGUGGUCUCCCAUUGGUUUACAUCCUGGGCUUCCUGACUCCGCCUCCCAGCCUUAACAAUGGGCCUCUCUGCUCCCCAGGCUUCUGACCCUGGUGCCAGCUUUGCCCAGAAGGCCACAGUCGGGCAGAGUCCUGGACUUUUGCAAAGCAAACGUGCAACCCCAAGCAGCGGUCUCCCGGGCCGGGGCUGCGCGGCCGCCGCUGUGCUGGCUUUUAACGGUGGGAGGGCACCAUCCUCUUGCUCUGCUCUCGUUCUCCAGAAGGCUGUCCCGGGGCCCCCACUCUCCGUCCCGCUCCGGGGACAGUGGCUCGCCUGCUAUGCGCGGCAGCCCGCGCCGGGGCCGGCACCAGCAGCGCCCGGGCGGAUGCAGCGAGCCCACGGAGGGGCAUGCUUCCACGCACCAAGUAUAACCGCUUCAGGAAUGACUCGGUGACAUCGGUCGAUGACCUUCUCCACAGCAUUCCCAUCCAAGUCCGGGUGGGCAGGUGGCUCUUGCCCCUUGGAUUGAGGAGCACGGGGGUCAGCCUCACGGCCCAGGGUGGCCGGCGCCAGCUAAUGAGGCUGUGGUCCCGCAGGAGCUGUUCCCCUCGCGUCAGGAGAAGCUCUACCCGGGCUGGGCGCGCGCCGCCUGUGUGCUGCUGUCCUUGCUGCCCGUGCUGUGGGUCCCGGUGGCCGCGCUUGCUCAGCUGCUCACCCGGCGGAGGCGGACGUGGAGGGACAGGGACGCGCGCCCAGACACGGACAUGCGCCCGGACACGGACACGCGCCCAGACACGGACAAGUUCCGUUUAUGGUCUGAUUUCCGGCCUCUCGCCUGCUCGCCCCGCCGCCCGCCUGUCCCGCUCCCUCCCUCCCGGGGACCCGGAGGAGAGGGGACCAUGCCGGAACCCGGGCCGGACGCUGCCGGCACCGCCAGCGCACAGCCCCAACCGCCGCCGCCCCCCCCACCCGCUCCCAAGGAGUCCCCGUUCUCCAUCAAGAACCUGCUCAACGGAGACCACCACCGGCCGCCCCCUAAGCCUCAGCCGCCCCCACGGACGCUCUUCGCGCCAGCCUCGGCUGCCGCCGCCGCCGCCGCUGCCGCUGCCGCGGCGGCCAAGCAGGGCCUGGUGGCGAGAGCGCGGCUGUCACUGCGCCCGAGCAUCCCAGAGCUUUCCGAGCGGACGAGCCGGCCGUGCCGGGCAUCCCCAGCCUCGCUACCCUCGCAGCACACGUCGAGCCCCGCACAGGCGAGGGUCCGGAACUUAGCCCAAAGCACGUUUCCCCUGGCAGCGCAGGAAACGCCCGGCCGCGCGCCGGCGCACGCCCCCCUCUCCUCCUUUGUUCCGGGGGUCGGCGGCCGCUCUCCUGCCAGCGUCGGGAUCUCGGCCCCGGGAGGCGGGCCGUCGGGCGCAGCCGCGAAGAUGCCGUUGGAACUGACGCAGAGCCGAGUGCAGAAGAUCUGGGUGCCCGUGGACCACGGACUACACUUCCCAGGAUGCGUCGGGGGAAGAGGCCACAGGGACAGGCAGAGGGAGGGGGCGGCCCCAGUCCUCCGGGGCGUCGCUGUUUCCAAGCGGCGAGAUCUCGCCUAGUAACCGGCAGCUGAGGUUCACUAGCGCGGCGUUGUGGCCCCGCCCCCGGAGCCCCGGCUGGAGGAAGAACCUGUCUCCCGCGGCGCCCCAGUGACGAAGUCCAUCCCCGGGUGCGGGAGGCGGGGAGGGGAGGGCAGGCAGAGGAUUUCGCUCGCUCGCCCGCGCGGGAUCCGGGACGCGCCGGUGGCGUCCGCUGGCAGCAGAGGCUCAGCCCCGACAAGGCGGCCGAGGUGCUGAGCCAGGGCGCUCACCUGGCGGCCGGGCCCGACGGCCGGACCAUCGACCGUUUCUCUCCCACCUAGAGCGCCCCUCGCCAGCCCGCUCUGUCGCUGCUGCGCGGCCCUGGCCCGCACCCCAGGGAGCGGCGGGGGCGGCGCGCAGGGCCCACUGUGCCCGGGACAACCGCAGCGUCGCCACAGUGGCGGCUCCACCUCUCGGCGGCCUCACCUGGCCUCACUGCUUCGUGCCUUAGCUCGGGGGUCGGGGGAGAACCCCGGGACGGGGGUGGGAUGGGGUAAGGGAAAUUUAUA
+>chr2
