# HG changeset patch # User erasmus-medical-center # Date 1487927902 18000 # Node ID 4d16cf9414cf4dd2a389635044ea3df040d4ca8d # Parent b7cf9b172cfe2e89f8687d8afffa0624e53f0936 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/segmentation_fold commit 3a3c1d069e0a079d8ea7c0b4ac856ef24141b1aa diff -r b7cf9b172cfe -r 4d16cf9414cf macros.xml --- a/macros.xml Wed Aug 03 04:54:40 2016 -0400 +++ b/macros.xml Fri Feb 24 04:18:22 2017 -0500 @@ -1,5 +1,5 @@ - smf-v1.6-5_utils-v2.1.0 + smf-v1.7-0_utils-v2.1.1 @@ -8,23 +8,16 @@ - segmentation-fold --version | head -n 2 | tail -n 1 | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' - segmentation-fold-utils --version - + + echo $(segmentation-fold --version | head -n 2 | tail -n 1 | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//')", "$(segmentation-fold-utils --version) + - python - numpy - pysam - htseq - segmentation-fold-utils - ]]> - - segmentation-fold - ]]> - - + + + segmentation-fold + + + diff -r b7cf9b172cfe -r 4d16cf9414cf segmentation-fold.xml --- a/segmentation-fold.xml Wed Aug 03 04:54:40 2016 -0400 +++ b/segmentation-fold.xml Fri Feb 24 04:18:22 2017 -0500 @@ -4,34 +4,27 @@ macros.xml - - segmentation-fold - + + - - - @VERSION_COMMAND_SMF@ - - $output_dbn + > '${output_dbn}' ]]> @@ -41,15 +34,15 @@ - + - + - - + + @@ -58,7 +51,7 @@ - + @@ -234,7 +227,7 @@ **Authors** -Youri Hoogstrate (yhoogstrate @ github) +Youri Hoogstrate (GitHub: @yhoogstrate) ]]> diff -r b7cf9b172cfe -r 4d16cf9414cf test-data/SNORD114-4-revised.scan-for-segments.txt --- a/test-data/SNORD114-4-revised.scan-for-segments.txt Wed Aug 03 04:54:40 2016 -0400 +++ b/test-data/SNORD114-4-revised.scan-for-segments.txt Fri Feb 24 04:18:22 2017 -0500 @@ -1,57 +1,74 @@ +>SNORD114-4 revised x Kt-42.dra +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 revised x Kt-42.eco +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 revised x Loop-E-Motif.bac +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 revised x Kt-CD-box.UAU +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 revised x Kt-CD-box.UGU +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 revised x Kt-CD-box.CAU +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 revised x Kt-42.tth +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 revised x Kt-G2nA-SAM-riboswitch (T. tengcongensi) +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA >SNORD114-4 revised x Kt-7 G2nA SAM riboswitch (H. marismortui) CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 revised x Kt-7 (T. thermophilus) +>SNORD114-4 revised x Kt-15.hma +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +.(((((((((.......)))))).((.((((..((..((((((..........)))))).))..))))..))))) .((((((....(((.((.....((((......))))((....))...)...))))...(((....))).)))))) -6.42471313477 +>SNORD114-4 revised x Kt-U4b.hsa +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 revised x Kt-CD-box.GGU CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA >SNORD114-4 revised x Kt-7 (E. coli) CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA >SNORD114-4 revised x Kt-7 (D. radiodurans) CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 revised x Kt-11 (T. thermophilus) -CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 revised x Kt-11.eco +>SNORD114-4 revised x Kt-58.hma CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 revised x Kt-15.hma +>SNORD114-4 revised x Kt-46.tth CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA -.(((((((((.......)))))).((.((((..((..((((((..........)))))).))..))))..))))) .((((((....(((.((.....((((......))))((....))...)...))))...(((....))).)))))) -6.42471313477 ->SNORD114-4 revised x Kt-23.tth +>SNORD114-4 revised x Kt-SAM-ribo.tte CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA >SNORD114-4 revised x Kt-23.eco CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA >SNORD114-4 revised x Kt-38.hma CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 revised x Kt-42.hma +>SNORD114-4 revised x Kt-46.dra CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 revised x Kt-42.tth -CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 revised x Kt-42.dra +>SNORD114-4 revised x Kt-CD-box.CGU CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 revised x Kt-42.eco -CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 revised x Kt-46.hma +>SNORD114-4 revised x Kt-T-box.bsu CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 revised x Kt-46.tth -CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 revised x Kt-46.dra +>SNORD114-4 revised x Kt-23.tth CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA >SNORD114-4 revised x Kt-46.eco CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 revised x Kt-58.hma +>SNORD114-4 revised x Kt-c-di-GMP-II.cac +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 revised x Kt-11 (T. thermophilus) +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 revised x Kt-CD-box.AAU +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 revised x Kt-L30e.sce +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 revised x Kt-7 (T. thermophilus) +CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +>SNORD114-4 revised x Kt-42.hma CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA >SNORD114-4 revised x Kt-U4a.hsa CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 revised x Kt-U4b.hsa -CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 revised x Kt-CD-box.CGU +>SNORD114-4 revised x Kt-G2nA-SAMribo.bsu CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 revised x Kt-CD-box.UGU +>SNORD114-4 revised x Kt-CD-box.GAU CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 revised x Kt-L30e.sce +>SNORD114-4 revised x Kt-11.eco CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 revised x Kt-SAM-ribo.tte -CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 revised x Kt-T-box.bsu +>SNORD114-4 revised x Kt-46.hma CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 revised x Kt-c-di-GMP-II.cac +>SNORD114-4 revised x Kt-CD-box.AGU CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA ->SNORD114-4 revised x Kt-G2nA-SAM-riboswitch (T. tengcongensi) -CUGAGCCAGUGAUGAAAACUGGUGGCAUAGAAGUCAAGGAUGCUGAAUAAUGUGUGUCUAGAACUCUGAGGUUCA +.