Mercurial > repos > rnateam > sshmm
changeset 0:4b01f0d7b350 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fasta_report_sequence_lengths.py Fri Jul 06 09:01:40 2018 -0400 @@ -0,0 +1,41 @@ +#!/usr/bin/env python + +import sys + +""" +Input: FASTA file +Output: Print sequence ID and corresponding sequence length + +Example output: +chr1 248956422 +chr2 242193529 +chr3 198295559 +... + +""" + +# Check input. +if not len(sys.argv) == 2: + exit("Usage: fasta_report_sequence_lengths.py <fasta_file>") + +fasta_file = sys.argv[1] + +seq_id = "id" +seq_len = 0 + +# Go through FASTA file, extract sequence lengths. +with open(fasta_file) as f: + for line in f: + if line.startswith(">"): + new_id = line[1:].strip() + if seq_len: + print("%s\t%i" % (seq_id, seq_len)) + seq_len = 0 + seq_id = new_id + else: + seq_len += len(line.strip()) + +# Print last sequence length. +if seq_len: + print("%s\t%i" % (seq_id, seq_len)) +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sshmm.xml Fri Jul 06 09:01:40 2018 -0400 @@ -0,0 +1,246 @@ +<tool id="sshmm" name="ssHMM" version="1.0.7"> + <description>- RNA sequence-structure motif finder</description> + <requirements> + <requirement type="package" version="1.0.7">sshmm</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python '$__tool_directory__/fasta_report_sequence_lengths.py' '$genome_fasta_file' > chrom.sizes && + mkdir prepro_out && + preprocess_dataset + prepro_out + prepro_id + '$input_bed_file' + '$genome_fasta_file' + chrom.sizes + #if $str_pred_method == 'rnashapes': + --disable_RNAstructure + #elif $str_pred_method == 'rnastructures': + --disable_RNAshapes + #end if + #if $advanced_prepro_params.advanced_prepro_params_selector == 'ap_specify': + $advanced_prepro_params.disable_filtering + --min_score $advanced_prepro_params.min_score + --min_length $advanced_prepro_params.min_length + --max_length $advanced_prepro_params.max_length + --elongation $advanced_prepro_params.elongation + #end if + && + mkdir results + && + train_seqstructhmm + prepro_out/fasta/prepro_id/positive.fasta + #if $str_pred_method == 'rnashapes': + prepro_out/shapes/prepro_id/positive.txt + #elif $str_pred_method == 'rnastructures': + prepro_out/structures/prepro_id/positive.txt + #end if + -o results + #if $advanced_train_params.advanced_train_params_selector == 'ap_specify': + --motif_length $advanced_train_params.motif_length + $advanced_train_params.init_random + --flexibility $advanced_train_params.flexibility + --block_size $advanced_train_params.block_size + --threshold $advanced_train_params.threshold + $advanced_train_params.only_best_shape + #end if + && + mv results/job_* results/res_out + ]]></command> + <inputs> + <param name="input_bed_file" type="data" format="bed" + label="Genomic binding sites BED file" + help="Genomic BED file containing protein binding sites"/> + <param name="genome_fasta_file" type="data" format="fasta" + label="Genome reference FASTA file" + help="Genomic FASTA file for extracting sequences defined in BED file"/> + <param name="str_pred_method" type="select" label="Select structure prediction method"> + <option value="rnashapes" selected="true">RNAshapes</option> + <option value="rnastructures">RNAstructures</option> + </param> + <conditional name="advanced_prepro_params"> + <param name="advanced_prepro_params_selector" type="select" label="Advanced preprocessing parameters"> + <option value="ap_not_specify" selected="true">Do not specify</option> + <option value="ap_specify">Manually specify</option> + </param> + <when value="ap_not_specify" /> + <when value="ap_specify"> + <param name="disable_filtering" truevalue="--disable_filtering" falsevalue="" checked="False" + label="Skip the filtering step?" type="boolean"/> + <param name="min_score" type="float" value="0.0" + label="Filtering: minimum score for binding site" /> + <param name="min_length" type="integer" value="8" + label="Filtering: minimum binding site length" /> + <param name="max_length" type="integer" value="75" + label="Filtering: maximum binding site length" /> + <param name="elongation" type="integer" value="20" + label="Elongation: span for up- and downstream elongation of binding sites" /> + </when> + </conditional> + <conditional name="advanced_train_params"> + <param name="advanced_train_params_selector" type="select" label="Advanced training parameters"> + <option value="ap_not_specify" selected="true">Do not specify</option> + <option value="ap_specify">Manually specify</option> + </param> + <when value="ap_not_specify" /> + <when value="ap_specify"> + <param name="motif_length" type="integer" value="6" + label="Length of the motif that shall be found"/> + <param name="init_random" truevalue="--random" falsevalue="" checked="False" + label="Initialize the model randomly?" type="boolean" + help="By default model is initialized with Baum-Welch optimized sequence motif"/> + <param name="flexibility" type="integer" value="10" + label="Greediness of Gibbs sampler" + help="Model parameters are sampled from among the top f configurations (default: 10); set f to 0 in order to include all possible configurations"/> + <param name="block_size" type="integer" value="1" + label="Number of sequences to be held out in each iteration"/> + <param name="threshold" type="integer" value="10" + label="Termination threshold" + help="The iterative algorithm is terminated if the given reduction in sequence structure log-likelihood is not reached for any of the 3 last measurements (default: 10)"/> + <param name="only_best_shape" truevalue="--only-best-shape" falsevalue="" checked="False" + label="Use only best structure for each sequence?" type="boolean" + help="Train only using best structure for each sequence (default: use all structures)"/> + </when> + </conditional> + <section name="output_options" title="Output options"> + <param name="output_prepro_files" type="boolean" value="False" + help="Set to output FASTA file and corresponding structures file for the extracted genomic regions" + label="Output FASTA file and corresponding structures file?"