| Previous changeset 0:773fdd1a02ea (2016-12-21) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/ commit fe9dd99a14770b6c5f26e24893599acb577e304f" |
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modified:
TargetFinder.xml |
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added:
macros.xml test-data/arabidopsis_thaliana_mRNA.fasta test-data/arabidopsis_thaliana_miRNA.fasta test-data/targetfinder_test_01.txt test-data/targetfinder_test_02.txt test-data/targetfinder_test_03.txt test-data/targetfinder_test_04.txt test-data/targetfinder_test_05.gff test-data/targetfinder_test_06.tab test-data/targetfinder_test_07.json test-data/targetfinder_test_08.tab |
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removed:
test-data/Antirrhinum_majus.mRNA.EST.fasta test-data/ath_miRNAs_predicted_targets.txt test-data/ath_miRNAs_test.fa |
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| diff -r 773fdd1a02ea -r c9d56748fbde TargetFinder.xml --- a/TargetFinder.xml Wed Dec 21 17:31:28 2016 -0500 +++ b/TargetFinder.xml Thu Mar 25 19:53:15 2021 +0000 |
| [ |
| b'@@ -1,73 +1,224 @@\n-<tool id="targetfinder" name="Plant small RNA target prediction tool" version="1.7.0">\n- <requirements>\n- <requirement type="package" version="1.7">targetfinder</requirement>\n- </requirements>\n+<tool id=\'targetfinder\' name=\'TargetFinder\' version=\'1.7.0+galaxy1\' profile=\'20.01\'>\n+ <description>plant small RNA target prediction tool</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro=\'edam\' />\n+ <expand macro=\'requirements\' />\n <stdio>\n- <exit_code range="1:" />\n+ <exit_code range=\'1:\' />\n </stdio>\n <command><![CDATA[\n targetfinder_threads.pl\n- -f $f\n- -d $d\n+ -f \'$f\'\n+ -d \'$d\'\n -c $c\n+ -p $output_format\n -t "\\${GALAXY_SLOTS:-12}"\n $r\n- -o $output1\n+ -o \'$output_file\'\n+ \n ]]></command>\n <inputs>\n- <param label="Input small RNA sequences file" help="(-f) FASTA-format" name="f" type="data" format="fasta" />\n- <param label="Target sequence database file" help="(-d) FASTA-format" name="d" type="data" format="fasta" />\n- <param label="Prediction score cutoff value" help="(-c) DEFAULT = 4" name="c" type="float" value="4.0" />\n- <param label="Search reverse strand for targets?" help="(-r) Use this option if the database is genomic DNA." name="r" type="boolean" falsevalue="" truevalue="-r" checked="false" />\n+ <param argument=\'-f\' type=\'data\' format=\'fasta\' label=\'Input small RNA sequences file\' help=\'FASTA-format\' />\n+ <param argument=\'-d\' type=\'data\' format=\'fasta\' label=\'Target sequence database file\' help=\'FASTA-format\' />\n+ <param argument=\'-c\' type=\'float\' value=\'4.0\' label=\'Prediction score cutoff value\' help=\'Predicted targets are printed out if they are equal to or lower than the cutoff score specified. DEFAULT = 4\' />\n+ <param argument=\'-c\' type=\'float\' value=\'4.0\' label=\'Prediction score cutoff value\' help=\'Predicted targets are printed out if they are equal to or lower than the cutoff score specified. DEFAULT = 4\' />\n+ <param argument=\'-r\' type=\'boolean\' falsevalue=\'\' truevalue=\'-r\' checked=\'false\' label=\'Search reverse strand for targets?\' help=\'Use this option if the database is genomic DNA.\' />\n+ <param name=\'output_format\' argument=\'-p\' type=\'select\' label=\'Output format\' help=\'Output format for small RNA-target pairs (Default = classic).\' >\n+ <option value=\'classic\'>Original TargetFinder base-pair format</option>\n+ <option value=\'gff\'>GFF</option>\n+ <option value=\'json\'>JavaScript Object Notation (JSON)</option>\n+ <option value=\'table\'>Tab-delimited format</option>\n+ </param>\n </inputs>\n <outputs>\n- <data name="output1" format="data"/>\n+ <data name=\'output_file\' format=\'txt\'>\n+ <change_format>\n+ <when input="output_format" value="gff" format="gff" />\n+ <when input="output_format" value="json" format="json" />\n+ <when input="output_format" value="table" format="tabular" />\n+ </change_format>\n+ </data>\n </outputs>\n <tests>\n <test>\n- <param name="f" value="ath_miRNAs_test.fa"/>\n- <param name="d" value="Antirrhinum_majus.mRNA.EST.fasta"/>\n- <param name="r" value=""/>\n- <param name="c" value="4.0"/>\n- <param name="t" value="1"/>\n- <output name="output1" file="ath_miRNAs_predicted_targets.txt" compare="contains"/>\n+ <param name=\'f\' value=\'arabidopsis_thaliana_miRNA.fasta\'/>\n+ <param name=\'d\' value=\'arabidopsis_thaliana_mRNA.fasta\'/>\n+ <param name=\'r\' value=\'false\'/>\n+ <param name=\'c\' value=\'4.0\'/>\n+ <param name=\'output_format\' value=\'classic\'/>\n+ <output name=\'output_file\' file=\'targetfinder_test_01.txt\' compa'..b't site sequece and the query sequence are base pair symbols. A \':\' (colon) symbol represents an ordinary Watson-Crick base pair, a \'.\' (period) represents a G:U base pair, and a \' \' (space) represents a mismatch.\n \n-Between the target site sequece and the query sequence are base pair symbols.\n+ ::\n+ \n+ target 5\' UAGGGCAAAUCUUCUUUGGCA 3\' \n+ .:::::::::::.:::::::: \n+ query 3\' GUCCCGUUUAGAGGAAACCGU 5\'\n \n-A ":" (colon) symbol represents an ordinary Watson-Crick base pair, a "." (period) represents a G:U base pair, and a " " (space) represents a mismatch.\n \n If a small RNA is predicted to target a sequence more than once, each target site will be output as separate output.\n+\n+\n+----\n+\n+.. class:: infomark\n+\n+**Additional output formats**\n+\n+In addition to the output described above (\'classic\' output), three new output format options were added to TargetFinder.