(((((((((.......)))))).((.((((..((..((((((..........)))))).))..))))..))))) .((((((...(((((.......((((......)))).((((((..........)))))).....))))))))))) 2.00271606445 diff -r b7cf9b172cfe -r 4d16cf9414cf test-data/SNORD118-revised.scan-for-segments.txt --- a/test-data/SNORD118-revised.scan-for-segments.txt Wed Aug 03 04:54:40 2016 -0400 +++ b/test-data/SNORD118-revised.scan-for-segments.txt Fri Feb 24 04:18:22 2017 -0500 @@ -1,57 +1,75 @@ +>SNORD118 revised x Kt-42.dra +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 revised x Kt-42.eco +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 revised x Loop-E-Motif.bac +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 revised x Kt-CD-box.UAU +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 revised x Kt-CD-box.UGU +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 revised x Kt-CD-box.CAU +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +.(((.((.(.(((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).)))).))))) .(((...((((((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).))))))))). 3.36520385742 +>SNORD118 revised x Kt-42.tth +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 revised x Kt-G2nA-SAM-riboswitch (T. tengcongensi) +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC >SNORD118 revised x Kt-7 G2nA SAM riboswitch (H. marismortui) AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 revised x Kt-7 (T. thermophilus) +>SNORD118 revised x Kt-15.hma +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 revised x Kt-U4b.hsa +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 revised x Kt-CD-box.GGU AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC >SNORD118 revised x Kt-7 (E. coli) AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC >SNORD118 revised x Kt-7 (D. radiodurans) AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 revised x Kt-11 (T. thermophilus) -AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 revised x Kt-11.eco +>SNORD118 revised x Kt-58.hma AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 revised x Kt-15.hma +>SNORD118 revised x Kt-46.tth AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 revised x Kt-23.tth +>SNORD118 revised x Kt-SAM-ribo.tte AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC >SNORD118 revised x Kt-23.eco AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC >SNORD118 revised x Kt-38.hma AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 revised x Kt-42.hma -AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 revised x Kt-42.tth -AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 revised x Kt-42.dra -AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 revised x Kt-42.eco -AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 revised x Kt-46.hma -AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 revised x Kt-46.tth -AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC >SNORD118 revised x Kt-46.dra AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 revised x Kt-46.eco -AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 revised x Kt-58.hma -AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 revised x Kt-U4a.hsa -AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 revised x Kt-U4b.hsa -AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC >SNORD118 revised x Kt-CD-box.CGU AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC .(((.((.(.(((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).)))).))))) (((((...((((((............))...))))...))......(((((((((...........))))))))).....)))...... -15.038848877 ->SNORD118 revised x Kt-CD-box.UGU +>SNORD118 revised x Kt-T-box.bsu +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 revised x Kt-23.tth +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 revised x Kt-46.eco +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 revised x Kt-c-di-GMP-II.cac +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 revised x Kt-11 (T. thermophilus) +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 revised x Kt-CD-box.AAU AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC >SNORD118 revised x Kt-L30e.sce AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 revised x Kt-SAM-ribo.tte +>SNORD118 revised x Kt-7 (T. thermophilus) +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 revised x Kt-42.hma AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 revised x Kt-T-box.bsu +>SNORD118 revised x Kt-U4a.hsa +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 revised x Kt-G2nA-SAMribo.bsu AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 revised x Kt-c-di-GMP-II.cac +>SNORD118 revised x Kt-CD-box.GAU +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +.(((.((.(.(((.(((((((((.((.((((.....)))).)))))))(((((((...........))))))).)))).)))).))))) (((.(((...(((((......))))))((((.....))))...)).(((((((((...........))))))))).....)))