/> + <param name="output_logo_files" type="boolean" value="False" + help="Set to output logo_global.png, logo_hairpin.png, and logo_best_sequences.png files" + label="Output logo files?"/> + <param name="output_raw_files" type="boolean" value="False" + help="Set to output final_model.xml, logo_best_sequences.txt, logo_global.txt, logo_hairpin.txt files" + label="Output raw logo and model files?"/> + </section> + </inputs> + <outputs> + <data format="fasta" name="positive_fasta_out_file" + label="${tool.name} on ${on_string} FASTA sequences (fasta)" + from_work_dir="prepro_out/fasta/prepro_id/positive.fasta"> + <filter> + output_options['output_prepro_files'] is True + </filter> + </data> + <data format="txt" name="positive_rnashapes_out_file" + label="${tool.name} on ${on_string} RNAshapes structures for sequences (txt)" + from_work_dir="prepro_out/shapes/prepro_id/positive.txt"> + <filter> + output_options['output_prepro_files'] is True and str_pred_method == 'rnashapes' + </filter> + </data> + <data format="txt" name="positive_rnastructures_out_file" + label="${tool.name} on ${on_string} RNAstructures structures for sequences (txt)" + from_work_dir="prepro_out/structures/prepro_id/positive.txt"> + <filter> + output_options['output_prepro_files'] is True and str_pred_method == 'rnastructures' + </filter> + </data> + <data format="png" name="final_graph_png" + label="${tool.name} on ${on_string} final graph (png)" + from_work_dir="results/res_out/final_graph.png"/> + <data format="png" name="logo_best_sequences_png" + label="${tool.name} on ${on_string} logo best sequences (png)" + from_work_dir="results/res_out/logo_best_sequences.png"> + <filter> + output_options['output_logo_files'] is True + </filter> + </data> + <data format="png" name="logo_global_png" + label="${tool.name} on ${on_string} logo global (png)" + from_work_dir="results/res_out/logo_global.png"> + <filter> + output_options['output_logo_files'] is True + </filter> + </data> + <data format="png" name="logo_hairpin_png" + label="${tool.name} on ${on_string} logo hairpin (png)" + from_work_dir="results/res_out/logo_hairpin.png"> + <filter> + output_options['output_logo_files'] is True + </filter> + </data> + <data format="txt" name="logo_best_sequences_txt" + label="${tool.name} on ${on_string} logo best sequences (txt)" + from_work_dir="results/res_out/logo_best_sequences.txt"> + <filter> + output_options['output_raw_files'] is True + </filter> + </data> + <data format="txt" name="logo_global_txt" + label="${tool.name} on ${on_string} logo global (txt)" + from_work_dir="results/res_out/logo_global.txt"> + <filter> + output_options['output_raw_files'] is True + </filter> + </data> + <data format="txt" name="logo_hairpin_txt" + label="${tool.name} on ${on_string} logo hairpin (txt)" + from_work_dir="results/res_out/logo_hairpin.txt"> + <filter> + output_options['output_raw_files'] is True + </filter> + </data> + + <data format="xml" name="final_model_xml" + label="${tool.name} on ${on_string} final model (xml)" + from_work_dir="results/res_out/final_model.xml"> + <filter> + output_options['output_raw_files'] is True + </filter> + </data> + </outputs> + <tests> + <test expect_num_outputs="10"> + <param name="input_bed_file" value="PUM2_sites_hsa_chrM.bed" ftype="bed"/> + <param name="genome_fasta_file" value="hsa_chrM.fa" ftype="fasta"/> + <param name="str_pred_method" value="rnastructures"/> + <param name="advanced_prepro_params_selector" value="ap_specify"/> + <param name="elongation" value="20"/> + <param name="output_prepro_files" value="True"/> + <param name="output_logo_files" value="True"/> + <param name="output_raw_files" value="True"/> + <output name="positive_fasta_out_file" file="hsa_chrM_positive.fasta" ftype="fasta"/> + <output name="positive_rnastructures_out_file" file="hsa_chrM_structures_positive.txt" ftype="txt"/> + <output name="final_graph_png" file="test_structure_final_graph.png" ftype="png" compare="sim_size" delta="40000"/> + <output name="logo_global_png" file="test_structure_logo_global.png" ftype="png" compare="sim_size" delta="5000"/> + <output name="logo_hairpin_png" file="test_structure_logo_hairpin.png" ftype="png" compare="sim_size" delta="5000"/> + <output name="logo_best_sequences_png" file="test_structure_logo_best_sequences.png" ftype="png" compare="sim_size" delta="5000"/> + <output name="logo_global_txt" file="test_structure_logo_global.txt" ftype="txt" compare="sim_size"/> + <output name="logo_hairpin_txt" file="test_structure_logo_hairpin.txt" ftype="txt" compare="sim_size"/> + <output name="logo_best_sequences_txt" file="test_structure_logo_best_sequences.txt" ftype="txt" compare="sim_size"/> + <output name="final_model_xml" file="test_structure_final_model.xml" ftype="xml" compare="sim_size"/> + </test> + <test expect_num_outputs="10"> + <param name="input_bed_file" value="PUM2_sites_hsa_chrM.bed" ftype="bed"/> + <param name="genome_fasta_file" value="hsa_chrM.fa" ftype="fasta"/> + <param name="str_pred_method" value="rnashapes"/> + <param name="output_prepro_files" value="True"/> + <param name="output_logo_files" value="True"/> + <param