# HG changeset patch # User rnateam # Date 1530882100 14400 # Node ID 4b01f0d7b350174b5b4d0f9ccec3a10a21e09ed6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/ commit b578a90031fd7061fbdaef48b6a66d895ac077c3 diff -r 000000000000 -r 4b01f0d7b350 fasta_report_sequence_lengths.py --- /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 = 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)) + diff -r 000000000000 -r 4b01f0d7b350 sshmm.xml --- /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 @@ + + - RNA sequence-structure motif finder + + sshmm + + 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 + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + +

+ + + + + output_options['output_prepro_files'] is True + + + + + output_options['output_prepro_files'] is True and str_pred_method == 'rnashapes' + + + + + output_options['output_prepro_files'] is True and str_pred_method == 'rnastructures' + + + + + + output_options['output_logo_files'] is True + + + + + output_options['output_logo_files'] is True + + + + + output_options['output_logo_files'] is True + + + + + output_options['output_raw_files'] is True + + + + + output_options['output_raw_files'] is True + + + + + output_options['output_raw_files'] is True + + + + + + output_options['output_raw_files'] is True + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10.1093/nar/gkx756 + + diff -r 000000000000 -r 4b01f0d7b350 test-data/PUM2_sites_hsa_chrM.bed --- /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 - diff -r 000000000000 -r 4b01f0d7b350 test-data/hsa_chrM.fa --- /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 diff -r 000000000000 -r 4b01f0d7b350 test-data/hsa_chrM.hg38.chrom.sizes --- /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 diff -r 000000000000 -r 4b01f0d7b350 test-data/hsa_chrM_positive.fasta --- /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 diff -r 000000000000 -r 4b01f0d7b350 test-data/hsa_chrM_shapes_positive.txt --- /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 diff -r 000000000000 -r 4b01f0d7b350 test-data/hsa_chrM_structures_positive.txt --- /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 diff -r 000000000000 -r 4b01f0d7b350 test-data/test_shapes_final_graph.png Binary file test-data/test_shapes_final_graph.png has changed diff -r 000000000000 -r 4b01f0d7b350 test-data/test_shapes_final_model.xml --- /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 @@ + + + + + + A + C + G + T + + + # + + + St + E1 + I1 + S1 + H1 + M1 + E2 + I2 + S2 + H2 + M2 + E3 + I3 + S3 + H3 + M3 + E4 + I4 + S4 + H4 + M4 + E5 + I5 + S5 + H5 + M5 + E6 + I6 + S6 + H6 + M6 + En + + + 0, 0, 0, 0, 1, 0 + 0 + + + 0.33333333, 0.16666667, 0.33333333, 0.16666667, 0, 0 + 1 + + + 0.25, 0.25, 0.25, 0.25, 0, 0 + 2 + + + 0.25, 0.25, 0.25, 0.25, 0, 0 + 3 + + + 0.5625, 0.1875, 0.1875, 0.0625, 0, 0 + 4 + + + 0.25, 0.25, 0.25, 0.25, 0, 0 + 5 + + + 0.16666667, 0.33333333, 0.16666667, 0.33333333, 0, 0 + 6 + + + 0.25, 0.25, 0.25, 0.25, 0, 0 + 7 + + + 0.25, 0.25, 0.25, 0.25, 0, 0 + 8 + + + 0.3125, 0.3125, 0.1875, 0.1875, 0, 0 + 9 + + + 0.25, 0.25, 0.25, 0.25, 0, 0 + 10 + + + 0.33333333, 0.16666667, 0.16666667, 0.33333333, 0, 0 + 11 + + + 0.25, 0.25, 0.25, 0.25, 0, 0 + 12 + + + 0.25, 0.25, 0.25, 0.25, 0, 0 + 13 + + + 0.1875, 0.1875, 0.1875, 0.4375, 0, 0 + 14 + + + 0.25, 0.25, 0.25, 0.25, 0, 0 + 15 + + + 0.33333333, 0.16666667, 0.16666667, 0.33333333, 0, 0 + 16 + + + 0.25, 0.25, 0.25, 0.25, 0, 0 + 17 + + + 0.25, 0.25, 0.25, 0.25, 0, 0 + 18 + + + 0.3125, 0.0625, 0.125, 0.5, 0, 0 + 19 + + + 0.25, 0.25, 0.25, 0.25, 0, 0 + 20 + + + 0.16666667, 0.16666667, 0.33333333, 0.33333333, 0, 0 + 21 + + + 0.25, 0.25, 0.25, 0.25, 0, 0 + 22 + + + 0.2, 0.1, 0.5, 0.2, 0, 0 + 23 + + + 0.6, 0.2, 0.1, 0.1, 0, 0 + 24 + + + 0.25, 0.25, 0.25, 0.25, 0, 0 + 25 + + + 0.16666667, 0.16666667, 0.16666667, 0.5, 0, 0 + 26 + + + 0.25, 0.25, 0.25, 0.25, 0, 0 + 27 + + + 0.33333333, 0.16666667, 0.25, 0.25, 0, 0 + 28 + + + 0.375, 0.375, 0.125, 0.125, 0, 0 + 29 + + + 0.25, 0.25, 0.25, 0.25, 0, 0 + 30 + + + 0, 0, 0, 0, 0, 1 + 31 + + + 0.15789474 + + + 0.052631579 + + + 0.052631579 + + + 0.68421053 + + + 0.052631579 + + + 0.42857143 + + + 0.14285714 + + + 0.14285714 + + + 0.14285714 + + + 0.14285714 + + + 0.2 + + + 0.2 + + + 0.2 + + + 0.2 + + + 0.2 + + + 0.2 + + + 0.2 + + + 0.2 + + + 0.2 + + + 0.2 + + + 0.058823529 + + + 0.058823529 + + + 0.058823529 + + + 0.76470588 + + + 0.058823529 + + + 0.2 + + + 0.2 + + + 0.2 + + + 0.2 + + + 0.2 + + + 0.42857143 + + + 0.14285714 + + + 0.14285714 + + + 0.14285714 + + + 0.14285714 + + + 0.2 + + + 0.2 + + + 0.2 + + + 0.2 + + + 0.2 + + + 0.2 + + + 0.2 + + + 0.2 + + + 0.2 + + + 0.2 + + + 0.058823529 + + + 0.058823529 + + + 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