\n+\n+Generic Feature Format (GFF3):\n+\n+ ::\n+\n+ AT2G33770.1 | Symbols: UBC24 | phosphate 2 | chr2:14277558-14283040 REVERSE LEN targetfinder rna_target 607 627 1.5 + . smallRNA=miR399a;target_seq=UAGGGCAAAUCUUCUUUGGCA;base_pairs=.:::::::::::.::::::::;miR_seq=GUCCCGUUUAGAGGAAACCGU\n+ AT2G33770.1 | Symbols: UBC24 | phosphate 2 | chr2:14277558-14283040 REVERSE LEN targetfinder rna_target 740 760 1.5 + . smallRNA=miR399a;target_seq=UAGGGCAUAUCUCCUUUGGCA;base_pairs=.:::::: :::::::::::::;miR_seq=GUCCCGUUUAGAGGAAACCGU\n+ AT2G33770.1 | Symbols: UBC24 | phosphate 2 | chr2:14277558-14283040 REVERSE LEN targetfinder rna_target 829 849 1.5 + . smallRNA=miR399a;target_seq=UUGGGCAAAUCUCCUUUGGCA;base_pairs=. :::::::::::::::::::;miR_seq=GUCCCGUUUAGAGGAAACCGU\n+\n+\n+Tab-deliminated Format:\n+\n+ ::\n+\n+ miR399a\tAT2G33770.1 | Symbols: UBC24 | phosphate 2 | chr2:14277558-14283040 REVERSE LEN\t607\t627\t+\t1.5\tUAGGGCAAAUCUUCUUUGGCA\t.:::::::::::.::::::::\tGUCCCGUUUAGAGGAAACCGU\n+ miR399a\tAT2G33770.1 | Symbols: UBC24 | phosphate 2 | chr2:14277558-14283040 REVERSE LEN\t740\t760\t+\t1.5\tUAGGGCAUAUCUCCUUUGGCA\t.:::::: :::::::::::::\tGUCCCGUUUAGAGGAAACCGU\n+ miR399a\tAT2G33770.1 | Symbols: UBC24 | phosphate 2 | chr2:14277558-14283040 REVERSE LEN\t829\t849\t+\t1.5\tUUGGGCAAAUCUCCUUUGGCA\t. :::::::::::::::::::\tGUCCCGUUUAGAGGAAACCGU\n+\n+JavaScript Object Notation Format (JSON):\n+\n+ ::\n+\n+ {\n+ \'miR399a\': {\n+ \'hits\' : [\n+ {\n+ \'Target accession\': \'AT2G33770.1 | Symbols: UBC24, ATUBC24, PHO2 | phosphate 2 | chr2:14277558-14283040 REVERSE LEN\',\n+ \'Score\': \'1.5\',\n+ \'Coordinates\': \'607-627\',\n+ \'Strand\': \'+\',\n+ \'Target sequence\': \'UAGGGCAAAUCUUCUUUGGCA\',\n+ \'Base pairing\': \'.:::::::::::.::::::::\',\n+ \'amiRNA sequence\': \'GUCCCGUUUAGAGGAAACCGU\'\n+ }\n+ ]\n+ }\n+ }\n+\n+\n+----\n+\n+.. class:: infomark\n+\n+**Method**\n+\n+TargetFinder searches for potential miRNA target sites in a FASTA-formated sequence database using three main steps.\n+\n+\n+ 1. The small RNA query sequence is aligned to every sequence in the FASTA-formated sequence database using `Smith-Waterman (SW) alignments <https://en.wikipedia.org/wiki/Smith%E2%80%93Waterman_algorithm>`_ implemented in the FASTA package (ssearch35_t).\n+ 2. The SW alignments are converted into RNA duplexes.\n+ 3. Each duplex is scored using a position-dependent scoring matrix.\n+\n+SW alignments are used to identify the best complementary regions between the small RNA query sequence and every sequence in the FASTA-formated sequence database.\n+\n ]]></help>\n- <citations>\n- <citation type="doi">10.1016/j.cell.2005.04.004</citation>\n- <citation type="doi">10.1371/journal.pone.0000219</citation>\n- <citation type="doi">10.1007/978-1-60327-005-2_4</citation>\n- </citations>\n+ <expand macro=\'citations\' />\n </tool>\n \n' |
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| diff -r 773fdd1a02ea -r c9d56748fbde macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Mar 25 19:53:15 2021 +0000 |
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| @@ -0,0 +1,34 @@ +<macros> + <token name='@TOOL_VERSION@'>1.7</token> + <xml name='edam'> + <edam_topics> + <edam_topic>topic_3170</edam_topic> + <edam_topic>topic_3308</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_0292</edam_operation> + </edam_operations> + </xml> + <xml name='requirements'> + <requirements> + <requirement type='package' version='@TOOL_VERSION@'>targetfinder</requirement> + </requirements> + </xml> + <xml name='citations'> + <citations> + <citation type='bibtex'> + @misc{githubTargetFinder, + author = {Fahlgren, Noah}, + year = {2016}, + title = {TargetFinder}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/carringtonlab/TargetFinder}, + } + </citation> + <citation type='doi'>10.1016/j.cell.2005.04.004</citation> + <citation type='doi'>10.1371/journal.pone.0000219</citation> + <citation type='doi'>10.1007/978-1-60327-005-2_4</citation> + </citations> + </xml> +</macros> |
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| diff -r 773fdd1a02ea -r c9d56748fbde test-data/Antirrhinum_majus.mRNA.EST.fasta --- a/test-data/Antirrhinum_majus.mRNA.EST.fasta Wed Dec 21 17:31:28 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,23 +0,0 @@ ->gi|51053470|gb|AJ787245.1|AJ787245 EST AJ787245 Antirrhinum majus whole plant Antirrhinum majus cDNA clone 018_1_01_o13, mRNA sequence. -CTCATACACCATGCTTTAAGCTTCATTGTACGGTCATCTTTCTCTTTTACCCTTGTTCTT -CCTTTTCTCTCCAAAAAGAAAAAAATGGATCCCAACATGCAAAACATGATGTCCTCTTAC -TTAAAAATCAAGAAACTTGTGGGAGATGAAGGGAGTGATTTTGAGGAGGAAGAAGAAGGT -GAAGACGAAGAAGAAGAAGAACAAGAAAGGGTTGTTAAAGTGAACTTTGCAGAGTCACAA -TTGAAGAAGAAAAAATTGAATCTTGGTGAAGGGTCTGGTGGAAAAAGTGGTGAGAAACAT -ACTGCTAGTGGTGGTGGAGTTGTGGCTCAGCCTTGTTGTTTGGTTGAGAATTGTGGTGCT -GATCTGAGGAATTGCAAGAAGTATTACCAAAGGCACAGGGTTTGTGAGGTTCATGCTAAG -GCTCCTGTGGTTTCTGTTGAGGGGTTGATGCAAAGGTTCTGTCAGCAATGTAGCAGGTTC -CATGATCTCTCGGAATTCGATCAGACAAAGAGGAGTTGTCGCCGACGTCTCGCTGGCCAC -AATGAACGGCGCCGTAAGAGTTCGCTCGAGTCTCACAAGGAGGGCAGAAGCCCAAGATAA -GGACAGCCTGATGAAACAAGTTTCCGTGTTATTGGAAAGTGTCTAGAATGCTTACTCTCT -TCTGTCACCTCGTGCC ->gi|51107699|gb|AJ792371.1|AJ792371 EST AJ792371 Antirrhinum majus whole plant Antirrhinum majus cDNA clone 018_2_11_f24, mRNA sequence. -TCTCTAATTCAGCACTGCTCTCTCTCTTCTGTCAAATAGTCCTGGGGCTCTAGAAACTCG -AACAATTTTCTTGGTACTAATGGAAACGGGCCAACCATAGTTCAGCCGTCTATTAACCCT -GGTGCTACAATTGGACAGTTTACCTGTCCCTCTTGGGGTTTTGGAGGCAACCCAGCTGAT -AACACCTCCCATGATATGCCTCCCAATCTGAATTTAGGACAATTTTCTCACTCCAGTAAC -AGTCACTATACTGGAGAGCCTGGGGTAGTCCAACTGAGCCACGGACAATTCCAGGACCTC -GATCACTCAAGAGGCTATGATTCTTCCGTTCAGGACATGCATTGGTCACTTTGAAGTATT -CCGATTCTGGACTCCCTCAATCTAGTGTTTTCAGTAACTTAAGTAAATTCCAGTGAATTA -TCAAACACCAGGGCTTTTGTGGTGTTGCCATGTGTTCTCTTAGGAATCTGAAACTTGTAT -GTGTGGGGTTATTTATGCTATTGCTTGTGGGCCTA |
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| diff -r 773fdd1a02ea -r c9d56748fbde test-data/arabidopsis_thaliana_mRNA.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/arabidopsis_thaliana_mRNA.fasta Thu Mar 25 19:53:15 2021 +0000 |