name="output_raw_files" value="True"/> + <output name="positive_fasta_out_file" file="hsa_chrM_positive.fasta" ftype="fasta"/> + <output name="positive_rnashapes_out_file" file="hsa_chrM_shapes_positive.txt" ftype="txt"/> + <output name="final_graph_png" file="test_shapes_final_graph.png" ftype="png" compare="sim_size" delta="40000"/> + <output name="logo_global_png" file="test_shapes_logo_global.png" ftype="png" compare="sim_size" delta="5000"/> + <output name="logo_hairpin_png" file="test_shapes_logo_hairpin.png" ftype="png" compare="sim_size" delta="5000"/> + <output name="logo_best_sequences_png" file="test_shapes_logo_best_sequences.png" ftype="png" compare="sim_size" delta="5000"/> + <output name="logo_global_txt" file="test_shapes_logo_global.txt" ftype="txt" compare="sim_size"/> + <output name="logo_hairpin_txt" file="test_shapes_logo_hairpin.txt" ftype="txt" compare="sim_size"/> + <output name="logo_best_sequences_txt" file="test_shapes_logo_best_sequences.txt" ftype="txt" compare="sim_size"/> + <output name="final_model_xml" file="test_shapes_final_model.xml" ftype="xml" compare="sim_size"/> + </test> + </tests> + <help><![CDATA[ + + ssHMM is an RNA motif finder that recovers sequence-structure motifs from RNA-binding protein data, such as CLIP-Seq data. The tool input consists of a BED file with genomic binding regions and the corresponding genome reference FASTA file. For structure prediction, the user can select between RNAshapes and RNAstructures. Advanced parameters can be set for both the preprocessing and the training stage. + + The output consists of a graph showing the found sequence motifs for the 5 structural contexts multiloop, hairpin, stem, internal loop, and exterior loop (output in .png format). The height of the nucleotides corresponds to their emission probabilities, while the thickness of the arrows corresponds to their transition probabilities. Additional files (intermediate, logo, model, raw) can be selected for output in the "Output options" section. + + For more details have a look at the online documentation: + + http://sshmm.readthedocs.io/en/latest/index.html + + ]]></help> + <citations> + <citation type="doi">10.1093/nar/gkx756</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/PUM2_sites_hsa_chrM.bed Fri Jul 06 09:01:40 2018 -0400 @@ -0,0 +1,15 @@ +chrM 574 595 chrM,574-595,+ 0 + +chrM 603 624 chrM,603-624,+ 0 + +chrM 908 929 chrM,908-929,+ 0 + +chrM 1512 1533 chrM,1512-1533,+ 0 + +chrM 2397 2418 chrM,2397-2418,+ 0 + +chrM 2512 2533 chrM,2512-2533,+ 0 + +chrM 3171 3192 chrM,3171-3192,+ 0 + +chrM 3187 3208 chrM,3187-3208,+ 0 + +chrM 4289 4310 chrM,4289-4310,+ 0 + +chrM 4390 4411 chrM,4390-4411,+ 0 + +chrM 4407 4428 chrM,4407-4428,+ 0 + +chrM 4423 4444 chrM,4423-4444,+ 0 + +chrM 15978 15999 chrM,15978-15999,- 0 - +chrM 14490 14511 chrM,14490-14511,- 0 - +chrM 5848 5869 chrM,5848-5869,- 0 -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hsa_chrM.fa Fri Jul 06 09:01:40 2018 -0400 @@ -0,0 +1,238 @@ +>chrM +GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG +GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC +CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA +ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC +ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA +AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC +TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA +CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC +AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC +ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA +GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC +AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA +ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA +TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT +CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC +ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC +AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC +CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA +CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC +AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT +GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA +AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA +TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA +GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA +GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG +ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA +ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC +AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA +AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT +AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC +CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG +TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC +ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG +TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC +AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA +AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC +ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA +AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT +TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA +TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT +AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG +TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA +GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG +ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG +AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT +ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA +ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT +TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA +TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC +CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC +ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC +CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG +CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC +AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC +TCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGG +CCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTTCGACCTTGCCGAAGGGGAGTC +CGAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAGGCCCCTTCGCCCTATTCTTCATAGCCGAATAC +ACAAACATTATTATAATAAACACCCTCACCACTACAATCTTCCTAGGAACAACATATGACGCACTCTCCC +CTGAACTCTACACAACATATTTTGTCACCAAGACCCTACTTCTAACCTCCCTGTTCTTATGAATTCGAAC +AGCATACCCCCGATTCCGCTACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCTA +GCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCCCCCTCAAACCTAAGAAATAT +GTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCCTTATTTCTAGGACTATGA +GAATCGAACCCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCTAAAGTAAGGTC +AGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTCCCGTACTAATTAATCCCCT +GGCCCAACCCGTCATCTACTCTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTT +TTTACCTGAGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTCTAACCAAAAAAATAAACCCTC +GTTCCACAGAAGCTGCCATCAAGTATTTCCTCACGCAAGCAACCGCATCCATAATCCTTCTAATAGCTAT +CCTCTTCAACAATATACTCTCCGGACAATGAACCATAACCAATACTACCAATCAATACTCATCATTAATA +ATCATAATAGCTATAGCAATAAAACTAGGAATAGCCCCCTTTCACTTCTGAGTCCCAGAGGTTACCCAAG +GCACCCCTCTGACATCCGGCCTGCTTCTTCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACCA +AATCTCTCCCTCACTAAACGTAAGCCTTCTCCTCACTCTCTCAATCTTATCCATCATAGCAGGCAGTTGA +GGTGGATTAAACCAAACCCAGCTACGCAAAATCTTAGCATACTCCTCAATTACCCACATAGGATGAATAA +TAGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTATCCTAACTACTAC +CGCATTCCTACTACTCAACTTAAACTCCAGCACCACGACCCTACTACTATCTCGCACCTGAAACAAGCTA +ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCTGCCCCCGCTAACCGGCTTTT +TGCCCAAATGGGCCATTATCGAAGAATTCACAAAAAACAATAGCCTCATCATCCCCACCATCATAGCCAC +CATCACCCTCCTTAACCTCTACTTCTACCTACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATA +TCTAACAACGTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCCCACACTCATCG +CCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATACTAATAATCTTATAGAAATTTAGGTTAAATAC +AGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGTAACAGCTAAGGACTGCAAAA +CCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAAGCCCTTACTAGACCAATGGGA +CTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCC +GCCGGGAAAAAAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGA +AAATCACCTCGGAGCTGGTAAAAAGAGGCCTAACCCCTGTCTTTAGATTTACAGTCCAATGCTTCACTCA +GCCATTTTACCTCACCCCCACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCACAAAGACATTGG +AACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCTCTAAGCCTCCTTATTCGAGCC +GAGCTGGGCCAGCCAGGCAACCTTCTAGGTAACGACCACATCTACAACGTTATCGTCACAGCCCATGCAT +TTGTAATAATCTTCTTCATAGTAATACCCATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAAT +AATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCTCCCTCTCTC +CTACTCCTGCTCGCATCTGCTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTTAG +CAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTACACCTAGCAGGTGTCTC +CTCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAAACCCCCTGCCATAACCCAATAC +CAAACGCCCCTCTTCGTCTGATCCGTCCTAATCACAGCAGTCCTACTTCTCCTATCTCTCCCAGTCCTAG +CTGCTGGCATCACTATACTACTAACAGACCGCAACCTCAACACCACCTTCTTCGACCCCGCCGGAGGAGG +AGACCCCATTCTATACCAACACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACCA +GGCTTCGGAATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGAACCATTTGGATACATAGGTA +TGGTCTGAGCTATGATATCAATTGGCTTCCTAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGG +AATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCACCGGCGTCAAA +GTATTTAGCTGACTCGCCACACTCCACGGAAGCAATATGAAATGATCTGCTGCAGTGCTCTGAGCCCTAG +GATTCATCTTTCTTTTCACCGTAGGTGGCCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCGT +ACTACACGACACGTACTACGTTGTAGCCCACTTCCACTATGTCCTATCAATAGGAGCTGTATTTGCCATC +ATAGGAGGCTTCATTCACTGATTTCCCCTATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAATCC +ATTTCACTATCATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGGCCTATCCGGAAT +GCCCCGACGTTACTCGGACTACCCCGATGCATACACCACATGAAACATCCTATCATCTGTAGGCTCATTC +ATTTCTCTAACAGCAGTAATATTAATAATTTTCATGATTTGAGAAGCCTTCGCTTCGAAGCGAAAAGTCC +TAATAGTAGAAGAACCCTCCATAAACCTGGAGTGACTATATGGATGCCCCCCACCCTACCACACATTCGA +AGAACCCGTATACATAAAATCTAGACAAAAAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAA +CCCCATGGCCTCCATGACTTTTTCAAAAAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAAT +TATAGGCTAAATCCTATATATCTTAATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCT +ATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCC +TGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAAATAGA +AACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTAC +ATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACG +AGTACACCGACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGCGA +CCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACA +TCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAACAGATGCAATTCCCGGACGTC +TAAACCAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGC +AAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATAGGGCCCGTATTT +ACCCTATAGCACCCCCTCTACCCCCTCTAGAGCCCACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTT +AAAGATTAAGAGAACCAACACCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACCAT +AATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATATTAAACACAAACTACCACCTA +CCTCCCTCACCAAAGCCCATAAAAATAAAAAATTATAACAAACCCTGAGAACCAAAATGAACGAAAATCT +GTTCGCTTCATTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTCTATTTCCCCCT +CTATTGATCCCCACCTCCAAATATCTCATCAACAACCGACTAATCACCACCCAACAATGACTAATCAAAC +TAACCTCAAAACAAATGATAACCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTT +AATCATTTTTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCATTTACACCAACCACCCAACTA +TCTATAAACCTAGCCATGGCCATCCCCTTATGAGCGGGCACAGTGATTATAGGCTTTCGCTCTAAGATTA +AAAATGCCCTAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTAGTTATTATCGA +AACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTAACCGCTAACATTACTGCAGGCCAC +CTACTCATGCACCTAATTGGAAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCA +TCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCTTAATCCAAGCCTACGTTTTCAC +ACTTCTAGTAAGCCTCTACCTGCACGACAACACATAATGACCCACCAATCACATGCCTATCATATAGTAA +AACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAGCCATGTGATT +TCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTAACCAACACACTAACCATATACCAATGATGG +CGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATACG +GGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAG +CCTAGCCCCTACCCCCCAATTAGGAGGGCACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAA +GTCCCACTCCTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCACCATAGTCTAA +TAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTATTACAATTTTACTGGGTCTCTATTTTACCCT +CCTACAAGCCTCAGAGTACTTCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGGCTCAACATTTTTT +GTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGCTCAACTTTCCTCACTATCTGCTTCATCCGCC +AACTAATATTTCACTTTACATCCAAACATCACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGT +AGATGTGGTTTGACTATTTCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTAGTATAAATAGT +ACCGTTAACTTCCAATTAACTAGTTTTGACAACATTCAAAAAAGAGTAATAAACTTCGCCTTAATTTTAA +TAATCAACACCCTCCTAGCCTTACTACTAATAATTATTACATTTTGACTACCACAACTCAACGGCTACAT +AGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCCCGCGTCCCTTTCTCCATAAAA +TTCTTCTTAGTAGCTATTACCTTCTTATTATTTGATCTAGAAATTGCCCTCCTTTTACCCCTACCATGAG +CCCTACAAACAACTAACCTGCCACTAATAGTTATGTCATCCCTCTTATTAATCATCATCCTAGCCCTAAG +TCTGGCCTATGAGTGACTACAAAAAGGATTAGACTGAACCGAATTGGTATATAGTTTAAACAAAACGAAT +GATTTCGACTCATTAAATTATGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACTAG +CATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATATCCTCCCTACTATGCCTAGA +AGGAATAATACTATCGCTGTTCATTATAGCTACTCTCATAACCCTCAACACCCACTCCCTCTTAGCCAAT +ATTGTGCCTATTGCCATACTAGTCTTTGCCGCCTGCGAAGCAGCGGTGGGCCTAGCCCTACTAGTCTCAA +TCTCCAACACATATGGCCTAGACTACGTACATAACCTAAACCTACTCCAATGCTAAAACTAATCGTCCCA +ACAATTATATTACTACCACTGACATGACTTTCCAAAAAACACATAATTTGAATCAACACAACCACCCACA +GCCTAATTATTAGCATCATCCCTCTACTATTTTTTAACCAAATCAACAACAACCTATTTAGCTGTTCCCC +AACCTTTTCCTCCGACCCCCTAACAACCCCCCTCCTAATACTAACTACCTGACTCCTACCCCTCACAATC +ATGGCAAGCCAACGCCACTTATCCAGTGAACCACTATCACGAAAAAAACTCTACCTCTCTATACTAATCT +CCCTACAAATCTCCTTAATTATAACATTCACAGCCACAGAACTAATCATATTTTATATCTTCTTCGAAAC +CACACTTATCCCCACCTTGGCTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACA +TACTTCCTATTCTACACCCTAGTAGGCTCCCTTCCCCTACTCATCGCACTAATTTACACTCACAACACCC +TAGGCTCACTAAACATTCTACTACTCACTCTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACTT +AATATGACTAGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACTTATGACTCCCT +AAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTACTTGCCGCAGTACTCTTAAAACTAGGCGGCT +ATGGTATAATACGCCTCACACTCATTCTCAACCCCCTGACAAAACACATAGCCTACCCCTTCCTTGTACT +ATCCCTATGAGGCATAATTATAACAAGCTCCATCTGCCTACGACAAACAGACCTAAAATCGCTCATTGCA +TACTCTTCAATCAGCCACATAGCCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCG +GCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTA +CGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTT +TGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTG +TGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGC +CCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAA +CCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACC +CCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAA +CAGAGGCTTACGACCCCTTATTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCCCCCATGTCTAAC +AACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCA +ACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCC +ATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCAT +CCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAA +CTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAATA +TTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACTGTGATATATAAACTCAGACC +CAAACATTAATCAGTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA +CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA +TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT +TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA +CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT +CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA +TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC +TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC +AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC +CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC +CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC +ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA +AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC +TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC +ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC +TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA +CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC +AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA +TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT +AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA +ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA +TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA +CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA +CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC +TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC +CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC +CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG +ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC +CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC +CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC +CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA +ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA +CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC +ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC +TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC +AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC +TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA +GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT +CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC +ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT +TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC +TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA +GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC +AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT +AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC +TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC +CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA +GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC +ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA +TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA +ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA +ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG +TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC +TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG +CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC +ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hsa_chrM.hg38.chrom.sizes Fri Jul 06 09:01:40 2018 -0400 @@ -0,0 +1,1 @@ +chrM 16569
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hsa_chrM_positive.fasta Fri Jul 06 09:01:40 2018 -0400 @@ -0,0 +1,30 @@ +>chrM:554-615(+) +aaccccaaagacaccccccaCAGTTTATGTAGCTTACCTCCtcaaagcaatacactgaaaa +>chrM:583-644(+) +tagcttacctcctcaaagcaATACACTGAAAATGTTTAGACgggctcacatcaccccataa +>chrM:888-949(+) +gccagccaccgcggtcacacGATTAACCCAAGTCAATAGAAgccggcgtaaagagtgtttt +>chrM:1492-1553(+) +ccctcctcaagtatacttcaAAGGACATTTAACTAAAACCCctacgcatttatatagagga +>chrM:2377-2438(+) +cccaatatctacaatcaaccAACAAGTCATTATTACCCTCActgtcaacccaacacaggca +>chrM:2492-2553(+) +cctgtttaccaaaaacatcaCCTCTAGCATCACCAGTATTAgaggcaccgcctgcccagtg +>chrM:3151-3212(+) +cttcacaaagcgccttccccCGTAAATGATATCATCTCAACttagtattatacccacaccc +>chrM:3167-3228(+) +cccccgtaaatgatatcatcTCAACTTAGTATTATACCCACacccacccaagaacagggtt +>chrM:4269-4330(+) +tgtctgataaaagagttactTTGATAGAGTAAATAATAGGAgcttaaacccccttatttct +>chrM:4370-4431(+) +tctccgtgccacctatcacaCCCCATCCTAAAGTAAGGTCAgctaaataagctatcgggcc +>chrM:4387-4448(+) +acaccccatcctaaagtaagGTCAGCTAAATAAGCTATCGGgcccataccccgaaaatgtt +>chrM:4403-4464(+) +taaggtcagctaaataagctATCGGGCCCATACCCCGAAAAtgttggttatacccttcccg +>chrM:15958-16019(-) +gaatagtttaaattagaatcTTAGCTTTGGGTGCTAATGGTggagttaaagactttttctc +>chrM:14470-14531(-) +gaggttatatgggtttaataGTTTTTTTAATTTATTTAGGGggaatgatggttgtctttgg +>chrM:5828-5889(-) +taaaatggctgagtgaagcaTTGGACTGTAAATCTAAAGACaggggttaggcctcttttta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hsa_chrM_shapes_positive.txt Fri Jul 06 09:01:40 2018 -0400 @@ -0,0 +1,38 @@ +>chrM:554-615(+) +EEEEEEEEEEEEEEEEEEEESSSSISSSIIISSSSHHHHHHHHHSSSSISSSISSSSEEEE 0.62376 +>chrM:583-644(+) +EESSSSHHHHHHHHHSSSSMMMMMMSSSSSHHHHSSSSSMMSSSHHHHHHHHHHSSSEEEE 0.3152474 +>chrM:888-949(+) +SSSISSHHHHSSSSSMSSSSIISSISSSSIIISSHHHHSSIIIISSISSISSIISSSSEEE 0.2931414 +SSSMSSSHHHHHSSSMMMMMSSSSHHHHHHSSSSMMMMMMMMMMSSSEEEEEEEEEEEEEE 0.0800483 +>chrM:1492-1553(+) +EEESSSSSIISSSSSIIIIIISSSHHHHHHHHHHHHHHHHSSSIIIIIIISSSSSISSSSS 0.1828745 +>chrM:2377-2438(+) +EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEESSSSHHHHHHHHHSSSSEEE 0.4065502 +>chrM:2492-2553(+) +EESSSSSHHHHHSSSSSMMMSSSSSSSISSHHHHHSSISSSSSSSEEEEEEEEEEEEEEEE 0.1278867 +EESSSSSHHHHHSSSSSMMMSSSSSSSISSHHHHHSSISSSSSSSMMMSSSHHHHHHHSSS 0.0410739 +>chrM:3151-3212(+) +EEEEEEEEESSSHHHHHHHHSSSMMSSSSSSSHHHHHHHHHHHHSSSSSSSEEEEEEEEEE 0.2376765 +>chrM:3167-3228(+) +EEEEEEEEESSSSSSSHHHHHHHHHHHHSSSSSSSMMMMMMMMMMSSSSHHHHHHHSSSSE 0.1810531 +>chrM:4269-4330(+) +EESSSHHHHHHSSSMSSSSSSHHHHHSSSSSSMMSSSSSSHHHHHHHHHHHHSSSSSSEEE 0.0392731 +EESSSSIIISSSSHHHHHSSSSIISSSSMMSSSSSSIISSHHHHHHHHHSSIISSSSSSEE 0.0283899 +>chrM:4370-4431(+) +EEEEESSSHHHHHHHHSSSMMSSSMMSSSHHHHHHSSSMMSSSSHHHHHSSSSMMMSSSEE 0.370664 +>chrM:4387-4448(+) +EEEEEEEEESSSHHHHHHSSSMMSSSSHHHHHSSSSMSSSSSHHHHHHHSSSSSEEEEEEE 0.2173924 +SSSMMMMMMSSSHHHHHHSSSMMSSSSHHHHHSSSSMSSSSSHHHHHHHSSSSSMMMSSSE 0.0593635 +>chrM:4403-4464(+) +ESSSSMMSSSSHHHHHSSSSMSSSSSHHHHHHHSSSSSMMMMMMMMMMMMMMMSSSSEEEE 0.1334685 +EEESSSISSSSSSIIIIIIIISSSSSHHHHHHHSSSSSIIIIISSSSSSIISSSEEEEEEE 0.0720459 +EEESSMMSSSSHHHHHSSSSMSSSSSHHHHHHHSSSSSMMMMMMMSSHHHHHSSMMMMSSE 0.0309876 +>chrM:15958-16019(-) +SSSISSSSSISSSSIIISSSSSSSSHHHHHHHSSSSSISSSIISSSSIISSSSSIISSSEE 0.2243046 +>chrM:14470-14531(-) +EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEESSSSSSISSSHHHHSSSISSSSSSE 0.0283177 +EEESSSSHHHHHHHHSSSSMMMMMMMMMMMMMMMMMSSSSSSISSSHHHHSSSISSSSSSE 0.0174045 +>chrM:5828-5889(-) +EEEEEEESSSHHHHHHSSSMSSSSSHHHHHHHSSSSSMMMMSSSSSHHHHHSSSSSEEEEE 0.0497615 +EEEEEEESSSHHHHHHSSSMMMMMMMMMMMMMMMMMMSSSISSSSSHHHHHSSSSSISSSE 0.0423085
