From 56a529904b02a1f7035120d0a03a20baed71f331 Mon Sep 17 00:00:00 2001 From: Melvin Alappat <melvin.alappat@unibas.ch> Date: Mon, 20 Dec 2021 20:59:31 +0100 Subject: [PATCH] Adding test-input files --- tests/resources/Energies_test.txt | 8 +++ tests/resources/transcript.fasta | 105 ++++++++++++++++++++++++++++++ 2 files changed, 113 insertions(+) create mode 100644 tests/resources/Energies_test.txt create mode 100644 tests/resources/transcript.fasta diff --git a/tests/resources/Energies_test.txt b/tests/resources/Energies_test.txt new file mode 100644 index 0000000..f734779 --- /dev/null +++ b/tests/resources/Energies_test.txt @@ -0,0 +1,8 @@ +RIblast ris result +input:primer.fasta,database:/RIblast/test_db,RepeatFlag:0,MaximalSpan:70,MinAccessibleLength:5,MaxSeedLength:20,InteractionEnergyThreshold:-4,HybridEnergyThreshold:-6,FinalThreshold:-8,DropOutLengthWoGap:5,DropOutLengthWGap:16 +Id,Query name, Query Length, Target name, Target Length, Accessibility Energy, Hybridization Energy, Interaction Energy, BasePair +0,NC_001137.3:100769-101251 Saccharomyces cerevisiae S288C chromosome V, complete sequence,483,NW_005196756.1:c68260-66684 Emiliania huxleyi CCMP1516 unplaced genomic scaffold EMIHUscaffold_7, whole genome shotgun sequence,1577,6.7775,-20.47,-13.6925,(12-31:1543-1527) +1,NC_001137.3:100769-101251 Saccharomyces cerevisiae S288C chromosome V, complete sequence,483,NW_005196756.1:c68260-66684 Emiliania huxleyi CCMP1516 unplaced genomic scaffold EMIHUscaffold_7, whole genome shotgun sequence,1577,2.50179,-10.96,-8.45821,(24-34:1505-1495) +2,NC_001137.3:100769-101251 Saccharomyces cerevisiae S288C chromosome V, complete sequence,483,NW_005196756.1:c68260-66684 Emiliania huxleyi CCMP1516 unplaced genomic scaffold EMIHUscaffold_7, whole genome shotgun sequence,1577,11.8919,-24.11,-12.2181,(14-47:1503-1468) + + diff --git a/tests/resources/transcript.fasta b/tests/resources/transcript.fasta new file mode 100644 index 0000000..2d25e4e --- /dev/null +++ b/tests/resources/transcript.fasta @@ -0,0 +1,105 @@ +>NW_005196756.1:c68260-66684 Emiliania huxleyi CCMP1516 unplaced genomic scaffold EMIHUscaffold_7, whole genome shotgun sequence +CUGAGCUCUUAGACACCAGGAUCACCAGGAGCGCGACGAGGGCCCUGCGCACACCCAUCCCUCCCCAUCC +CUCCCCUCAGGGUCCCUCCCUCUCUCUGCCGAGAGGGGCGGCCCUCGCCGCUCGCCCCCUCCCGCCAUCG +CGCGUUCCUCGCGUGCGGCGCUCAGCCGCCCCCCGCGCCUGGCGCCCUCUGCACACACGCUCCCCCUCUG +GCUGCGCGCCGCGCGACCAACGGCGCCGGCUGGUGUCGCAGGCAUGCUGUCCUUCCUUCUCACCACCGCG +GCCGCGGUCACCGCCUUUAACGCGCCCGUCGCGGCGCCGAGCAGCAGCUUCGCGCAGCCGCGUGUCGCAG +CCUCGCCUGUGAUGGGUGCCACCAUCCGCGAGCUGCGCGACCGCGUGGGCUCGGUCAAAAACACGAAGAA +AAUCACGUCUGCUAUGCGCCUCGUCGCCGCCGCCAAGGUGCGCCGCGCGCAGGAGGCUUGCCUGCGCUCG +CGCCCCUUCUCGGAGACGCUGGAGCGCAUCCUCGGCGGCCUCCUCCAGCGCCUCUCAACCGAGGCGCUGG +ACAUCCCGCUGCUGCAGCAGCGCGAGGCGAAAAAGGUGGGCCUGUUGGUCAUCACCGGGGACCGCGGCCU +GUGCGGCUCCUACAAUUCUGCCGCCAUCAAGAAGACCGAGGGCCGCAUCGCUGAGCUGAAGGCGCAGGGC +GUUGAGGCCGAGCUCAUCACUGUGGGCAACAAGGGCUCGACCUACUUCAAGCGCCGCUCGGACCCGUCCU +CGCCCCAGUACGCCGCGCCGCUGCGCAAGGCAGUGCCGUGCGGCCAGGCCCCGACCGCCGAGAUGGCGAC +GGAGCUCGCCUCCGAGCUGCUCUCCUCGUACUAUGCCGGCGAGCUCGACCGCGUCGAGCUCAUCUACACC +UCCUUCGUCUCUAUGAUCUCCUCCAUCCCGUCGGUCCGCACGAUGAUCCCGCUCACGCCGCAGGGCAUCG +AGACCGAGGGCGACGAGAUCUUCAAGAUGACCACCAAGGAUGGCGAUUUCGCCAUCGAGAAGGAGAAGGU +GGACAAGGCGGAGCCGCAGCAGUUUGCCGCCGACAUGAUCUUCGAGCAGGAGCCGUCGCAGCUGCUCAAC +GCCAUCCUGCCGCUCUACCUCAACGGCCAGAUCCUGCGCACGCUGCAGGAGUCGGUCGCGUCGGAGCUCG +CGUCGCGCAUGACCGCGAUGCAGUCGGCUACGGACAACGCCAAGGAGCUGCAAAAGACGCUCGAGCUCCA +GAUGAACCGCGCGCGCCAGGCCAAGAUCACCCAGGAGCUGAUGGAGAUCAUCGCGGGCGCGGACUCGGUU +UAGAGGGCUGUGGGAGCAAAAGGGGGGAUGGGGGGCGUGGCGAGGUCGCUUGCCAGUCGUAGCUCUGGGA +GCGACUGACGAUUCUCACAUUGAACUCGAGCGAACUGUCGAUGCUGCGAGCCGCCCGCCGCGCGCGUGAU +CUGGGGGGCGGGGGGGGGUGUGCACGGGAUGGGGGUUGGGGAGAGAGUCGUCGCGGCGGAGGGGCGGCAG +GACACUUUCGCGCGAAAAAUACGUUCGUCCCGUUGAA + + +>NC_000012.12:c6970753-6965327 Homo sapiens chromosome 12, GRCh38.p13 Primary Assembly +UCCGUAUGCGCGAUUCCUGUGCGCGAAGUUCGGGUCCGUAGUGGGCUAAGGGGGAGGGUUUCAAAGGGAG 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+GCGCCCGCCACCACGCCCGGCUAAUUUUUGUAUUUUAGUAGAGACGGGGUUUCACUAUGUAGAUCAAGCU +GGUCUCGAACUCCUGACCUCAAAUGAUCCGCCCGCCUCGGCCUCCCAAAGUGCUGGGAUUACAGGCGUGA +GCCACCGCGCCCGGCCGAAACUGUGGCCUCUUAAUACCUAUCCCUGUCCUCUCCAGGAUCCCUUGGUUCC +AGUACCCCAUUAUCUAUGACAUUCGGGCCAGACCUCGAAAAAUCUCCUCCCCUACAGGCUCCAAAGGUAG +GUCUGAGCACUUGGUAAUCACAUGGCAGGUGGGAUGAUCAAGGUAGCUGGCAAGAAACCCCAGGGGAAUA +UGGUAGUGUCAGGCCUUUAGGCCUCUUUCCACAUCUGCAAGAGCUGUAACAAAAAUACCUGCCUCCUGGG +GUCAAAGCAGCAAAUUCUGAACACACUGUGUUUGCGUGCUUUUUACUGUCUCCUCCCUGACGUGUAUUCA +AUAAGAGUAUUGUUUGUCCCUCGUCUUGUUCACUGCCUAGAUCAAAGCUUUGUUUUAAAGCCUUUUUUUU +CUAACUGCUUGACUUACUAUAUCUACAGUUACAUCCACUAGUACACUCUGUUCUGGAGAAGUUUGUCCCU +AAGCUUGACUAGUUCACCUGUUCUCUCCUUCUAGACCAUACAUAAAAGCCGUGCCUUUGAGUUCCCCAGA +CCUCUUCCUCCUCCCCACCCACGCACACAUAUACACCCUGGGUCAGGUAGCUCACCUGUAACCUGUAAUG +UACUUCUUUGUGCUAUACCUAGUGCAGGUCGCUUAUUCAUUUACUAGACUGGGCCCUGGGAAUAAAAGAU +UCAUUAAACACAAUUCUUGUCCCCCAAGUCCUUACAGGAGACAUGAUUACGGUACAGCACGAAAGCGCCC 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