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| b'@@ -0,0 +1,5173 @@\n+>AT1G01200.1 | Symbols: RABA3, ATRABA3, ATRAB-A3 | ARABIDOPSIS RAB GTPASE HOMOLOG A3, RAB GTPase homolog A3 | chr1:86486-88409 REVERSE LENGTH=1207\n+ATTTCAACGACTTAAACCAAACCAAATTTACGAAATTTTGGTTTGTAGCAGTTTTAGTTTTATTAAATATGGTTGCGAATGGTTATGAGTGAATCCAACC\n+AATCTCACTGAAGTGGTTCAGAATTTTTGTTAATTCGGTATATTCGTACTGAACCATATAAAACCAAATTTCTTCTCCTTTCTTCTCTTTTCTCTGTTTC\n+ACTCACTCCCACTTTACTCAAAAGAGACTTAAACTTTATAGTTGTTTTCTTCATCAGCGCAATAATGAACGAAGAGATGAGCGGTGAGTCGCCGGAGAAT\n+AACAAACACGTAAAGAAACCGACGATGCCGGAAAAGATCGATTACGTGTTCAAGGTGGTGGTCATTGGAGATTCTGCTGTCGGGAAAACGCAGCTCCTCT\n+CACGTTTTACACACAACGAGTTCTGTTATGATTCAAAATCAACCATTGGTGTCGAGTTTCAGACACGGACCATCACTCTTCGGGGCAAACTCGTCAAAGC\n+TCAGATCTGGGACACCGCCGGTCAAGAGAGATACAGAGCGGTGACTAGCGCCTACTACAGAGGTGCGTTAGGTGCGATGGTGGTTTACGACATTACCAAA\n+CGCCTCTCATTCGACCACGTTGCACGTTGGGTCGAGGAATTACGTGCTCACGCCGATGATTCCGCCGTGATCATGCTCGTCGGAAACAAAGCCGATCTCT\n+CCGTTGGTAAACGTGCCGTTCCTACGGAGGATGCAGTCGAATTCGCCGAGACTCAACGGCTTTTTTTCTCGGAAGTCTCGGCTCTAAGCGGCGGAAACGT\n+CGACGAAGCTTTTTTCCGTTTACTCGAGGAGATTTTCAGCCGCGTTGTTGTTTCGAGAAAAGCTATGGAATCCGACGGTGGAGCCACCGTGAAACTTGAC\n+GGTTCGAGAATTGATGTCATCTCTGGTTCGGATCTTGAGACTAGTAATATCAAGGAACAAGCTTCGTGCTCGTGTTGAAATTTTGAGTGATAGGCCATAA\n+AATCAAAAGCCAATTATTGGGCCTTTCTTTAAGCCCATATATGACTCGGATCTTTGTTTGGGTTTTTCATGTTTAGAGAATTAGAGGTGGTGCTTATAGT\n+AAAATCAAAAAGCTATTCATGTGTCACTCGTAATCTCTTTGACATTCTTGTATATGTAAAGAAAAAACAATTCTTTTATTCTGTCAAGTTCCAAGGAGTT\n+TCTTCTA\n+>AT1G01600.1 | Symbols: CYP86A4 | "cytochrome P450, family 86, subfamily A, polypeptide 4" | chr1:218834-221286 FORWARD LENGTH=2323\n+ACATACATATGATCATTTAATGAAATTCATTAAATGAAACTATTCCTTTCGCTGCAAAATTAGGTACCAGTAAAGCATAAACACCACTTTACCACTTCTT\n+GAATTCCAAATCTGAAAGCTCTGTCATTATATATGTATAAACCAATTTAAACATATACATGTCTCACCGATAACAACGGAGGTTCATTAATGAGGGTTTG\n+ATTATGATACTTACGAGTGACAGATTGTGAATATCAAAGAGAAGCTTCTTCCTCCCTTTTTTCTCCCTATAAATTTCCGTAGAAAAATCATTCATTCGCA\n+TCTCTTCTCTTCTCAAAAATCACCACATTTCTTTACTTCTCTGGGAAACAATAATAAAAGAGCTACATGGAAATATCCAATGCCATGCTTCTTGTAGCGA\n+TCGTAACAGGGTATTGGCTATGGTTCAAGAGGATCTCACGGTGGCTAAAGGGTCCACGTGTCTGGCCTCTGTTGGGTAGTCTTCCTGGTCTGATAGAGCA\n+ACGTGACAGGATGCATGAATGGATCACCGAGAACCTTCGTGCGTGCGGCGGCACTTACCAGACTTGTATCTTTGCCGTGCCTTTCTTGGCTAAGAAGCAA\n+GGTCTCGTGACTGTCACGTGTGACCCTAAGAATCTCGAACACATGCTCAAGACCCGGTTCGATAACTACCCTAAAGGTCCTACATGGCAATCCGTCTTCC\n+ACGATCTCCTGGGTCAAGGTATTTTCAACTCCGACGGTGACACCTGGCTCTTCCAACGCAAAACCGCCGCTCTTGAATTCACAACAAGGACGTTGCGGCA\n+AGCCATGGGTAGGTGGGTAAACCGAGGAATTAAGCTCCGGTTCTGTCCGATTCTTGCAACGGCTCAAGACAATGCAGAACCAGTTGATCTCCAAGACTTA\n+ATACTACGGCTCACATTCGACAACATTTGCGGATTGGCGTTCGGTAAGGACACACGAACCTGCGCACCGGGGCTTCCCGAGAATGGCTTTGCCTCGGCAT\n+TCGATCGAGCCACCGAAGCCTCGCTTCAACGGTTTATCATACCGAAGTTTATGTGGAAGCTGAAGAAATGGCTTGGGCTCGGTTTAGAAGTAAGCTTGAG\n+CCGAAGCTTAGGAGAAATCGATGAATATCTTGCTGCTGTTATAAATACACGTAAGCAAGAACTGATGAGTCAGCAAGAAAGTGGAACCCACCAGAGACAC\n+GACGATCTCCTCTCGCGTTTCATGATGAAGAAAACAGAATCTTACAGTGACACGTTTCTCCAACACGTGGCGCTTAACTTTATCCTAGCTGGACGTGACA\n+CGTCATCAGTTGCGCTGAGCTGGTTCTTCTGGCTTATCACGATGCATCCAACCGTCGAGGATAAAATCGTCCGCGAGATCTGCTCCGTCCTGATCGAGAC\n+ACGTGGCACTGATGACGTCGCGTCGTGGACTGAGGAGCCTCTAGGGTTCGACGAAATCGACCGTTTGGTTTACCTGAAGGCGGCGATCTCGGAGACGCTC\n+AGGCTTTACCCATCGGTGCCGGAAGATTCAAAACACGTCGAGAACGACGACGTTTTACCAGATGGGACCTTCGTTCCGGCGGGATCATCGGTGACGTACT\n+CGATTTACGCGGCGGGGAGGATGAAGTCGACTTGGGGAGAAGATTGTCTGGAATTCAATCCGGAGAGATGGATTTCTCCGATCGACGGAAAATTTATCAA\n+TCACGATCAATATCGGTTCGTGGCGTTCAATGCTGGACCAAGGATCTGCTTGGGGAAAGATCTGGCGTATCTTCAGATGAAAACAATAGCGGCAGCGGTG\n+CTTCTCCGTCACCGGCTTACGGTGGTTCCGGGACATAAAGTGGAGCAGAAGATGTCGTTGACGCTATTTATGAAGAACGGACTTCTGGTGAATCTGTATA\n+AGAGAGATCTCCAAGGAATCATAAAGAGTCTAGTGGTGAAGAAGAGCGACGGTGTCTCTAACGGTCAATGTAACGGCGTTATTGGTGAAGGCGTCGCCGT\n+TTACTTAAATACGGGAGTTGCAGTGGTTTAACAAGGCCAATCACGTCCCTGATTTATTCATATACACTTTTTTTCTTTAATTCCAAAAGAAAACACTTGA\n+ACAAAAATACAGCTTGTAATTTTTGTTCAATATGAAATTGTAAGCAATATACTCCAGCCGACAAAAAAAAGAAAGAAAAAGCAATATACTCCAATTAGTA\n+ATTTTACCGGGTTCTTTTCTTTTTCTATTTTTTTGCAAACCTTTTTATTTTCTTTATGGGAAATTATTGTAAGCAAATCATATACGTTTATATAGTCTAA\n+AATAAATACATTTTACTTCGTAC\n+>AT1G01620.1 | Symbols: TMP-B, PIP1;3, PIP1C | plasma membrane intrinsic protein 1C, PLASMA ME'..b'TTGATGGCGGCTACTGCGACGGA\n+GGATGGAGGATTAAGCTTCACTGTGGCTTCAGTAATGGAGGATGTGTTGCAGCAACATGGAAATGGGCTTAGAGATCATGATTTAGTGTCTCGTCGAGCT\n+GAAGAAGCTGCATCGAGGAGATATGAGGCGGCTAATTGGCTGAGAAGGATGGTTGGAGTTGTTGGAGCTAAGGATTTGCCTGCAGAGCCAACAGAAGAAG\n+GGCTTAGGCTTGGTTTAAGAAGTGGAATTATCCTTTGTAAAGTCCTCAATAAGGTTCAACCTGGAGCTGTCTCAAAGGTTGTGGAAAGTCCTTGTGATGC\n+CATTCTTGTTGCGGATGGAGCTCCGTTATCAGCATTTCAGTATTTTGAGAATGTTAGGAACTTTCTTGTTGCTATACAGGAAATGGGGTTTCCAACATTT\n+GAGGCATCTGATCTCGAGCAAGGAGGAAATGCTTCTCGAGTTGTGAATTGTGTTTTGGCTATCAAATCATATGATGAATGGAAACAAAGTGGTGGAATTG\n+GAGTTTGGAAATTTGGTGGCAACATTAAGCCTCCTGCACTTGGGAAGTCATCTTTTGTCAGAAAAAACTCAGAGCCATTCATGAACTCTTTATCGAGAAC\n+CTCCTCGATCAACAATGAGAAAGCTCCCTCTGAGAATGATTCTAACAAGCTGTCCAGTCCCAGTTCCTTGAGCACACTTGTTCGCGCTGTTCTATCAGAT\n+AAAAAGCCTGAGGATGTGCCCAAACTGATTGAATCTCTGCTGAGTAAAGTAGTCGAAGAGTTTGAAAATCGAGTTACAAATCAGTATGAGTTGGTTAGAG\n+CAGCTCCAAGAGAATCAACTTCGTCACAGAACAACAGATCATTTCTTAAACCTCTTGGTGAAAGAGAGAGGGAAGAGAAGAGTTTCAAAGCAATAAAGAA\n+AGATGATCACAATAGTCAGATTCTTGACGAAAAGATGAAAACTCGCCAATTTAAACAACTGACAATCTTCAACCAACAACAAGAAGATATAGAAGGACTA\n+AGACAGACGCTCTACACAACAAGGGCTGGTATGCAATTTATGCAGAAGAAATTTCAAGAAGAGTTCTCTTCTCTTGGTATGCACGTTCATGGCCTTGCTC\n+ATGCTGCTTCTGGCTATCACCGAGTTCTTGAAGAAAACCGAAAACTTTATAATCAAGTGCAGGATCTCAAGGGTAGCATCCGTGTTTATTGTCGGGTGCG\n+GCCATTTTTGCCTGGACAATCCAGCTTTTCTAGTACAATTGGGAACATGGAGGATGATACCATAGGGATCAATACTGCATCTAGACATGGAAAATCACTC\n+AAATCCTTCACTTTCAACAAAGTCTTTGGCCCATCTGCAACTCAAGAAGAGGTATTTTCTGATATGCAGCCATTGATCCGTTCTGTTCTTGATGGATACA\n+ATGTCTGCATATTTGCATATGGTCAAACTGGATCAGGAAAAACATTCACAATGAGTGGACCAAGAGATCTAACGGAGAAGAGCCAGGGAGTTAATTACAG\n+AGCACTTGGTGATCTGTTTCTTCTTGCTGAACAAAGAAAAGACACATTCCGCTACGATATTGCAGTTCAGATGATTGAGATTTACAATGAGCAAGTTAGA\n+GACCTTTTGGTTACTGATGGAAGCAATAAAAGGTTAGAGATCAGGAATAGCTCTCAAAAGGGTCTAAGTGTACCGGATGCAAGTCTTGTTCCAGTCTCTT\n+CAACATTTGATGTTATTGATCTAATGAAAACTGGGCACAAGAATCGAGCCGTTGGATCAACAGCCTTGAATGATCGAAGCAGTCGTTCTCATAGCTGCTT\n+GACTGTTCATGTTCAAGGAAGAGACTTGACTTCAGGAGCTGTGCTTCGAGGATGCATGCATCTTGTGGATCTAGCAGGCAGTGAGAGGGTAGACAAATCC\n+GAGGTTACTGGAGACAGACTAAAAGAAGCACAGCACATCAATAGATCGCTCTCTGCTTTAGGAGATGTGATTGCTTCGCTAGCTCACAAGAACCCACATG\n+TTCCTTACAGAAACAGCAAACTCACACAACTCCTTCAGGACTCTCTTGGAGGACAAGCAAAGACATTGATGTTTGTCCACATTAGTCCTGAGGCAGATGC\n+AGTTGGGGAAACAATAAGCACTTTGAAGTTTGCAGAGAGAGTAGCTACGGTTGAGCTTGGGGCTGCACGAGTGAACAATGATACTTCAGATGTTAAGGAA\n+CTCAAAGAACAGATTGCTACTCTTAAAGCAGCACTCGCGAGAAAAGAAGCAGAGTCACAGCAGAACAACATCTTGAAAACTCCTGGTGGCTCTGAGAAAC\n+ACAAAGCCAAAACTGGTGAAGTAGAGATTCATAACAATAACATCATGACAAAGAAATCTGAGAGTTGTGAAGTGGAGGAGATTACAGTGAACTCACCACC\n+TTGGCCACCAGTAGCAAGTCCAGGACAAGCCTACAGAGAGGATGACCGAAGTTTCGGGTCCAGCGAGTGGGTTGACAAGGTGATGGTGAATAACAGACAA\n+GACGAGATGAGAAGAGTGGAGAGTCTTTGGGGAGGAGCCACAACAGAGAATGGTATTGGTATTCTGCCGGAAGATTTTTACAGGAGAGATTTGGCTTCAG\n+ACACTTCAAGAATATTCTCTGAACATTCTTACAACATCTTCATGGGAAACAACAACAGCACAGACGATCTAGATGCAGCCACAAGTGACTCATCTGAGCC\n+AGATTTGCTCTGGCAATTCAACCAGTCCACCAAGATACCTACAAGAAGCAATATTGAGTCAAAACTCAAGAAACCCGTCTCAAAACCTATAAGAAGTCCT\n+CAATCCAGGAACAACTCAAACAACACGGTTTCACGTCCTTTGGCTTCACAGAAGGTAGGGAATGGTCCTCGTGGCATGAAACAGTTCGGTCCTGCTGATA\n+TGAAGCGGAAAGCTACTAACGCCAGACATTGAAGGCCACTCACTCACACGGATACATACATACACACTCACATGGCTTCTTATTGGTTTTGATTTGTTTA\n+TTTTTCATCCATTGGTTTTTATTGTTTCTTCTTCTCTCGTTTGGTTGTGCGAGCTTTTATATACATAACACAGACAAAGACAATAGCTAGACAATGCAAC\n+AACAGTTTCTTCTTGTTGCTCTCTTTCTTGGGTTTTGTTTTACTTTTCTGTTCTATGTATATTCTTCCACTAGCTGAACATAAAAAATATGAAAGATTTG\n+TTTGTTAACTATTTGCTTGAGAGTTTTTTTAGTATATTC\n+>AT3G02830.1 | Symbols: ZFN1, PNT1 | zinc finger protein 1, PENTA 1 | chr3:613772-616145 FORWARD LENGTH=1726\n+TTTTTCTCAAAATTTCTTGTTTGATTTGTGTGGAGGTGAGACGAGAACGCTTTTTTGCTTTTCGTCTTTCTCTCTCTCTTTCTTTCTTCACTACCTCTCA\n+CCTCTCTGTTTACACGATTCTTCTTCTTCTTCTTCTTCTTCTTTAGATGTCTTCTTCCTCCATTGTCATCTACCTCTCTACACTTCATTTTCTTGTTGGA\n+AGAAGATCGATTACCGGTGACTCATTCTTAGTGATGACAGTATAATGTCTGATGCTTATTATCATCATCATCATCATCGGAGACATTCTTCCTCTTCACG\n+TCTATGGATTTTAATGCCGGAGTTCCCATGTCTTCTCTTTCACCTTTGATGAATCAAGATGCAATGTGGCAAATGAATTTGAGTTCAGATGAAACAATGG\n+AAACTGGTTCTTACCCTGAACGACCAGGAGAGCCTGATTGTTCTTATTACATAAGAACTGGTCTTTGTAGATTTGGCTCTACTTGTCGGTTCAACCATCC\n+TCGTGATCGGGAACTGGTTA\n\\ No newline at end of file\n' |
| b |
| diff -r 773fdd1a02ea -r c9d56748fbde test-data/arabidopsis_thaliana_miRNA.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/arabidopsis_thaliana_miRNA.fasta Thu Mar 25 19:53:15 2021 +0000 |
| b |
| @@ -0,0 +1,54 @@ +>Ath-miR156c +TGACAGAAGAGAGTGAGCAC +>Ath-miR156e +TGACAGAAGAGAGTGAGCAC +>Ath-miR156g +CGACAGAAGAGAGTGAGCAC +>Ath-miR165a +TCGGACCAGGCTTCATCCCCC +>Ath-miR165b +TCGGACCAGGCTTCATCCCCC +>Ath-miR168a +TCGCTTGGTGCAGGTCGGGAA +>Ath-miR170 +TGATTGAGCCGTGTCAATATC +>Ath-miR171a +TGATTGAGCCGCGCCAATATC +>Ath-miR171c +TTGAGCCGTGCCAATATCACG +>Ath-miR393a +TCCAAAGGGATCGCATTGATCC +>Ath-miR393b +TCCAAAGGGATCGCATTGATC +>Ath-miR395a +CTGAAGTGTTTGGGGGAACTC +>Ath-miR395b +CTGAAGTGTTTGGGGGGACTC +>Ath-miR395c +CTGAAGTGTTTGGGGGGACTC +>Ath-miR395d +CTGAAGTGTTTGGGGGAACTC +>Ath-miR395e +CTGAAGTGTTTGGGGGAACTC +>Ath-miR395f +CTGAAGTGTTTGGGGGGACTC +>Ath-miR829 +AGCTCTGATACCAAATGATGGAAT +>Ath-miR851 +TGGGTGGCAAACAAAGACGAC +>Ath-miR861 +GATGGATATGTCTTCAAGGAC +>Ath-miR2111a +TAATCTGCATCCTGAGGTTTA +>Ath-miR2111b +TAATCTGCATCCTGAGGTTTA +>Ath-miRN118 +TGAGCTGTGATGAAATTGGC +>Ath-miRN132 +AAGTCCTCGTGTTGCATCGCT +>Ath-miRN134 +TCTGGGATGAATTTGGATCT +>Ath-miRN143 +TTGGCCCATGTCGTTATGATT +>Ath-miRN146 +GGGGTTTATAGACCTCGAATC |
| b |
| diff -r 773fdd1a02ea -r c9d56748fbde test-data/ath_miRNAs_predicted_targets.txt --- a/test-data/ath_miRNAs_predicted_targets.txt Wed Dec 21 17:31:28 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,12 +0,0 @@ -query=ath-miR156g, target=gb|AJ787245.1|AJ787245 EST AJ787245 Antirrhinum majus whole plant Antirrhinum maju, score=2.5, range=0-0, strand=1 - -target 5' AUGCUUACUCUCUUCUGUCA 3' - ::::.::::::::::::: -query 3' CACGAGUGAGAGAAGACAGC 5' - -query=ath-miR156g, target=gb|AJ792371.1|AJ792371 EST AJ792371 Antirrhinum majus whole plant Antirrhinum maju, score=3, range=0-0, strand=1 - -target 5' CUGCUCUCUCUCUUCUGUCA 3' - ::::: :::::::::::: -query 3' CACGAGUGAGAGAAGACAGC 5' - |
| b |
| diff -r 773fdd1a02ea -r c9d56748fbde test-data/ath_miRNAs_test.fa --- a/test-data/ath_miRNAs_test.fa Wed Dec 21 17:31:28 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ ->ath-miR156g -CGACAGAAGAGAGUGAGCAC |
| b |
| diff -r 773fdd1a02ea -r c9d56748fbde test-data/targetfinder_test_01.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/targetfinder_test_01.txt Thu Mar 25 19:53:15 2021 +0000 |
| b |
| @@ -0,0 +1,37 @@ +No results for Ath-miR2111b +No results for Ath-miR395b +No results for Ath-miR851 +No results for Ath-miR171c +No results for Ath-miRN146 +No results for Ath-miR393a +No results for Ath-miR393b +No results for Ath-miRN143 +No results for Ath-miR170 +No results for Ath-miRN134 +No results for Ath-miRN132 +No results for Ath-miR156g +No results for Ath-miR395f +No results for Ath-miR171a +No results for Ath-miR2111a +No results for Ath-miR829 +No results for Ath-miR168a +query=Ath-miR156c, target=AT1G26890.1 | Symbols: no symbol available | no full name available | chr1:9317589-9319246 FOR, score=4, range=948-967, strand=1 + +target 5' GAGAUCUCUUUCUUCUGUCA 3' + : : :: ::.:::::::::: +query 3' CACGAGUGAGAGAAGACAGU 5' + +No results for Ath-miR395d +No results for Ath-miR395a +No results for Ath-miR165a +query=Ath-miR156e, target=AT1G26890.1 | Symbols: no symbol available | no full name available | chr1:9317589-9319246 FOR, score=4, range=948-967, strand=1 + +target 5' GAGAUCUCUUUCUUCUGUCA 3' + : : :: ::.:::::::::: +query 3' CACGAGUGAGAGAAGACAGU 5' + +No results for Ath-miR395c +No results for Ath-miR165b +No results for Ath-miR861 +No results for Ath-miR395e +No results for Ath-miRN118 |
| b |
| diff -r 773fdd1a02ea -r c9d56748fbde test-data/targetfinder_test_02.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/targetfinder_test_02.txt Thu Mar 25 19:53:15 2021 +0000 |
| b |