...... -8.30844116211 +>SNORD118 revised x Kt-11.eco AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC ->SNORD118 revised x Kt-G2nA-SAM-riboswitch (T. tengcongensi) +>SNORD118 revised x Kt-46.hma AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC +>SNORD118 revised x Kt-CD-box.AGU +AGAACAUGAUGAUUGGAGAUGCAUGAAACGUGAUUAACGUCUCUGCGUAAUCAGGACUUGCAACACCCUGAUUGCUCCUGUCUGAUUUC diff -r b7cf9b172cfe -r 4d16cf9414cf test-data/SNORD13-revised.scan-for-segments.txt --- a/test-data/SNORD13-revised.scan-for-segments.txt Wed Aug 03 04:54:40 2016 -0400 +++ b/test-data/SNORD13-revised.scan-for-segments.txt Fri Feb 24 04:18:22 2017 -0500 @@ -1,57 +1,74 @@ +>SNORD13 revised x Kt-42.dra +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 revised x Kt-42.eco +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 revised x Loop-E-Motif.bac +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 revised x Kt-CD-box.UAU +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 revised x Kt-CD-box.UGU +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 revised x Kt-CD-box.CAU +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 revised x Kt-42.tth +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 revised x Kt-G2nA-SAM-riboswitch (T. tengcongensi) +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC >SNORD13 revised x Kt-7 G2nA SAM riboswitch (H. marismortui) GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 revised x Kt-7 (T. thermophilus) +>SNORD13 revised x Kt-15.hma +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 revised x Kt-U4b.hsa +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 revised x Kt-CD-box.GGU GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC >SNORD13 revised x Kt-7 (E. coli) GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC >SNORD13 revised x Kt-7 (D. radiodurans) GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 revised x Kt-11 (T. thermophilus) -GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 revised x Kt-11.eco +>SNORD13 revised x Kt-58.hma GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 revised x Kt-15.hma +>SNORD13 revised x Kt-46.tth GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 revised x Kt-23.tth +>SNORD13 revised x Kt-SAM-ribo.tte GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC >SNORD13 revised x Kt-23.eco GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC >SNORD13 revised x Kt-38.hma GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 revised x Kt-42.hma -GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 revised x Kt-42.tth -GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 revised x Kt-42.dra -GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 revised x Kt-42.eco -GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 revised x Kt-46.hma -GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 revised x Kt-46.tth -GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC >SNORD13 revised x Kt-46.dra GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 revised x Kt-46.eco -GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 revised x Kt-58.hma -GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 revised x Kt-U4a.hsa -GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 revised x Kt-U4b.hsa -GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC >SNORD13 revised x Kt-CD-box.CGU GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC (((((.(..((.(((....((((((((((((....)))))))(((((((..(.((((((...))).))).)..)))))))))))))))))..)))))) (((((.(.(...((((((.((((((((((((....)))))))(((((((..(.((((((...))).))).)..))))))))))))))))))))))))) 3.37054443359 ->SNORD13 revised x Kt-CD-box.UGU +>SNORD13 revised x Kt-T-box.bsu +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 revised x Kt-23.tth +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 revised x Kt-46.eco +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 revised x Kt-c-di-GMP-II.cac +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 revised x Kt-11 (T. thermophilus) +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 revised x Kt-CD-box.AAU GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC >SNORD13 revised x Kt-L30e.sce GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 revised x Kt-SAM-ribo.tte +>SNORD13 revised x Kt-7 (T. thermophilus) +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 revised x Kt-42.hma GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 revised x Kt-T-box.bsu +>SNORD13 revised x Kt-U4a.hsa +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 revised x Kt-G2nA-SAMribo.bsu GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 revised x Kt-c-di-GMP-II.cac +>SNORD13 revised x Kt-CD-box.GAU +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +(((((.(..((.(((....((((((((((((....)))))))(((((((..(.((((((...))).))).)..)))))))))))))))))..)))))) (((((((.((((...((((((((((....))))))..)))))...)))))............((((.((((.