| Next changeset 1:85010d0eaa6c (2024-03-27) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit 236a9bc5da1e5f73ba2c27b0664ac28ee14bb6da |
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added:
macros.xml mirmachine.xml test-data/ref.fa |
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| diff -r 000000000000 -r f2e87c81497d macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Mar 15 16:16:00 2024 +0000 |
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| @@ -0,0 +1,94 @@ +<macros> + <token name="@TOOL_VERSION@">0.2.13</token> + <token name="@SUFFIX_VERSION@">0</token> + <xml name="edam_ontology"> + <edam_topics> + <edam_topic>topic_0659</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_0362</edam_operation> + </edam_operations> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">mirmachine</requirement> + </requirements> + </xml> + <xml name="creator"> + <creator> + <organization name="IZW" url="https://www.izw-berlin.de/en/home.html"/> + </creator> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1016/j.xgen.2023.100348</citation> + </citations> + </xml> + <xml name="node_options"> + <option value="Acanthomorpha">Acanthomorpha</option> + <option value="Ambulacraria">Ambulacraria</option> + <option value="Amniota">Amniota</option> + <option value="Amphibia">Amphibia</option> + <option value="Annelida">Annelida</option> + <option value="Archelosauria">Archelosauria</option> + <option value="Archosauria">Archosauria</option> + <option value="Arthropoda">Arthropoda</option> + <option value="Bilateria">Bilateria</option> + <option value="Boreoeutheria">Boreoeutheria</option> + <option value="Branchiostoma">Branchiostoma</option> + <option value="Caenorhabditis">Caenorhabditis</option> + <option value="Catarrhini">Catarrhini</option> + <option value="Cephalopoda">Cephalopoda</option> + <option value="Chelicerata">Chelicerata</option> + <option value="Chondrichthyes">Chondrichthyes</option> + <option value="Chordata">Chordata</option> + <option value="Chromadorea">Chromadorea</option> + <option value="Clupeocephala">Clupeocephala</option> + <option value="Cnidaria">Cnidaria</option> + <option value="Coleoidea">Coleoidea</option> + <option value="Cyclostomata">Cyclostomata</option> + <option value="Daphnia">Daphnia</option> + <option value="Demospongiae">Demospongiae</option> + <option value="Deuterostomia">Deuterostomia</option> + <option value="Diapsida">Diapsida</option> + <option value="Diptera">Diptera</option> + <option value="Drosophila">Drosophila</option> + <option value="Ecdysozoa">Ecdysozoa</option> + <option