| @@ -0,0 +1,61 @@ +No results for Ath-miRN134 +No results for Ath-miR170 +No results for Ath-miR395c +No results for Ath-miR395f +No results for Ath-miR156g +No results for Ath-miR2111b +No results for Ath-miR168a +No results for Ath-miRN132 +No results for Ath-miR861 +No results for Ath-miR165b +query=Ath-miR156c, target=AT1G04680.1 | Symbols: no symbol available | no full name available | chr1:1303467-1307973 REV, score=3.5, range=1263-1281, strand=-1 + +target 5' GUGUCCACUCUCUUC-GUCA 3' + :::. :::::::::: :::: +query 3' CACGAGUGAGAGAAGACAGU 5' + +query=Ath-miR156c, target=AT1G26890.1 | Symbols: no symbol available | no full name available | chr1:9317589-9319246 FOR, score=4, range=948-967, strand=1 + +target 5' GAGAUCUCUUUCUUCUGUCA 3' + : : :: ::.:::::::::: +query 3' CACGAGUGAGAGAAGACAGU 5' + +query=Ath-miR156c, target=AT2G33420.1 | Symbols: no symbol available | no full name available | chr2:14158671-14162618 F, score=4, range=671-689, strand=-1 + +target 5' CUG-UCACUCUGUUCUGUCA 3' + :: ::::::: :::::::: +query 3' CACGAGUGAGAGAAGACAGU 5' + +No results for Ath-miR395a +No results for Ath-miRN118 +No results for Ath-miR829 +No results for Ath-miR393b +No results for Ath-miR2111a +No results for Ath-miR395e +No results for Ath-miR851 +No results for Ath-miR393a +No results for Ath-miR395d +No results for Ath-miRN146 +No results for Ath-miR171a +No results for Ath-miR171c +No results for Ath-miR165a +No results for Ath-miRN143 +query=Ath-miR156e, target=AT1G04680.1 | Symbols: no symbol available | no full name available | chr1:1303467-1307973 REV, score=3.5, range=1263-1281, strand=-1 + +target 5' GUGUCCACUCUCUUC-GUCA 3' + :::. :::::::::: :::: +query 3' CACGAGUGAGAGAAGACAGU 5' + +query=Ath-miR156e, target=AT1G26890.1 | Symbols: no symbol available | no full name available | chr1:9317589-9319246 FOR, score=4, range=948-967, strand=1 + +target 5' GAGAUCUCUUUCUUCUGUCA 3' + : : :: ::.:::::::::: +query 3' CACGAGUGAGAGAAGACAGU 5' + +query=Ath-miR156e, target=AT2G33420.1 | Symbols: no symbol available | no full name available | chr2:14158671-14162618 F, score=4, range=671-689, strand=-1 + +target 5' CUG-UCACUCUGUUCUGUCA 3' + :: ::::::: :::::::: +query 3' CACGAGUGAGAGAAGACAGU 5' + +No results for Ath-miR395b |
| b |
| diff -r 773fdd1a02ea -r c9d56748fbde test-data/targetfinder_test_03.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/targetfinder_test_03.txt Thu Mar 25 19:53:15 2021 +0000 |
| b |
| b"@@ -0,0 +1,252 @@\n+No results for Ath-miR395d\n+query=Ath-miR395b, target=AT1G66400.1 | Symbols: CML23 | calmodulin like 23 | chr1:24770419-24771393 REVERSE LENGTH=975, score=6, range=189-209, strand=1\n+\n+target 5' CUCUCUCUCCAAACGCUUCAC 3'\n+ ::.:.::::::.::::: \n+query 3' CUCAGGGGGGUUUGUGAAGUC 5'\n+\n+query=Ath-miR393a, target=AT1G09812.1 | Symbols: no symbol available | no full name available | chr1:3187442-3188854 FOR, score=5.5, range=452-474, strand=1\n+\n+target 5' CGAUGAAUGCGAUCUCAUUUGGG 3'\n+ ::: :::::::::.: :::::.\n+query 3' CCUAGUUACGCUAGGG-AAACCU 5'\n+\n+query=Ath-miR393a, target=AT2G33380.1 | Symbols: AtRD20, PXG3, CLO-3, CLO3, RD20, AtCLO3 | caleosin 3, Arabidopsis thali, score=5.5, range=719-739, strand=1\n+\n+target 5' AUGGCAAU-CGAUCCUUUUGGA 3'\n+ . :::: ::::::.::::::\n+query 3' CCUAGUUACGCUAGGGAAACCU 5'\n+\n+No results for Ath-miR171a\n+query=Ath-miR156g, target=AT2G12400.1 | Symbols: no symbol available | no full name available | chr2:5004884-5008442 REV, score=5, range=347-365, strand=1\n+\n+target 5' GUGUUUACUCUCUUC-GUUU 3'\n+ :::.:.::::::::: ::. \n+query 3' CACGAGUGAGAGAAGACAGC 5'\n+\n+query=Ath-miR156g, target=AT1G26890.1 | Symbols: no symbol available | no full name available | chr1:9317589-9319246 FOR, score=5, range=948-967, strand=1\n+\n+target 5' GAGAUCUCUUUCUUCUGUCA 3'\n+ : : :: ::.::::::::: \n+query 3' CACGAGUGAGAGAAGACAGC 5'\n+\n+query=Ath-miR156g, target=AT1G29025.1 | Symbols: no symbol available | no full name available | chr1:10124286-10127098 R, score=5.5, range=1649-1668, strand=1\n+\n+target 5' UUGUCUGCUCACUUCUGUCG 3'\n+ ::. ..::: :::::::::\n+query 3' CACGAGUGAGAGAAGACAGC 5'\n+\n+query=Ath-miR156g, target=AT2G17660.1 | Symbols: no symbol available | no full name available | chr2:7673145-7673712 FOR, score=6, range=82-101, strand=1\n+\n+target 5' CUGUUUUCUCUCUUCUCUCC 3'\n+ ::.:. ::::::::: :: \n+query 3' CACGAGUGAGAGAAGACAGC 5'\n+\n+query=Ath-miR156g, target=AT1G22470.1 | Symbols: no symbol available | no full name available | chr1:7932777-7933604 REV, score=6, range=570-590, strand=1\n+\n+target 5' CUUCUUAUUACUCUUCUGUCU 3'\n+ : ::.:.: :::::::::: \n+query 3' CACGAGUGA-GAGAAGACAGC 5'\n+\n+query=Ath-miR156g, target=AT1G11960.1 | Symbols: no symbol available | no full name available | chr1:4039566-4044021 REV, score=6, range=1472-1490, strand=1\n+\n+target 5' UUCCUCACUUUCUUCU-UCA 3'\n+ : ::::::.:::::: :: \n+query 3' CACGAGUGAGAGAAGACAGC 5'\n+\n+query=Ath-miR395c, target=AT1G66400.1 | Symbols: CML23 | calmodulin like 23 | chr1:24770419-24771393 REVERSE LENGTH=975, score=6, range=189-209, strand=1\n+\n+target 5' CUCUCUCUCCAAACGCUUCAC 3'\n+ ::.:.::::::.::::: \n+query 3' CUCAGGGGGGUUUGUGAAGUC 5'\n+\n+query=Ath-miRN134, target=AT1G60030.1 | Symbols: NAT7, ATNAT7 | nucleobase-ascorbate transporter 7, ARABIDOPSIS NUCLEOBA, score=5, range=1655-1675, strand=1\n+\n+target 5' AGAACAAAAUUCAUCCUCGGA 3'\n+ ::: : :::::::::: :.::\n+query 3' UCUAGGUUUAAGUAGG-GUCU 5'\n+\n+query=Ath-miRN134, target=AT1G30280.1 | Symbols: no symbol available | no full name available | chr1:10662621-10664668 R, score=6, range=761-779, strand=1\n+\n+target 5' GGAUCCGAAUUCCUUC-AGA 3'\n+ .:::::.::::: :.: :::\n+query 3' UCUAGGUUUAAGUAGGGUCU 5'\n+\n+query=Ath-miRN134, target=AT1G73010.1 | Symbols: PS2, ATPS2, AtPPsPase1, PPsPase1 | pyrophosphate-specific phosphatase1,, score=6, range=1149-1167, strand=1\n+\n+target 5' AGAUU-GAAUUUAUCCUAAA 3'\n+ ::::. .::::.::::.: :\n+query 3' UCUAGGUUUAAGUAGGGUCU 5'\n+\n+query=Ath-miR170, target=AT1G26770.2 | Symbols: ATHEXP ALPHA 1.1, ATEXPA10, AT-EXP10, EXPA10, ATEXP10, EXP10 | expansin, score=5.5, range=321-341, strand=1\n+\n+target 5' GGUGUUUACCUGGCUCAAUCG 3'\n+ :.:.:: :: .:::::::::.