+CAGUCACCACCUCACACAUGAGGAAGCUGAGGCUGGAGACUUAGGUGACCUGGCCUAGAGUUUCAGGGCGCCGGGAUCCUGUCGAAGGUCCCACCCACCUGGCUCUGCUGCAGCGCCCUCUCUCUGUCCUCUAGGUGUGUUUGGUGGCCGGGGCCGAGGUGGGAUCCCGGGCACAGGCAGAGGCCAGCCAGAGAAGAAGCCUGGCAGACAGGCGGGCAAACAGUGAGCGCCCACCCAGACCGGCUGCUGCGCCCCCUCCUGCCAGGGUGGCGAUUCCGCUCCACAGUCUCGGACGGAUCUGCUCAGAAAGGAAGAGGCAGGUCUGGCACGGUGAAGAGACGUGAGAGGUGUAGAAUAAGUGGGAGGCCCCCGGCGCCCCCCGGUGUCCCCGCGAGGGGUCCAGGGCGGGGUCUGCCGGCCCUGCGGGCCGCCGGUGAAAUACCACUACUCUGAUCGUUUUUUCACUGACCCGGUGAGGCGGGGGGGCGAGCCCUGAGGGGCUCUCGCUUCUGGCGCCAAGCGCCCGGCCGCACGCAAAAGAGCUCCUGAAGGAAGCGCUAAACAUGGAAAGGAACAACGGGUACCAGCCGCUGCAAAAUCAUGCCAAAAUGUAAAGACCAUCGAGACUAGGAAGAAACUGCAUCAACUAACGAGCAAAAUCACCAGCUAAAGUUCCGUUUAUGGUCUGAUUUCCGGCCUCUCGCCUGCUCGCCCCGCCGCCCGCCUGUCCCGCUCCCUCCCUCCCGGGGACCCGGAGGAGAGGGGACCAUGCCGGAACCCGGGCCGGACGCUGCCGGCACCGCCAGCGCACAGCCCCAACCGCCGCCGCCCCCCCCACCCGCUCCCAAGGAGUCCCCGUUCUCCAUCAAGAACCUGCUCAACGGAGACCACCACCGGCCGCCCCCUAAGCCUCAGCCGCCCCCACGGACGCUCUUCGCGCCAGCCUCGGCUGCCGCCGCCGCCGCCGCUGCCGCUGCCGCGGCGGCCAAGCAGGCAUGCGCUGCCUAGCCCCGUGUGGUUAACAUGUCCGUAUUUAAAGAACACACAAUUAAUUGCCUAAAAGCAUUAUCCUUCUCAGCACUCUCCUAUCCUUCAGAUCUAACCUUUAGGCACUGCCGGCUGCCGGCGGGGUCCAGGACCCAGCGGGGCUGGGCGCGCGGAGCAGCGCUGGGUGCAGCGCCUGCGCCGGCAGCUGCAAGGGCCGCAGAAAUUAAACGCGAGUGUCCAGAAUCGGGCAUUGUGGGUUUAAAUCCUGAAUCCACUGGUCACUAUCUGAGACUUUCCCCUGUCACAAAUUAGUUACCUUCUUACUUUUGCAAAGCAAACGUGCAACCCCAAGCAGCGGUCUCCCGGGCCGGGGCUGCGCGGCCGCCGCUGUGCUGGCUUUUAACGGUGGGAGGGCACCAUCCUCUUGCUCUGCUCUCGUUCUCCAGAAGGCUGUCCCGGGGCCCCCACUCUCCGUCCCGCUCCGGGGACAGUGGCUCGCCUGCUAUGCGCGGCAGCCCGCGCCGGGGCCGGCACCAGCAGCGCCCGGGCGGAUGCAGCGAGCCCACGGAGGGGCAUGCUUCCACGCACCAAGUAUAACCGCUUCAGGAAUGACUCGGUGACAUCGGUCGAUGACCUUCUCCACAGGCCUUGGCCCCGCCCCCGCCGCCGCGCAGGCGCUGACGCAAGCGCAGCAGGCGCGCGCUGUUUCCGGAAGUCGCGGCCGGCGUCACCGCUGCGGCUGCCUCAGCUACUGCCGCAGUCGCCGCGGAAUUCGGCGAGUAGAACCGCUGAGGCGGGCGCGGGCCCGGGUGGGGCCAAGGUUCCGGCCACUCUGCAGAAUGGAGAUAAUCAGGAGCAGUGCGUGUCCGCCGUACACCUCCCCGCCUCCCCACACCCGGCUGCCCCUGGCCUGCUAGGCCGAGACCAUGGCCGGCGUGUUUGGCUGGGCCUGGGGCUGAGGCAGCCCUGUUGUGUAUCACUCACUGAGGCUGGACAAGAGGGAAGGCGGAGAAGCCUGGCCACAUGUCUCCUGAGGGCUCCAGGCAGGGCCCUCUCACCUGCUGCCAGGGUCCCAGCCCGCAGGAGCUUCCCGUCCACCUCUGAACUCACGGUCCACAUGGCGCUGGAGCGUCGGGCACCAUCUACAGGGCUUGAGGCCAGCAGCCUAGCCUCUGGGUCCACUGGGGCAGGCAAGGUGAGUCCUGCUGUCUGUGGAGCCAGCGUGCUGGGCCGGGCAGGGGGCCUCGUUGGCUGGGGUGGCUGCAGCUCCGCCCUGCCUGGGGCAUU
diff -r 000000000000 -r 7c6c282ecf5a test-data/genome.fa.fai
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome.fa.fai	Fri Dec 09 17:40:27 2022 +0000
@@ -0,0 +1,2 @@
+chr1	2290	6	2290	2291
+chr2	2274	2303	2274	2275
diff -r 000000000000 -r 7c6c282ecf5a test-data/genome.sizes
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome.sizes	Fri Dec 09 17:40:27 2022 +0000
@@ -0,0 +1,2 @@
+chr1	2292
+chr2	2276
diff -r 000000000000 -r 7c6c282ecf5a test-data/mixed_context_150_st_off.npz
Binary file test-data/mixed_context_150_st_off.npz has changed
diff -r 000000000000 -r 7c6c282ecf5a 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 17:40:27 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 7c6c282ecf5a test-data/train_1.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/train_1.fa	Fri Dec 09 17:40:27 2022 +0000
@@ -0,0 +1,4 @@
+>chr1
+CCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCCGUGGCGGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCGGUGCCGCGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCCGUGGCGGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCGGUGCCGGGUGAGGCGGGGGGGCGAGCCCUGAGGGGCUCUCGCUUCUGGCGCCAAGCCCAGCGGGGCUGGGCGCGCGGAGUAGGGGGCGGGCUCCGGCGCUGCCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACGCGCGUGCGCCCGAGCGCGGCCCGGUGGUCCCUCCCGGACAGGCGUUCGUGCGACGUGUGCGCGCGUGCGCCCGAGCGCGGCCCGGUGGUCCCUCCCGGACAGGCGUUCGUGCGACGUGUGCCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGANANANANACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGAAGGGAGAAGGGUCGGGGCAGGGCCCCGGGGAGCCCGGCGGCCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGAGUAGGGGGCGGGCUCCGGCGCUGCCCAGCGGGGCUGGGCGCGCGGAGUAGGGGGCGGGCUCCGGCGCUGCCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGANACCCCGGGGAGCCCGGCGGGUAGGGGGCGGGCUCCGGCGCUGCCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGAGGUGAGGCGGGGGGGCGAGCCCUGAGGGGCUCUCGCUUCUGGCGCCAAGGGUGAGGCGGGGGGGCGAGCCCUGAGGGGCUCUCGCUUCUGGCGCCAAGAGGGAGAAGGGUCGGGGCAGGGGUAGGGGGCGGGCUCCGGCGCUGCCCAGCGGGGCUGGGCGCGCGGACCCCGGGGAGCCCGGCGGCCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGAGUAGGGGGCGGGCUCCGGCGCUGCGGAUCCGAGUCACGGCACCAAACCCAGCGGGGCUGGGCGCGCGGAGUAGGGGGCGGGCUCCGGCGCUGGUAGGGGGCGGGCUCCGGCGCUGGUAGGGGGCGGGCUCCGGCGCUGGUAGGGGGCGGGCUCCGGCGCUGCCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCA
+>chr2
+GUUGCGGCUGGACGAGGCGCAGUGGCCGCGGCGCGAGCCGGGGGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCGGUGCCGCGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCCGUGGCGGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCGGUGCCGCGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCCGUGGCACUGGUGAAGAGACAUGAGAGGAUGGGCGCGCGCCGGGCCCGUGCCGUUCCCUCCUCCUCCUCCCCUGCCGCGGCGAGCCGGGCCCUGGGGGCCCUUCCCGUGCGCGGGCGAGCCGGGCCCGAUGCCUUCCCCGUCCGUCCGUCCGUCCGUCCAUCCGUCCACCCCCGGGCCGGGCACCGCCCCCGGGCCGGGCACCGCGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAGAAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCGGGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAGAAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCGGGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAGAAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCGGGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAGAAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCGGGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGNANANANAGGACGGGCCCUUCCCGUGGCGCUGCGCGAGCCGGGCGCUGCGGCUGGAUGAGGCGCUCGCCCUCUCUCUCUCUCUCUCUGUCUCUCUCUCUCUCUGGAGCCGGGGGGGGGGGGGGGGGGGGGGGGGGGCAGGCGGCGCCGCCGCCCUCUCCCACCCCAGAAAAGGUGUUGGUUGAUAUAGACAGCAGGACGGUGGCCAUGGAAGUCAGAAUCCACUAAGGAGUGUGUAACAACUCACCUGCCGAAUCAACUAGCCCUGAAAAUGGAUGGCACUGGAGCAUCAGGCCCAUACCCGGCCAUCGCCAGCAGUCCGGCCGCCGCGGCGCGCGCCCGGGUCCCCCGCCGCCCCUCCGGUGCUCCCUCCCCACCCCGCAGUGAUGCCUUCCCCGUCCGUCCGUCCGUCCGUCCAUCCGUCCACGCCUCCCUCCCCACCCCGCGAGCCUCCCUCCCCACCCCGCGAGCCUCCCUCCCCACCCCGCGAGCCUCCCUCCCCACCCCGCGAGCCUCCCUCCCCACCCCGCGAAUACUUACCUGGCAGGGGAGAUACCAUGAUCACGAAGGUGGUUUUCCCAGGGCGAGGCUUAUCCAUUGCACUC
diff -r 000000000000 -r 7c6c282ecf5a 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 17:40:27 2022 +0000
@@ -0,0 +1,2 @@
+chr1	1888
+chr2	1652
diff -r 000000000000 -r 7c6c282ecf5a 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 17:40:27 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 7c6c282ecf5a test-data/train_2.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/train_2.fa	Fri Dec 09 17:40:27 2022 +0000
@@ -0,0 +1,4 @@
+>chr1
+CCCAGCGGGGCUGGGCGCGCGGAGGUGAGGCGGGGGGGCGAGCCCUGAGGGGCUCUCGCUUCUGGCGCCAAGAGGCCCCGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCCGUGGCGGCCGCGGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCGGUGAGGCCCCGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCCGUGGCGGCCGCGGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCGGUGCCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGAGUAGGGGGCGGGCUCCGGCGCCCCAGCGGGGCUGGGCGCGCGGACGCGCGUGCGCCCGAGCGCGGCCCGGUGGUCCCUCCCGGACAGGCGUUCGUGCGACGCGCGUGCGCCCGAGCGCGGCCCGGUGGUCCCUCCCGGACAGGCGUUCGUGCGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGAGUAGGGGGCGGGCUCCGGCGCUGGCGUCCCCUUCCCCGCCGGCCGCCUUUCUCGCGCGCGACUGCGGCGGCGGUGGUGGGGGGAGCCGCGGGGAUCCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGAUGGCGUCCCCUUCCCCGCCGGCCGCCUUUCUCGCGCGCGACUGCGGCGGCGGUGGUGGGGGGAGCCGCGGGGAUNANANANACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGAGUAGGGGGCGGGCUCCGGCGCGGUGAGGCGGGGGGGCGAGCCCUGAGGGGCUCUCGCUUCUGGCGCCAAGCCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGAAGGGAGAAGGGUCGGGGCAGNANACCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGAGGUGAGGCGGGGGGGCGAGCCCUGAGGGGCUCUCGCUUCUGGCGCCAAGGGUGAGGCGGGGGGGCGAGCCCUGAGGGGCUCUCGCUUCUGGCGCCAAGGGUGAGGCGGGGGGGCGAGCCCUGAGGGGCUCUCGCUUCUGGCGCCAAGCCCCGGGGAGCCCGGCGGNANANANAGUAGGGGGCGGGCUCCGGCGCCCCAGCGGGGCUGGGCGCGCGGACCCAGCGGGGCUGGGCGCGCGGAGGUGAGGCGGGGGGGCGAGCCCUGAGGGGCUCUCGCUUCUGGCGCCAAGCCCAGCGGGGCUGGGCGCGCGGACC
+>chr2
+GUUGCGGCUGGACGAGGCGCAGCUGGUGAAGAGACAUGAGAGGAUGCCGCGGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCGGUGAGGCCCCGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCCGUGGCGGCCGCGGGGAUCGCCGAGGGCCGGUCGGCCGCCCCGGGUGCCGCGCGGUGAGGCCCCGCGCGUGUGUCCCGGCUGCGGUCGGCCGCGCUCGAGGGGUCCCCGUGGCGGCUGCGGCUGGAUGAGGCGGGGCCGCGGCGCGAGCCGGGCUGGGGGCCCUUCCCGUGGUUCCCUCCUCCUCCUCCCCUGGCGCGCGCCGGGCCCGUGCCGCCCCGGGCCGGGCACCGCCCCCGGGCCGGGCACCGCGCCGCGGCGAGCCGGGCCGGACGGGCCCUUCCCGUGUGCCUUCCCCGUCCGUCCGUCCGUCCGUCCAUCCGUCCACCGCGACUGCGGCGGCGGUGGUGGGGGGAGCCGCGGGGAUUGGCGUCCCCUUCCCCGCCGGCCGCCUUUCUCGCGGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAGAAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCGGGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAGAAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCGGGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAGAAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCGGGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAGAAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCGGGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGCGCGACUGCGGCGGCGGUGGUGG
diff -r 000000000000 -r 7c6c282ecf5a 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 17:40:27 2022 +0000
@@ -0,0 +1,2 @@
+chr1	1416
+chr2	1180
diff -r 000000000000 -r 7c6c282ecf5a 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 17:40:27 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 7c6c282ecf5a 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 7c6c282ecf5a test-data/training_data_mixed_context_100_st_on.npz
Binary file test-data/training_data_mixed_context_100_st_on.npz has changed