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hsa_chrM_structures_positive.txt Fri Jul 06 09:01:40 2018 -0400 @@ -0,0 +1,31 @@ +>chrM:554-615(+) +EEEEEEEEEEEEEEEEEEEESSSSISSSIIISSSSHHHHHHHHHSSSSISSSISSSSEEEE 1 +>chrM:583-644(+) +EESSSSHHHHHHHHHSSSSMMMMMMSSSSSHHHHSSSSSMMSSSHHHHHHHHHHSSSEEEE 1 +>chrM:888-949(+) +SSSISSHHHHSSSSSMSSSSIISSISSSSIIISSHHHHSSIIIISSISSISSIISSSSEEE 1 +>chrM:1492-1553(+) +EEESSSSSIISSSSSIIIIIISSSHHHHHHHHHHHHHHHHSSSIIIIIIISSSSSISSSSS 1 +>chrM:2377-2438(+) +EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEESSSSHHHHHHHHHSSSSEEE 1 +>chrM:2492-2553(+) +EESSSSSHHHHHSSSSSMMMSSSSSSSISSHHHHHSSISSSSSSSSSSHHHHHHHHHHSSS 1 +>chrM:3151-3212(+) +EEEEEEEEESSSHHHHHHHHSSSMMSSSSSSSHHHHHHHHHHHHSSSSSSSEEEEEEEEEE 1 +>chrM:3167-3228(+) +EEEEEEEEESSSSSSSHHHHHHHHHHHHSSSSSSSMMMMMMMMMMSSSSHHHHHHHSSSSE 1 +>chrM:4269-4330(+) +EESSSHHHHHHSSSMSSSSSSSHHHSSSSSSSMMSSSSSSHHHHHHHHHHHHSSSSSSEEE 1 +>chrM:4370-4431(+) +EEEEESSSHHHHHHHHSSSMSSSIIIIIIIIIIIIISSSISSSSHHHHHSSSSSSSSSSEE 1 +>chrM:4387-4448(+) +EEEEEEEEESSSHHHHHHSSSMMSSSSHHHHHSSSSMSSSSSHHHHHHHSSSSSEEEEEEE 1 +>chrM:4403-4464(+) +EEEEEEESSSSHHHHHSSSSMSSSSSHHHHHHHSSSSSMMMMMMMSSSHHHSSSEEEEEEE 1 +EEESSSISSSSSSIIIIIIIISSSSSHHHHHHHSSSSSIIIIISSSSSSIISSSEEEEEEE 1 +>chrM:15958-16019(-) +SSSISSSSSISSSSIIISSSSSSSSHHHHHHHSSSSSISSSIISSSSIISSSSSIISSSEE 1 +>chrM:14470-14531(-) +EEEEEEEESSSSSSSISSHHHHHHHHSSSSSSSSSMSSSSSSISSSHHHHSSSISSSSSSE 1 +>chrM:5828-5889(-) +EEEEEEESSSHHHHHHSSSMMSSSSHHHHHHHSSSSMSSSISSSSSSHHHSSSSSSISSSE 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_shapes_final_model.xml Fri Jul 06 09:01:40 2018 -0400 @@ -0,0 +1,584 @@ +<?xml version="1.0" encoding="ISO-8859-1"?> +<!DOCTYPE mixture PUBLIC "-//ghmm.org//DOCUMENT ghmm V1.0//EN" "http://ghmm.sourceforge.net/xml/1.0/ghmm.dtd"> +<mixture version="1.0" noComponents="1"> + <HMM name="stateHMM" type="labeled discrete"> + <alphabet id="0"> + <symbol code="0">A</symbol> + <symbol code="1">C</symbol> + <symbol code="2">G</symbol> + <symbol code="3">T</symbol> + <symbol code="4">+</symbol> + <symbol code="5">#</symbol> + </alphabet> + <classAlphabet> + <symbol code="0">St</symbol> + <symbol code="1">E1</symbol> + <symbol code="2">I1</symbol> + <symbol code="3">S1</symbol> + <symbol code="4">H1</symbol> + <symbol code="5">M1</symbol> + <symbol code="6">E2</symbol> + <symbol code="7">I2</symbol> + <symbol code="8">S2</symbol> + <symbol code="9">H2</symbol> + <symbol code="10">M2</symbol> + <symbol code="11">E3</symbol> + <symbol 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<transition source="17" target="24"> + <probability>0.2</probability> + </transition> + <transition source="17" target="25"> + <probability>0.2</probability> + </transition> + <transition source="18" target="21"> + <probability>0.2</probability> + </transition> + <transition source="18" target="22"> + <probability>0.2</probability> + </transition> + <transition source="18" target="23"> + <probability>0.2</probability> + </transition> + <transition source="18" target="24"> + <probability>0.2</probability> + </transition> + <transition source="18" target="25"> + <probability>0.2</probability> + </transition> + <transition source="19" target="21"> + <probability>0.058823529</probability> + </transition> + <transition source="19" target="22"> + <probability>0.058823529</probability> + </transition> + <transition source="19" target="23"> + <probability>0.41176471</probability> + </transition> + <transition source="19" target="24"> + <probability>0.41176471</probability> + </transition> + <transition source="19" target="25"> + <probability>0.058823529</probability> + </transition> + <transition source="20" target="21"> + <probability>0.2</probability> + </transition> + <transition source="20" target="22"> + <probability>0.2</probability> + </transition> + <transition source="20" target="23"> + <probability>0.2</probability> + </transition> + <transition source="20" target="24"> + <probability>0.2</probability> + </transition> + <transition source="20" target="25"> + <probability>0.2</probability> + </transition> + <transition source="21" target="26"> + <probability>0.42857143</probability> + </transition> + <transition source="21" target="27"> + <probability>0.14285714</probability> + </transition> + <transition source="21" target="28"> + <probability>0.14285714</probability> + </transition> + <transition source="21" target="29"> + <probability>0.14285714</probability> + </transition> + <transition source="21" target="30"> + <probability>0.14285714</probability> + </transition> + <transition source="22" target="26"> + <probability>0.2</probability> + </transition> + <transition source="22" target="27"> + <probability>0.2</probability> + </transition> + <transition source="22" target="28"> + <probability>0.2</probability> + </transition> + <transition source="22" target="29"> + <probability>0.2</probability> + </transition> + <transition source="22" target="30"> + <probability>0.2</probability> + </transition> + <transition source="23" target="26"> + <probability>0.090909091</probability> + </transition> + <transition source="23" target="27"> + <probability>0.090909091</probability> + </transition> + <transition source="23" target="28"> + <probability>0.63636364</probability> + </transition> + <transition source="23" target="29"> + <probability>0.090909091</probability> + </transition> + <transition source="23" target="30"> + <probability>0.090909091</probability> + </transition> + <transition source="24" target="26"> + <probability>0.090909091</probability> + </transition> + <transition