value="Echinodermata">Echinodermata</option> + <option value="Eleutherozoa">Eleutherozoa</option> + <option value="Endopterygota">Endopterygota</option> + <option value="Enteropneusta">Enteropneusta</option> + <option value="Euarchontoglires">Euarchontoglires</option> + <option value="Eumetazoa">Eumetazoa</option> + <option value="Eutheria">Eutheria</option> + <option value="Glires">Glires</option> + <option value="Gnathostomata">Gnathostomata</option> + <option value="Gymnophiona">Gymnophiona</option> + <option value="Laurasiatheria">Laurasiatheria</option> + <option value="Lepidoptera">Lepidoptera</option> + <option value="Lepidosauria">Lepidosauria</option> + <option value="Lophotrochozoa">Lophotrochozoa</option> + <option value="Mammalia">Mammalia</option> + <option value="Marsupialia">Marsupialia</option> + <option value="Metazoa">Metazoa</option> + <option value="Mollusca">Mollusca</option> + <option value="Muridae">Muridae</option> + <option value="Neoaves">Neoaves</option> + <option value="Neognathae">Neognathae</option> + <option value="Neoptera">Neoptera</option> + <option value="Neopterygii">Neopterygii</option> + <option value="Neotrochozoa">Neotrochozoa</option> + <option value="Octopus">Octopus</option> + <option value="Olfactores">Olfactores</option> + <option value="Osteichthyes">Osteichthyes</option> + <option value="Pancrustacea">Pancrustacea</option> + <option value="Platytrochozoa">Platytrochozoa</option> + <option value="Protostomia">Protostomia</option> + <option value="Sarcopterygii">Sarcopterygii</option> + <option value="Silicispongia">Silicispongia</option> + <option value="Tetrapoda">Tetrapoda</option> + <option value="Theria">Theria</option> + <option value="Vertebrata">Vertebrata</option> + <option value="Xenopus">Xenopus</option> + </xml> +</macros> |
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| diff -r 000000000000 -r f2e87c81497d mirmachine.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mirmachine.xml Fri Mar 15 16:16:00 2024 +0000 |
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| @@ -0,0 +1,67 @@ +<tool id="mirmachine" name="MirMachine" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="22.05"> + <description>A tool to detect miRNA homologs in genome sequences</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + ln -sf '$genome' ./genome.fasta && + MirMachine.py + -n '$input_node' + -s '$input_species' + --genome ./genome.fasta + -c \${GALAXY_SLOTS:-8} + && + mv results/predictions/filtered_gff/*.PRE.gff species_filtered.PRE.gff && + mv results/predictions/gff/*.PRE.gff species.PRE.gff && + mv results/predictions/fasta/*.PRE.fasta species.PRE.fasta + ]]></command> + <inputs> + <param type="data" name="genome" format="fasta" label="Genome fasta file"/> + <param name="input_node" type="select" label="Node name" help="e.g. Caenorhabditis"> + <expand macro="node_options"/> + </param> + <param type="text" name="input_species" label="Scientific species name" help="Separated by underscore e.g. Caenorhabditis_elegans"> + <sanitizer invalid_char=""> + <valid initial="string.letters"> + <add value="_"/> + </valid> + </sanitizer> + <validator type="regex">[a-zA-Z_]+</validator> + </param> + </inputs> + <outputs> + <data name="gff_file" format="gff" from_work_dir="species.PRE.gff" label="${tool.name} on ${on_string}: GFF file"/> + <data name="filtered_gff_file" format="gff" from_work_dir="species_filtered.PRE.gff" label="${tool.name} on ${on_string}: filtered GFF file"/> + <data name="fasta_file" format="fasta" from_work_dir="species.PRE.fasta" label="${tool.name} on ${on_string}: fasta sequence of annotation miRNAs"/> + </outputs> + <tests> + <test expect_num_outputs="3"> + <param name="genome" value="ref.fa"/> + <param name="input_node" value="Caenorhabditis"/> + <param name="input_species" value="Caenorhabditis_elegans"/> + <output name="gff_file"> + <assert_contents> + <has_n_lines n="24" delta="0"/> + </assert_contents> + </output> + <output name="filtered_gff_file"> + <assert_contents> + <has_n_lines n="15" delta="0"/> + </assert_contents> + </output> + <output name="fasta_file"> + <assert_contents> + <has_n_lines n="24" delta="0"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + +Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements. MirMachine facilitates automated genome annotation pipelines and deeper studies into the evolution of genome regulation, even in extinct organisms. + + ]]></help> + <expand macro="citations"/> + <expand macro="creator"/> +</tool> |
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| diff -r 000000000000 -r f2e87c81497d test-data/ref.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ref.fa Fri Mar 15 16:16:00 2024 +0000 |
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| b'@@ -0,0 +1,16668 @@\n+>chrI_9000001-10000000:. \n+CCTGGAAAATAATCTGAATATATTGGTAAAGGTGAGTTTCCAGAAGACATTAATCAATTG\n+TATCAAGAAAGAGGATCAGTGTCTGAATATTTAAACTTTTTTCATAGAAAACTGTTTATT\n+TTTCATTCAATAAAGGCGGCAAAGAACATGTAAGATAATAAAATATAAAGATATATTTAA\n+AATTGAATCAATATTAAGAATTACAATGGATTGTTTTAGAAACATTTTCCATCAGTTACA\n+ACTTTGGTTAGTAGTTTGCTCTTGTTAAAATCTGATCATGCATTCGCAAACTTTGCATGC\n+TTGAAATTACAAATAACAACATTACACAAATTATAAAACCCGCATTTAATCTAATATACA\n+ACAATTTTAATCTCTAATTTCACAGAAAAAAAAATAGAAAGTGAATAATGTTTACTCATA\n+ATTTTTTAGAATTGATTATCCTCAACGTTCACTAATCACTGCGAACTCCTTCGTTCTGGT\n+AAGTATGAACTTCTTGTGGAACCACTTTGGAAAGTAGCTTGTTCTGACTGAAATTACGTA\n+GATCATATGATTAGTAATATTTTAAAATTAGGGATTACCTGATAGTTAGGTTTCTTTGGA\n+TAAATGAACATGAATTGTCTTGAAGGGCTTTCAACTTCGACGGGATTTGTGTGAACTCTG\n+AAAATTAATTTATGAAGTTTCAAACATTTCAAACCATTAATGTTTGAGTATCTCAGTACG\n+CTTCTTCCCATTATACAGATCATGTTAAAATTTAACAATAGCAATTTTCAAAGTGAAGAA\n+ATTAACAAGTGTTTCAATTTTCCATATTAATGAATTTTCATCTGATAACGTTCGTAAAAA\n+CATGAAAACACCTTTTTAGTGAATTAAAAAAAATATATATAAATTCTAAACAAACCTTCG\n+AACTGGTGGTTTTGTGTAAGCTGTAGGTGTCGGAGGAAGTGAAGTATTTGGAAGTGATTT\n+GATTACTCGAATTGTTGATCTTTTTGGAGATATTCCAGTTTCAATATCCTCCGTTTTTCC\n+CGATTTTCGACCCAAACATTTTTGAAATGGTTTACGCATTCGAGTTGAATACTGAAAAAA\n+AGTTAAGTTGGTTGGAATGGCATATTGTTGGAAACTGCTAAAATGTGCTGGTGAAAGCAA\n+ACATAACAGTGCAAAGCTTCCGATCATGAACCTATAAATCTGTTGCGGCCCTACCGTAGT\n+CTACAGTACTCAACTTAGACATTCATGACAGGCCTGCCAGTATTTCGGTTTTTTTCTTTT\n+TGTTTTTTGCGGTACCTGGTTACCTGGTTgtacctggttgtggtgacacgattgaaaatg\n+tttaaatgaaagcttcgaaaaggaatgtgcgcctttaaggagtactgtagctctcacatc\n+tcactgcttcactgttttcaAATAGCCCTTTCCCGGCCTTTTTTAGCATTCAACTTTCAG\n+AAAACGAAGTATTTATTAATCTTGGCTTTTTATACTTATTATATCATAAAACTCACCATA\n+AACAATAAAATAAGTGTAGCTACCGCTAAGGCGGCTAAAATAATAGCAACGAGCACAAAA\n+TCAATAATACTTTCAGCCATTTTAAAGGTCTATGTTCTGCAGTAAGTTGGAGAGTAAAAG\n+AAAAGAGAAGATTTGCGTAAAACTTTTCGTTTTATACAGCAGCGGCGGTAGTGCGAATTC\n+AGAATTTCACAAGTGCGTCAATCGGCCGTTAGGTTTGGCTGAAAAAATGAAATCACTGTT\n+TTTTCCGAAAAGGAGAAAAAACGTGTTTAGAGCCGAACCCGTGTTTGCCACACTGATCGG\n+ATTTGCATAAGTTTTTTATTTCATTTTTTCCCGGTCGATCATCATTTCATCGGTCAAATG\n+ATCCCGATCATTCTTCTTCTCTGAAAAGAACGTCAAAGCAGTACGTCATATTCAATCAAT\n+ACATTTTATTGAGAAAAATTCGAAAAAAAGCAACGAGAGGGAAGTTAGTACAATTGAGGA\n+GTTGAACATATTTTAGACTTAGGTTAGACTGTATACAAACACATGACTTATAATAAAAGC\n+TCGATTCTCAGTATGTTTTTCAAATAAATATAGGACAGGAAGCATATTCACAGAACAGAG\n+ACACTCCTATTACTTAGCCAGGTAGAGGGTTAATCCAATGATAAAGATAAGAATAACAAA\n+GAAACAGAGAAGGAGAAGCTTCTTTTGACGGGCTTTCTGATTGTAGTAGACGGCTTGTTG\n+CACATTTTGAGCACCCTTAATTTATTTTTTATTAAAATGGAATACCCACTATTTTTCAAC\n+TTTGAAAGTACCTAAACGTGTATATTTTTAGATAAATTAAAGTTTTTTTTGCAGATTTTC\n+GTTTTCATCGCTTCATTCTCGAACAATTCTGTGATTCTCCGAATTTTTACCTGTTCAACG\n+TAAATCTGTGCATGCTCCACATTTGCCTCAATCGAATCCACCATATCTCCTTGTTCGTGT\n+ACGATATTCGCGAGTTCGGCGAAAATCTGAAAATTAATTAATGTTACTTAATCTTGAAGA\n+GTTATTTTTCGTATGGCACATCCTCTAACCGCTTTTAATGAAATTAATAGAAATTAAAAA\n+ATAATAATTTTTAAATTGGTCATTATAACTTCAATTGAATAAAGCCTACCGCATTAACAT\n+CTCCAATATCTCGTTCCAATTGTTGTAATGCATTTTGTCGTTCTTTCATATCTTGCAAAT\n+TTCCTTGTTGCTGTGCCGTCATCTGCATCTGTCCACCACTTCGTCCATTATTTCCGTACA\n+TATCGTATTCGGCAGCATCACGTGCCGCTTGAGCATCCATTTCTGCTGCAACCATTCCAG\n+CTTTTTCAGTTTGTGCAGCTTTTCGTTGAGATGCTTGAAGGCGGTTGAGCACTCCGATAT\n+ACTCATTTTGAAGACGCTCTCGGACTCCTCGTAAGTTCTTCTGAAATATTTTAATGTTGT\n+TGATAATACTATAATAAAATATTCCTTCAAAGACATCTCTCCCAAACGTGTATTTCCTAT\n+TTTCATATGAATATCAATACAAAATGAGTTTGAAATCAATTTTCAGAAAATTTaaatttc\n+ggatttaaaaattgatttatgaggttattcaagtagagtcggaaaattgtagacaaatgg\n+cgccacaactgtaatcaaatacatacaaaaacatgtattttaatatagttgtgacgtcat\n+tttctacactttttaattttccgatactacttgaataggccACTTATTATCAAAATATAT\n+AAACTGTCATGTGAAACGTGGCTTATTTTTTATTTTGTTTTTTATTTAAGCTCCTCCCAT\n+TTTTTTAAAATGAACTAATAAATACAAACTTTAACGAAAGGTCAGGAATGGGAGGAGCTT\n+GAATAAAAAACAAAATAAAAAATAAGCCACTTTACACATGCCAGTTTATATATTTTGATA\n+ATAAGATTATTTCAAATTATTTTTTTAAGTTTTTTTTATTTAACAAAAATCGTGTGATTT\n+TATGATTTATTTTTGAATGTTATAAAATTTTAAAACCTTAGGATAATTTTTTTAAAATAT\n+AAATTCATTGAAAAATTTTGCCTTCACCAAAGTTTAATATAAAAATTTATACTGAAACTC\n+ACATCAGAGTTGCTCATCACAACTAATCTTTTCAGCAGGGCATTGGTTTCCTTCGAGAGT\n+TCCTGAGCATTATGAGCTTTCTGAAATATTTTAATGTAATATTAATTAATAGAGAGTAAT\n+AACTAACGCGATTGAAAAGCTCCCGTTCTCTTTGTCCTGATTCACTGCTATCTGATAGAT\n+TTGTGATAAAGGATTCCAATTGAATAACTGAAACGAAATTTAGTG'..b'TTAATTATTTCAAAAGTCCCTCTTTCATTTTCTTCTCTCATCAAAAACAT\n+GCCCATTTAGTTTTGAAAAAGGCCCAACTTATTGTAATGACTAATAAGTGTAATACTCAA\n+TAATGGTTCTCCCCCACTCAAAAACTTCTCTTCTTCCATTTAGAAGCTTCTCATAATTAA\n+ATATTCGTTCGAGTCACTCAATTAGCCGACTTTAAGAAAAAAGAAAATGAAGTATAATTG\n+ATTTGGGTTGAAATGGGATATGGAATTGCAATATGAGAGAAAATAAGAAAATTAGATAAT\n+TCACAACAAAATTAGAGAAAAGTTACGGTACCTGGATATTCAAGCAAAGGTTCTATGCAA\n+AATTCGTGAGGTACCAGGAAATTGGTGGGGATTTTTTTTGAAGTTTTTATTTTTTCCAGG\n+TTCACTTGGAAGTTTCAAATTTCTGGACAAAATTGCAAGAAACCCCCTTTTTATTGTAAA\n+ATTTCATAAATAACCACCAATTTCTAAATTCAAATATAGATTCTATATTTTGATCATAAA\n+TCATTTCTAATCTTTCTCTCTTCTATTATTCCTCTGCTTCGCCCATTTTCAACCCCCCGG\n+ATGGGAAGCTATTGCTCTCTATTATTACATGTTGTAAACTCTGGTGGTCTCCCTCCTCAT\n+CCCATTATATTCCCCCtttttacaatcattattattattattattatgtttaaaatgttt\n+tattttattGCGTCAAGTCTGTCAGAAACCCATCAAAAGAGCATGTTTTTGAAAATAAAT\n+TAAATTGATTATCCACAAAAAGAGTTTTTAGTAGTCATCGTGTGTTTTTGATGTTAACTA\n+TAATAAGTAGCCACTTCAATTTTTTGTTGAAAACTTCAAAATGACACACACGATGACGCA\n+CCTCTGAAAGTTTATCGATACTTCCAAACTTTTCCCAGAATACTCCACCGTTTGATGGGG\n+AAATTGAAGGATTCTGAAAACACCAAAAACATAATGTTTGATATTACAAAAAATGACAGG\n+AACTTGGTTGTTTAATTGTAGATTTGCAGAGGGTGCAAGGAAATTTTTCATAAATTATTT\n+TTCCACATTCTTCAATTTTAACAGCGAATATCTCCCTTGGCTTTTGTTTTGGCATATAGC\n+CAACAAACAAACTATTTGGAATTTCTGTTTCTGTAATTTTTTTGTTCGTTTTCCTTTTGT\n+ACCGTTGAAATACGCCAAAATATATTCTTTCAAAGTGGAGTGGAGTGCCCAACTAATAGA\n+AAAAATATGACAAACTATGTTTCGAACTTTAATCTCTCTAATATTCTGATCATTCCCACT\n+TAATCAGCTGATAACAGTGTTAAAAAGTGAACACACACATGTTCTATGCTTTTCCATTCT\n+TTTCTTCCAACATTATTAATCTATTTGATTCGAGCAGCCAATCGGCTCCGCAAACAAATG\n+CTCTTGCGCACTCAAATTCTCTCCGTAGACTCCGCCCAGAAAGTTAATGCAAGTTTTATA\n+TTGATTCAAAATTAAAAAGTAGTACTGTATCGGTTTCAAATTTAAAAAAAAAGTTGAAAT\n+CAAAGGAATCAAGCTAATCCTAGACTAGTTGAAAGCAGTTTTAGATTAGGTGTGGTCTGA\n+CACTTGTGAAAACTTTTCTTTATTTTTCTAGATGCCAATGAGAAATGATTAACGTGGTCC\n+AGATCTTGGCTAGTATTTTCTGAAATAAATCTAACAAATAATATTTATCTCAGAATATAT\n+CTCAAAATCAAAAACTATAAATAATTCATTAGTGAGACTTATTGTATATATCTAACTCAT\n+AATTGATTAGTTGTACATAGGTAAAACAAATGGCCTTTCTCTTTCTCATATTACCCCTCA\n+CAAGTTGACAACACGAAGCGAATTAGTGATTCCGAAGGTGTGAACAATAGATTTGTAAAT\n+GTGTGAACACAATGCTTCATCATCTATTCTTTCAAGGAATCACTTGAGATACGGTAGCTA\n+CGAAAGAAAGTTGTTGCACACATAATTAACTAAAATGCTTCTCCATCTTTGCTCGTCACT\n+ATGGTAATTGGAGATGAATACGGAATTAAGATGAGAAGGGGGAAAACACTGAGAAATTCT\n+GAATACATTTCTAAAATTTGTTCTAGATTTTCAATTTTTCAATTAATTTAACGTTGGAAA\n+ATCTACATGTTGCACAAAAAAGGTATCAAAGTAATTTAATTTATTATATGACGAATAGGA\n+AATTTGCCTTTTGTGAAGACAATAGCGCTCCGCGACTATGTAGAAAAAACGCTCATCATA\n+TATTTTCCGGTTGTTGTTAATTATTGTTTTATTGTAAAATTGGAACCCAATAAATCTGTA\n+ACTCAAATTTTTTCATTAACACTAccgtatttcctctattagtaaggcatgcaaaactaa\n+ttttcggacacctaatttgatgcaaaactaatggaggtgcaaaactaattttcgaacagg\n+ttttttctcatgtttcccattaagttatgacataatatcaccaatttcaatgacaaatta\n+tgaaccgaaatggacgaattttacgactgatacgcaaaaattgtccgaattgtactcata\n+ttttgcctattttgacttgttataccaagtctgtaagagttttcctaatttttagaacga\n+ctttataatgcaaattttgaattcctaaaattagggaacaaatgaagcggtgcaaaacta\n+ttaaggtgcaaaactaatggaggtgcaaaactaatagaggtgcctaactaatagaggaaa\n+tacggTATTCAATTTTTTTATTGAACTTTAACTATTCCTATCGTTTGCCCATAAAGCATG\n+GTTTATCCCAAAAAGGCTAACCTGCTTAAACTGTTCTTCGTATGACCATGCTGGACCAGA\n+TGCATTTATACCAGATTCTGATGGTTCTTCTGATTTCACTGATGTTTCTTTTCTGAATCC\n+TCCTAATGTCAAATCTTCTGGTTCTCCTTGATTAGTGTTCTCTTCGTCATAGTCGTCAAG\n+TCCCGGAGAAATTGCTGTTAAGCCTGACGCAAGACCTAGAAGCTGTTGCTGAATACTGAA\n+TGGACCCTGAAGTGCTTGAAAGATCGGTGGTAAATTGAGAGGCGCTCGTAGATTTGACAG\n+ATTCAATTGTGAATTTAGAAGTCGTTGAACTACTTTTTGCCGGGATTCCAGGTCGAATAC\n+GTTTAGGTTTGCTGTTAGATCGGGAGAAGCTGGAGGTGATTTCTGCTGAAATTTTTTTAT\n+TGGATTGTCAGTTTTGGATATTTCAGAAGTTTCAGACCTGCACAGATTTGCCAATAAATA\n+TTGAAGAAACTAAATTTTCCGAAAATCCGAGCTACACTAAAAATTCAGTGAAGACGTCAA\n+ATTTTAAAAGTCAAAGAAAGCAAGATGTCGAATTTGTGGTTTTTGAAGCTCCGAAAATGC\n+CTTCGTAAAAATCTTGCTAATGTAAATTGAAAATACTTTTTGCTCACTTATCAAGCTTTG\n+AAAAACTGTTCAAATTGAAAAATAAAAAAGTGAACAAAATAAAGAAGTGAAAAAGTGCCA\n+TCAATTTACATTATAGTCAgaaaaattcaagtaaccgtactccttataaacgcacacttt\n+cctgcatttaacaaaataattgatcgtgtcggaccggtcaccgtattAAGAGTTAAAAAT\n+AAAGCCAAACCTCTTCTGTTTGATCATCAACTCGTTCATCACAATTACTGCTTGAATCAT\n+CATGATGTCCACCAACATTAACAGTTTCTTGAGTCGGCTCCTTTGACATACTGACGAACA\n+GTTGCGGTTCGTCAATCCTTACGGACATCTGCAAGAAAATACAAACTCTTAGAATTCATT\n+TTCcatcatccatcgtcatcatcacggtcatcaAAAGAAC\n' 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