\n+query 3' CUAUAACUGUGCCGAGUUAGU 5'\n+\n+query=Ath-miR170, target=AT1G10340.1 | Symbols: no symbol available | no full name available | chr1:3390475-3392633 REV, score=6, range=716-736, strand=1\n+\n+target 5' UAUA"..b"AT1G11960.1 | Symbols: no symbol available | no full name available | chr1:4039566-4044021 REV, score=5, range=1472-1490, strand=1\n+\n+target 5' UUCCUCACUUUCUUCU-UCA 3'\n+ : ::::::.:::::: :::\n+query 3' CACGAGUGAGAGAAGACAGU 5'\n+\n+query=Ath-miR156e, target=AT1G29025.1 | Symbols: no symbol available | no full name available | chr1:10124286-10127098 R, score=6, range=1649-1668, strand=1\n+\n+target 5' UUGUCUGCUCACUUCUGUCG 3'\n+ ::. ..::: ::::::::.\n+query 3' CACGAGUGAGAGAAGACAGU 5'\n+\n+query=Ath-miR156e, target=AT2G17660.1 | Symbols: no symbol available | no full name available | chr2:7673145-7673712 FOR, score=6, range=82-101, strand=1\n+\n+target 5' CUGUUUUCUCUCUUCUCUCC 3'\n+ ::.:. ::::::::: :: \n+query 3' CACGAGUGAGAGAAGACAGU 5'\n+\n+query=Ath-miR156e, target=AT1G22470.1 | Symbols: no symbol available | no full name available | chr1:7932777-7933604 REV, score=6, range=570-590, strand=1\n+\n+target 5' CUUCUUAUUACUCUUCUGUCU 3'\n+ : ::.:.: :::::::::: \n+query 3' CACGAGUGA-GAGAAGACAGU 5'\n+\n+query=Ath-miR156e, target=AT2G44740.1 | Symbols: CYCP4;1 | cyclin p4;1 | chr2:18441828-18443405 REVERSE LENGTH=1169, score=6, range=68-88, strand=1\n+\n+target 5' UUUUUCUUUCUCUCUCUGUCA 3'\n+ : .:: .::::: :::::::\n+query 3' CACGAGUGAGAGA-AGACAGU 5'\n+\n+No results for Ath-miR395a\n+No results for Ath-miR165b\n+No results for Ath-miR2111a\n+query=Ath-miR171c, target=AT2G32800.1 | Symbols: LecRK-S.2, AP4.3A | L-type lectin receptor kinase S.2 | chr2:13916440-1, score=6, range=1659-1679, strand=1\n+\n+target 5' GUUGAUUUUGGUACGGCUUAU 3'\n+ :::: ::::.::::::.: \n+query 3' GCACUAUAACCGUGCCGAGUU 5'\n+\n+query=Ath-miR393b, target=AT1G09812.1 | Symbols: no symbol available | no full name available | chr1:3187442-3188854 FOR, score=4.5, range=453-474, strand=1\n+\n+target 5' GAUGAAUGCGAUCUCAUUUGGG 3'\n+ ::: :::::::::.: :::::.\n+query 3' CUAGUUACGCUAGGG-AAACCU 5'\n+\n+query=Ath-miR393b, target=AT2G33380.1 | Symbols: AtRD20, PXG3, CLO-3, CLO3, RD20, AtCLO3 | caleosin 3, Arabidopsis thali, score=4.5, range=720-739, strand=1\n+\n+target 5' UGGCAAU-CGAUCCUUUUGGA 3'\n+ . :::: ::::::.::::::\n+query 3' CUAGUUACGCUAGGGAAACCU 5'\n+\n+query=Ath-miR393b, target=AT1G20070.1 | Symbols: no symbol available | no full name available | chr1:6958010-6959148 REV, score=5, range=72-91, strand=1\n+\n+target 5' UAUCAAAACGAUCC-UUUGGA 3'\n+ ::::: :::::: ::::::\n+query 3' CUAGUUACGCUAGGGAAACCU 5'\n+\n+query=Ath-miR393b, target=AT1G63300.1 | Symbols: no symbol available | no full name available | chr1:23481907-23486220 F, score=6, range=1397-1416, strand=1\n+\n+target 5' GAUCCAUG-GGUUCUUUUGGA 3'\n+ :::: ::: :.:.:.::::::\n+query 3' CUAGUUACGCUAGGGAAACCU 5'\n+\n+No results for Ath-miR829\n+No results for Ath-miR2111b\n+query=Ath-miRN146, target=AT1G62620.1 | Symbols: no symbol available | no full name available | chr1:23182644-23185151 F, score=6, range=242-263, strand=1\n+\n+target 5' CAUUCAAGCGUCUAUAGAUCUC 3'\n+ :::: :: :::::::.:.:.:\n+query 3' CUAAGCUC-CAGAUAUUUGGGG 5'\n+\n+No results for Ath-miR165a\n+No results for Ath-miR168a\n+query=Ath-miRN118, target=AT1G78720.1 | Symbols: no symbol available | no full name available | chr1:29605457-29607678 F, score=5.5, range=523-542, strand=1\n+\n+target 5' GCUAUUCUUAUCAUAGUUCA 3'\n+ ::.: : :.::::.::.:::\n+query 3' CGGUUAAAGUAGUGUCGAGU 5'\n+\n+query=Ath-miRN118, target=AT1G01200.1 | Symbols: RABA3, ATRABA3, ATRAB-A3 | ARABIDOPSIS RAB GTPASE HOMOLOG A3, RAB GTPas, score=6, range=484-503, strand=1\n+\n+target 5' GGCAAACUCGUCAAAGCUCA 3'\n+ : ::: ::.::: ::::::\n+query 3' CGGUUAAAGUAGUGUCGAGU 5'\n+\n+query=Ath-miR395f, target=AT1G66400.1 | Symbols: CML23 | calmodulin like 23 | chr1:24770419-24771393 REVERSE LENGTH=975, score=6, range=189-209, strand=1\n+\n+target 5' CUCUCUCUCCAAACGCUUCAC 3'\n+ ::.:.::::::.::::: \n+query 3' CUCAGGGGGGUUUGUGAAGUC 5'\n+\n+No results for Ath-miR851\n+No results for Ath-miR395e\n+No results for Ath-miRN143\n" |
| b |
| diff -r 773fdd1a02ea -r c9d56748fbde test-data/targetfinder_test_04.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/targetfinder_test_04.txt Thu Mar 25 19:53:15 2021 +0000 |
| b |
| @@ -0,0 +1,37 @@ +No results for Ath-miR395b +No results for Ath-miR171a +No results for Ath-miRN143 +No results for Ath-miR395c +No results for Ath-miR851 +No results for Ath-miR395f +No results for Ath-miRN134 +No results for Ath-miR861 +No results for Ath-miR156g +No results for Ath-miRN146 +query=Ath-miR156c, target=AT1G26890.1 | Symbols: no symbol available | no full name available | chr1:9317589-9319246 FOR, score=4, range=948-967, strand=1 + +target 5' GAGAUCUCUUUCUUCUGUCA 3' + : : :: ::.:::::::::: +query 3' CACGAGUGAGAGAAGACAGU 5' + +No results for Ath-miR165a +No results for Ath-miR393a +No results for Ath-miR168a +No results for Ath-miR395d +No results for Ath-miR393b +No results for Ath-miR165b +No results for Ath-miRN132 +No results for Ath-miR2111a +No results for Ath-miR395e +No results for Ath-miR171c +query=Ath-miR156e, target=AT1G26890.1 | Symbols: no symbol available | no full name available | chr1:9317589-9319246 FOR, score=4, range=948-967, strand=1 + +target 5' GAGAUCUCUUUCUUCUGUCA 3' + : : :: ::.:::::::::: +query 3' CACGAGUGAGAGAAGACAGU 5' + +No results for Ath-miRN118 +No results for Ath-miR829 +No results for Ath-miR2111b +No results for Ath-miR395a +No results for Ath-miR170 |
| b |
| diff -r 773fdd1a02ea -r c9d56748fbde test-data/targetfinder_test_05.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/targetfinder_test_05.gff Thu Mar 25 19:53:15 2021 +0000 |
| b |