source="24" target="27"> + <probability>0.090909091</probability> + </transition> + <transition source="24" target="28"> + <probability>0.27272727</probability> + </transition> + <transition source="24" target="29"> + <probability>0.45454545</probability> + </transition> + <transition source="24" target="30"> + <probability>0.090909091</probability> + </transition> + <transition source="25" target="26"> + <probability>0.2</probability> + </transition> + <transition source="25" target="27"> + <probability>0.2</probability> + </transition> + <transition source="25" target="28"> + <probability>0.2</probability> + </transition> + <transition source="25" target="29"> + <probability>0.2</probability> + </transition> + <transition source="25" target="30"> + <probability>0.2</probability> + </transition> + <transition source="26" target="31"> + <probability>1</probability> + </transition> + <transition source="27" target="31"> + <probability>1</probability> + </transition> + <transition source="28" target="31"> + <probability>1</probability> + </transition> + <transition source="29" target="31"> + <probability>1</probability> + </transition> + <transition source="30" target="31"> + <probability>1</probability> + </transition> + <transition source="31" target="31"> + <probability>1</probability> + </transition> + </HMM> +</mixture>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_shapes_logo_best_sequences.txt Fri Jul 06 09:01:40 2018 -0400 @@ -0,0 +1,7 @@ +A C G T +0.578947368421 0.157894736842 0.210526315789 0.0526315789474 +0.263157894737 0.315789473684 0.157894736842 0.263157894737 +0.210526315789 0.210526315789 0.157894736842 0.421052631579 +0.315789473684 0.0526315789474 0.105263157895 0.526315789474 +0.368421052632 0.157894736842 0.315789473684 0.157894736842 +0.368421052632 0.210526315789 0.157894736842 0.263157894737
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_shapes_logo_global.txt Fri Jul 06 09:01:40 2018 -0400 @@ -0,0 +1,7 @@ +A C G T +0.476973684211 0.194078947368 0.220394736842 0.108552631579 +0.274460047177 0.297709346897 0.202290653103 0.225539952823 +0.230152274532 0.205089642668 0.205089642668 0.359668440131 +0.293683667816 0.145821174691 0.176068753437 0.384426404055 +0.323937667837 0.177301370012 0.293371370423 0.205389591728 +0.292889941685 0.236277914204 0.206327031782 0.264505112329
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_shapes_logo_hairpin.txt Fri Jul 06 09:01:40 2018 -0400 @@ -0,0 +1,7 @@ +A C G T +0.5625 0.1875 0.1875 0.0625 +0.3125 0.3125 0.1875 0.1875 +0.1875 0.1875 0.1875 0.4375 +0.3125 0.0625 0.125 0.5 +0.6 0.2 0.1 0.1 +0.375 0.375 0.125 0.125
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_structure_final_model.xml Fri Jul 06 09:01:40 2018 -0400 @@ -0,0 +1,584 @@ +<?xml version="1.0" encoding="ISO-8859-1"?> +<!DOCTYPE mixture PUBLIC "-//ghmm.org//DOCUMENT ghmm V1.0//EN" "http://ghmm.sourceforge.net/xml/1.0/ghmm.dtd"> +<mixture version="1.0" noComponents="1"> + <HMM name="stateHMM" type="labeled discrete"> + <alphabet id="0"> + <symbol code="0">A</symbol> + <symbol code="1">C</symbol> + <symbol code="2">G</symbol> + <symbol code="3">T</symbol> + <symbol code="4">+</symbol> + <symbol code="5">#</symbol> + </alphabet> + <classAlphabet> + <symbol code="0">St</symbol> + <symbol code="1">E1</symbol> + <symbol code="2">I1</symbol> + <symbol code="3">S1</symbol> + <symbol code="4">H1</symbol> + <symbol code="5">M1</symbol> + <symbol code="6">E2</symbol> + <symbol code="7">I2</symbol> + <symbol code="8">S2</symbol> + <symbol code="9">H2</symbol> + <symbol code="10">M2</symbol> + <symbol code="11">E3</symbol> + 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</transition> + <transition source="27" target="31"> + <probability>1</probability> + </transition> + <transition source="28" target="31"> + <probability>1</probability> + </transition> + <transition source="29" target="31"> + <probability>1</probability> + </transition> + <transition source="30" target="31"> + <probability>1</probability> + </transition> + <transition source="31" target="31"> + <probability>1</probability> + </transition> + </HMM> +</mixture>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_structure_logo_best_sequences.txt Fri Jul 06 09:01:40 2018 -0400 @@ -0,0 +1,7 @@ +A C G T +0.421052631579 0.105263157895 0.315789473684 0.157894736842 +0.263157894737 0.210526315789 0.263157894737 0.263157894737 +0.421052631579 0.263157894737 0.157894736842 0.157894736842 +0.368421052632 0.157894736842 0.105263157895 0.368421052632 +0.210526315789 0.368421052632 0.105263157895 0.315789473684 +0.421052631579 0.210526315789 0.105263157895 0.263157894737
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_structure_logo_global.txt Fri Jul 06 09:01:40 2018 -0400 @@ -0,0 +1,7 @@ +A C G T +0.384984520124 0.147213622291 0.320588235294 0.147213622291 +0.259590643275 0.227938596491 0.274400584795 0.238070175439 +0.327199882562 0.26038871185 0.206205702794 0.206205702794 +0.321786111248 0.176320123839 0.177234517667 0.324659247247 +0.235785812673 0.292484260816 0.177506621579 0.294223304932 +0.349524327816 0.23630361257 0.180298105303 0.233873954311
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_structure_logo_hairpin.txt Fri Jul 06 09:01:40 2018 -0400 @@ -0,0 +1,7 @@ +A C G T +0.25 0.25 0.25 0.25 +0.25 0.25 0.25 0.25 +0.285714285714 0.428571428571 0.142857142857 0.142857142857 +0.5 0.166666666667 0.0833333333333 0.25 +0.230769230769 0.384615384615 0.153846153846 0.230769230769 +0.384615384615 0.230769230769 0.0769230769231 0.307692307692