| @@ -0,0 +1,27 @@ +No results for Ath-miRN143 +No results for Ath-miR2111a +No results for Ath-miR861 +No results for Ath-miR395b +No results for Ath-miRN132 +No results for Ath-miR829 +No results for Ath-miR165b +No results for Ath-miR395c +No results for Ath-miR156g +AT1G26890.1 | Symbols: no symbol available | no full name available | chr1:9317589-9319246 FOR targetfinder rna_target 948 967 4 + . smallRNA=Ath-miR156c;target_seq=GAGAUCUCUUUCUUCUGUCA;base_pairs=: : :: ::.::::::::::;miR_seq=CACGAGUGAGAGAAGACAGU +No results for Ath-miR395d +No results for Ath-miR851 +No results for Ath-miR393a +No results for Ath-miR393b +No results for Ath-miR395e +No results for Ath-miR395a +No results for Ath-miRN118 +No results for Ath-miR171c +No results for Ath-miR395f +No results for Ath-miR171a +No results for Ath-miR170 +No results for Ath-miRN134 +No results for Ath-miR2111b +No results for Ath-miR168a +AT1G26890.1 | Symbols: no symbol available | no full name available | chr1:9317589-9319246 FOR targetfinder rna_target 948 967 4 + . smallRNA=Ath-miR156e;target_seq=GAGAUCUCUUUCUUCUGUCA;base_pairs=: : :: ::.::::::::::;miR_seq=CACGAGUGAGAGAAGACAGU +No results for Ath-miRN146 +No results for Ath-miR165a |
| b |
| diff -r 773fdd1a02ea -r c9d56748fbde test-data/targetfinder_test_06.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/targetfinder_test_06.tab Thu Mar 25 19:53:15 2021 +0000 |
| b |
| @@ -0,0 +1,27 @@ +No results for Ath-miR393b +No results for Ath-miR2111b +No results for Ath-miR829 +No results for Ath-miR861 +No results for Ath-miRN134 +No results for Ath-miR2111a +Ath-miR156c AT1G26890.1 | Symbols: no symbol available | no full name available | chr1:9317589-9319246 FOR 948 967 + 4 GAGAUCUCUUUCUUCUGUCA : : :: ::.:::::::::: CACGAGUGAGAGAAGACAGU +No results for Ath-miR156g +No results for Ath-miR165b +No results for Ath-miR395f +Ath-miR156e AT1G26890.1 | Symbols: no symbol available | no full name available | chr1:9317589-9319246 FOR 948 967 + 4 GAGAUCUCUUUCUUCUGUCA : : :: ::.:::::::::: CACGAGUGAGAGAAGACAGU +No results for Ath-miR851 +No results for Ath-miR395a +No results for Ath-miR395e +No results for Ath-miR168a +No results for Ath-miR395c +No results for Ath-miRN118 +No results for Ath-miR395d +No results for Ath-miR393a +No results for Ath-miR171a +No results for Ath-miRN146 +No results for Ath-miR165a +No results for Ath-miRN143 +No results for Ath-miRN132 +No results for Ath-miR395b +No results for Ath-miR171c +No results for Ath-miR170 |
| b |
| diff -r 773fdd1a02ea -r c9d56748fbde test-data/targetfinder_test_07.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/targetfinder_test_07.json Thu Mar 25 19:53:15 2021 +0000 |
| [ |
| @@ -0,0 +1,27 @@ +{ + "Ath-miR156e": { + "hits" : [ + { + "Target accession": "AT1G26890.1 | Symbols: no symbol available | no full name available | chr1:9317589-9319246 FOR", + "Score": "4", + "Coordinates": "948-967", + "Strand": "+", + "Target sequence": "GAGAUCUCUUUCUUCUGUCA", + "Base pairing": ": : :: ::.::::::::::", + "amiRNA sequence": "CACGAGUGAGAGAAGACAGU" + } + ] + } "Ath-miR156c": { + "hits" : [ + { + "Target accession": "AT1G26890.1 | Symbols: no symbol available | no full name available | chr1:9317589-9319246 FOR", + "Score": "4", + "Coordinates": "948-967", + "Strand": "+", + "Target sequence": "GAGAUCUCUUUCUUCUGUCA", + "Base pairing": ": : :: ::.::::::::::", + "amiRNA sequence": "CACGAGUGAGAGAAGACAGU" + } + ] + } +} |
| b |
| diff -r 773fdd1a02ea -r c9d56748fbde test-data/targetfinder_test_08.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/targetfinder_test_08.tab Thu Mar 25 19:53:15 2021 +0000 |
| b |
| b'@@ -0,0 +1,135 @@\n+Ath-miRN143\tAT1G08500.1 | Symbols: ENODL18, AtENODL18 | early nodulin-like protein 18 | chr1:2688880-26902\t372\t391\t+\t6.5\tAAUUAUCA-GAAAUGGGCCGA\t:::.:: : :: :::::::.:\tUUAGUAUUGCUGUACCCGGUU\n+Ath-miR165a\tAT2G01260.1 | Symbols: no symbol available | no full name available | chr2:135223-137916 REVER\t293\t312\t-\t6\tCGGCGAAGAAGCUUGGUC-GA\t :: :: :::::.::::: ::\tCCCCCUACUUCGGACCAGGCU\n+Ath-miRN134\tAT1G60030.1 | Symbols: NAT7, ATNAT7 | nucleobase-ascorbate transporter 7, ARABIDOPSIS NUCLEOBA\t1655\t1675\t+\t5\tAGAACAAAAUUCAUCCUCGGA\t::: : :::::::::: :.::\tUCUAGGUUUAAGUAGG-GUCU\n+Ath-miRN134\tAT1G65330.1 | Symbols: PHE1, AGL37 | AGAMOUS-like 37, PHERES1 | chr1:24266257-24267336 REVERSE\t706\t726\t-\t5\tAGAUCCAAAUUCAUACUCUGA\t:::::::::::::: :.: ::\tUCUAGGUUUAAGUA-GGGUCU\n+Ath-miRN134\tAT2G18700.1 | Symbols: TPS11, ATTPSB, ATTPS11 | trehalose phosphatase/synthase 11, TREHALOSE-6\t1442\t1461\t-\t5.5\tGGCACCAAAUUCAUCCCAUC\t.: :::::::::::::: \tUCUAGGUUUAAGUAGGGUCU\n+Ath-miRN134\tAT1G30280.1 | Symbols: no symbol available | no full name available | chr1:10662621-10664668 R\t761\t779\t+\t6\tGGAUCCGAAUUCCUUC-AGA\t.:::::.::::: :.: :::\tUCUAGGUUUAAGUAGGGUCU\n+Ath-miRN134\tAT1G73010.1 | Symbols: PS2, ATPS2, AtPPsPase1, PPsPase1 | pyrophosphate-specific phosphatase1,\t1149\t1167\t+\t6\tAGAUU-GAAUUUAUCCUAAA\t::::. .::::.::::.: :\tUCUAGGUUUAAGUAGGGUCU\n+Ath-miRN134\tAT1G30080.1 | Symbols: no symbol available | no full name available | chr1:10550855-10553295 R\t1131\t1151\t-\t6\tCAAUCCAUAAUUCCUCUCAGA\t ::::: ::::: ::.::::\tUCUAGGU-UUAAGUAGGGUCU\n+Ath-miRN134\tAT1G29670.1 | Symbols: no symbol available | no full name available | chr1:10375754-10377871 F\t1063\t1082\t-\t6\tAGGGUGAAAUGCGUCCCAGA\t::. . :::: :.:::::::\tUCUAGGUUUAAGUAGGGUCU\n+Ath-miRN134\tAT1G60030.1 | Symbols: NAT7, ATNAT7 | nucleobase-ascorbate transporter 7, ARABIDOPSIS NUCLEOBA\t1525\t1543\t-\t6\tAGCUCCAAAUUUA-CCAAGA\t:: ::::::::.: :: :::\tUCUAGGUUUAAGUAGGGUCU\n+Ath-miRN134\tAT2G47500.1 | Symbols: no symbol available | no full name available | chr2:19492867-19498189 F\t1211\t1230\t+\t6.5\tAGAAUCAACUUCGUCACAGA\t::: .::: :::.:: ::::\tUCUAGGUUUAAGUAGGGUCU\n+Ath-miRN134\tAT1G62430.1 | Symbols: CDS1, ATCDS1 | CDP-diacylglycerol synthase 1 | chr1:23105905-23109534 R\t1610\t1628\t+\t6.5\tAGAUUCUGAUUC-UCCAAGA\t::::.: .:::: ::: :::\tUCUAGGUUUAAGUAGGGUCU\n+Ath-miRN134\tAT1G30280.1 | Symbols: no symbol available | no full name available | chr1:10662621-10664668 R\t468\t486\t+\t6.5\tAGAUC-GAAUUCAUCGUCGA\t::::: .:::::::: . ::\tUCUAGGUUUAAGUAGGGUCU\n+Ath-miRN134\tAT2G14960.1 | Symbols: GH3.1 | | chr2:6451319-6453797 REVERSE LENGTH=2240\t536\t555\t-\t6.5\tACAUACAAAUUCAUUACGGG\t: :: :::::::::. :.:.\tUCUAGGUUUAAGUAGGGUCU\n+Ath-miRN134\tAT1G58340.1 | Symbols: ABS4, ZF14, BCD1, ZRZ | BUSH-AND-CHLOROTIC-DWARF 1, ZRIZI, Arabidopsis\t2041\t2059\t-\t6.5\tAAAUUCACAUUC-UCCUAGA\t: ::.:: :::: :::.:::\tUCUAGGUUUAAGUAGGGUCU\n+Ath-miR861\tAT2G41190.1 | Symbols: no symbol available | no full name available | chr2:17167279-17170559 R\t1974\t1994\t+\t5.5\tGACCUUGGGGACAUAUUCUUC\t: :::::..:::::::.: ::\tCAGGAACUUCUGUAUAGGUAG\n+Ath-miR861\tAT1G04240.1 | Symbols: SHY2, IAA3 | SHORT HYPOCOTYL 2, indole-3-acetic acid inducible 3 | chr1\t798\t819\t-\t5.5\tUUUCUUGAAGAUAUAUCUCAUA\t :.::::::::.::::: ::: \tCAGGAACUUCUGUAUAG-GUAG\n+Ath-miR861\tAT1G29025.1 | Symbols: no symbol available | no full name available | chr1:10124286-10127098 R\t449\t469\t-\t5.5\tAACUUGGAAGACAUAUCCUUC\t :.: :::::::::::: ::\tCAGGAACUUCUGUAUAGGUAG\n+Ath-miR861\tAT1G14520.1 | Symbols: MIOX1 | myo-inositol oxygenase 1 | chr1:4968134-4970311 REVERSE LENGTH=\t1310\t1330\t-\t6\tAUUCAUCAAGGCAUAUCCGUU\t :.: : :::.:::::::.:.\tCAGGAACUUCUGUAUAGGUAG\n+Ath-miR861\tAT1G52750.1 | Symbols: no symbol available | no full name available | chr1:19646465-19649340 R\t2066\t2086\t-\t6.5\tGUUCUCGCAGAUGUUUCCAUC\t::.:: : :::..: ::::::\tCAGGAACUUCUGUAUAGGUAG\n+Ath-miR393a\tAT1G09812.1 | Symbols: no symbol available | no full name available | chr1:3187442-3188854 FOR\t452\t474\t+\t5.5\tCGAUGAAUGCGAUCUCAUUUGGG\t ::: :::::::::.: :::::.\tCCUAGUUACGCUAGGG-AAACCU\n+Ath-miR393a\tAT2G33380.1 | Symbols: AtRD20, PXG3, CLO-3, CLO3, RD20, AtCLO'..b'02 R\t975\t994\t-\t5.5\tGCGUUCCCUCUCUUCUGUAU\t: :.:: ::::::::::: \tCACGAGUGAGAGAAGACAGC\n+Ath-miR156g\tAT2G17660.1 | Symbols: no symbol available | no full name available | chr2:7673145-7673712 FOR\t82\t101\t+\t6\tCUGUUUUCUCUCUUCUCUCC\t ::.:. ::::::::: :: \tCACGAGUGAGAGAAGACAGC\n+Ath-miR156g\tAT1G22470.1 | Symbols: no symbol available | no full name available | chr1:7932777-7933604 REV\t570\t590\t+\t6\tCUUCUUAUUACUCUUCUGUCU\t : ::.:.: :::::::::: \tCACGAGUGA-GAGAAGACAGC\n+Ath-miR156g\tAT1G11960.1 | Symbols: no symbol available | no full name available | chr1:4039566-4044021 REV\t1472\t1490\t+\t6\tUUCCUCACUUUCUUCU-UCA\t : ::::::.:::::: :: \tCACGAGUGAGAGAAGACAGC\n+Ath-miR156g\tAT2G18700.1 | Symbols: TPS11, ATTPSB, ATTPS11 | trehalose phosphatase/synthase 11, TREHALOSE-6\t2669\t2688\t-\t6\tUUGCUCUGUUUCUUCUGUUG\t ::::: :.::::::::.:\tCACGAGUGAGAGAAGACAGC\n+Ath-miR156g\tAT2G30985.1 | Symbols: no symbol available | no full name available | chr2:13186716-13187200 F\t410\t430\t-\t6\tAUUUUCAUGUUUCUUCUGUCG\t : .:::. :.::::::::::\tCACGAGUG-AGAGAAGACAGC\n+Ath-miR156g\tAT1G01600.1 | Symbols: CYP86A4 | "cytochrome P450, family 86, subfamily A, polypeptide 4" | ch\t2159\t2178\t-\t6.5\tUUUCUUUCUUUUUUUUGUCG\t : ::. ::.:.::.:::::\tCACGAGUGAGAGAAGACAGC\n+Ath-miR156g\tAT2G35860.1 | Symbols: FLA16 | FASCICLIN-like arabinogalactan protein 16 precursor | chr2:1505\t1097\t1116\t-\t6.5\tGUACAUACUCUCCUCUGUUU\t:: : .:::::: :::::. \tCACGAGUGAGAGAAGACAGC\n+Ath-miR156g\tAT1G09932.1 | Symbols: no symbol available | no full name available | chr1:3230716-3233259 REV\t154\t172\t-\t6.5\tCUUCUUCUUCUCUUCU-UCG\t : ::. .:::::::: :::\tCACGAGUGAGAGAAGACAGC\n+Ath-miR171a\tAT1G26770.2 | Symbols: ATHEXP ALPHA 1.1, ATEXPA10, AT-EXP10, EXPA10, ATEXP10, EXP10 | expansin\t321\t341\t+\t6.5\tGGUGUUUACCUGGCUCAAUCG\t:.:.:: : .:::::::::.\tCUAUAACCGCGCCGAGUUAGU\n+Ath-miR395e\tAT1G48480.1 | Symbols: RKL1 | receptor-like kinase 1 | chr1:17918207-17921116 FORWARD LENGTH=2\t2273\t2294\t-\t6\tGAUUUCUCCCCAACCAUUUCAU\t:: ::: :::::: ::.:::: \tCUCAAG-GGGGUUUGUGAAGUC\n+Ath-miR395e\tAT1G62440.1 | Symbols: LRX2 | leucine-rich repeat/extensin 2 | chr1:23112933-23115293 FORWARD\t871\t891\t-\t6\tGAGCUGUUCCAAACUCUUCAU\t::: : ..:::::: ::::: \tCUCAAGGGGGUUUGUGAAGUC\n+Ath-miR395e\tAT2G23170.1 | Symbols: GH3.3 | | chr2:9863855-9866562 REVERSE LENGTH=2118\t1787\t1808\t+\t6.5\tGGGUUGUAUCUACACACUUCAG\t:.::: . .:.: :::::::::\tCUCAAGG-GGGUUUGUGAAGUC\n+Ath-miR2111a\tAT1G74420.2 | Symbols: FUT3, ATFUT3 | fucosyltransferase 3 | chr1:27967894-27969871 REVERSE LE\t1212\t1232\t-\t5.5\tUCAACUUCAGGAAGCAGCUUA\t: :::.:::::: :::: :::\tAUUUGGAGUCCUACGUCUAAU\n+Ath-miR395b\tAT1G66400.1 | Symbols: CML23 | calmodulin like 23 | chr1:24770419-24771393 REVERSE LENGTH=975\t189\t209\t+\t6\tCUCUCUCUCCAAACGCUUCAC\t ::.:.::::::.::::: \tCUCAGGGGGGUUUGUGAAGUC\n+Ath-miR395b\tAT1G07720.1 | Symbols: KCS3 | 3-ketoacyl-CoA synthase 3 | chr1:2390655-2392500 REVERSE LENGTH=\t812\t833\t-\t6\tGCGUCCUUACCAAACACCUUAG\t: ::::.. :::::::: :.::\tCUCAGGGG-GGUUUGUGAAGUC\n+Ath-miR395b\tAT1G62440.1 | Symbols: LRX2 | leucine-rich repeat/extensin 2 | chr1:23112933-23115293 FORWARD\t871\t891\t-\t6.5\tGAGCUGUUCCAAACUCUUCAU\t::: . ..:::::: ::::: \tCUCAGGGGGGUUUGUGAAGUC\n+Ath-miR171c\tAT2G32800.1 | Symbols: LecRK-S.2, AP4.3A | L-type lectin receptor kinase S.2 | chr2:13916440-1\t1659\t1679\t+\t6\tGUUGAUUUUGGUACGGCUUAU\t :::: ::::.::::::.: \tGCACUAUAACCGUGCCGAGUU\n+Ath-miR171c\tAT1G01600.1 | Symbols: CYP86A4 | "cytochrome P450, family 86, subfamily A, polypeptide 4" | ch\t407\t428\t+\t6.5\tCAGGGUAUUGGCUAUGGUUCAA\t: :.::::::: :.::.::::\tGCACUAUAACCG-UGCCGAGUU\n+Ath-miR171c\tAT1G08570.1 | Symbols: ACHT4 | atypical CYS HIS rich thioredoxin 4 | chr1:2712694-2714833 FOR\t924\t944\t-\t6.5\tCGUGGCAUUGGUACAGCUAAA\t::::. :::::.:: ::: ::\tGCACUAUAACCGUGCCGAGUU\n+Ath-miR171c\tAT2G02640.1 | Symbols: no symbol available | no full name available | chr2:732291-734271 FORWA\t1458\t1478\t-\t6.5\tCUUGAUAAUUGAACGGCUCAG\t: ::::: : : ::::::::.\tGCACUAUAACCGUGCCGAGUU\n+Ath-miR171c\tAT1G75780.1 | Symbols: TUB1 | tubulin beta-1 chain | chr1:28451138-28453820 REVERSE LENGTH=180\t760\t779\t-\t6.5\tAGUUGCAUUG-UACGGCUCAA\t :: . :::: .:::::::::\tGCACUAUAACCGUGCCGAGUU\n' |