((........)))))))))).))))) -9.90228271484 +>SNORD13 revised x Kt-11.eco GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC ->SNORD13 revised x Kt-G2nA-SAM-riboswitch (T. tengcongensi) +>SNORD13 revised x Kt-46.hma GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC +>SNORD13 revised x Kt-CD-box.AGU +GUUCAUGAGCGUGAUGAUUGGGUGUUCAUACGCUUGUGUGAGAUGUGCCACCCUUGAACCUUGUUACGACGUGGGCACAUUACCCGUCUGACCUGAAC diff -r b7cf9b172cfe -r 4d16cf9414cf test-data/SNORD48-revised.scan-for-segments.txt --- a/test-data/SNORD48-revised.scan-for-segments.txt Wed Aug 03 04:54:40 2016 -0400 +++ b/test-data/SNORD48-revised.scan-for-segments.txt Fri Feb 24 04:18:22 2017 -0500 @@ -1,56 +1,74 @@ +>SNORD48 revised (2 extra bases on 5' end) x Kt-42.dra +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 revised (2 extra bases on 5' end) x Kt-42.eco +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 revised (2 extra bases on 5' end) x Loop-E-Motif.bac +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 revised (2 extra bases on 5' end) x Kt-CD-box.UAU +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 revised (2 extra bases on 5' end) x Kt-CD-box.UGU +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 revised (2 extra bases on 5' end) x Kt-CD-box.CAU +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 revised (2 extra bases on 5' end) x Kt-42.tth +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 revised (2 extra bases on 5' end) x Kt-G2nA-SAM-riboswitch (T. tengcongensi) +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC >SNORD48 revised (2 extra bases on 5' end) x Kt-7 G2nA SAM riboswitch (H. marismortui) GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised (2 extra bases on 5' end) x Kt-7 (T. thermophilus) +>SNORD48 revised (2 extra bases on 5' end) x Kt-15.hma +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 revised (2 extra bases on 5' end) x Kt-U4b.hsa +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 revised (2 extra bases on 5' end) x Kt-CD-box.GGU GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC >SNORD48 revised (2 extra bases on 5' end) x Kt-7 (E. coli) GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC >SNORD48 revised (2 extra bases on 5' end) x Kt-7 (D. radiodurans) GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised (2 extra bases on 5' end) x Kt-11 (T. thermophilus) -GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised (2 extra bases on 5' end) x Kt-11.eco +>SNORD48 revised (2 extra bases on 5' end) x Kt-58.hma GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised (2 extra bases on 5' end) x Kt-15.hma +>SNORD48 revised (2 extra bases on 5' end) x Kt-46.tth GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised (2 extra bases on 5' end) x Kt-23.tth +>SNORD48 revised (2 extra bases on 5' end) x Kt-SAM-ribo.tte GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC >SNORD48 revised (2 extra bases on 5' end) x Kt-23.eco GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC >SNORD48 revised (2 extra bases on 5' end) x Kt-38.hma GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised (2 extra bases on 5' end) x Kt-42.hma +>SNORD48 revised (2 extra bases on 5' end) x Kt-46.dra GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised (2 extra bases on 5' end) x Kt-42.tth -GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised (2 extra bases on 5' end) x Kt-42.dra +>SNORD48 revised (2 extra bases on 5' end) x Kt-CD-box.CGU GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised (2 extra bases on 5' end) x Kt-42.eco -GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised (2 extra bases on 5' end) x Kt-46.hma +>SNORD48 revised (2 extra bases on 5' end) x Kt-T-box.bsu GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised (2 extra bases on 5' end) x Kt-46.tth -GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised (2 extra bases on 5' end) x Kt-46.dra +>SNORD48 revised (2 extra bases on 5' end) x Kt-23.tth GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC >SNORD48 revised (2 extra bases on 5' end) x Kt-46.eco GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised (2 extra bases on 5' end) x Kt-58.hma +>SNORD48 revised (2 extra bases on 5' end) x Kt-c-di-GMP-II.cac +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 revised (2 extra bases on 5' end) x Kt-11 (T. thermophilus) +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 revised (2 extra bases on 5' end) x Kt-CD-box.AAU +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 revised (2 extra bases on 5' end) x Kt-L30e.sce +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 revised (2 extra bases on 5' end) x Kt-7 (T. thermophilus) +GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +>SNORD48 revised (2 extra bases on 5' end) x Kt-42.hma GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC >SNORD48 revised (2 extra bases on 5' end) x Kt-U4a.hsa GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised (2 extra bases on 5' end) x Kt-U4b.hsa -GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised (2 extra bases on 5' end) x Kt-CD-box.CGU +>SNORD48 revised (2 extra bases on 5' end) x Kt-G2nA-SAMribo.bsu GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised (2 extra bases on 5' end) x Kt-CD-box.UGU -GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised (2 extra bases on 5' end) x Kt-L30e.sce +>SNORD48 revised (2 extra bases on 5' end) x Kt-CD-box.GAU GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised (2 extra bases on 5' end) x Kt-SAM-ribo.tte -GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised (2 extra bases on 5' end) x Kt-T-box.bsu +((((((.((.((((((((((.....)))).).).)))).((((...))))...)).)))))).... (((((...(((((((...))).....))))).....(((((............))))))))).... -10.9268188477 +>SNORD48 revised (2 extra bases on 5' end) x Kt-11.eco GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised (2 extra bases on 5' end) x Kt-c-di-GMP-II.cac +>SNORD48 revised (2 extra bases on 5' end) x Kt-46.hma GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC ->SNORD48 revised (2 extra bases on 5' end) x Kt-G2nA-SAM-riboswitch (T. tengcongensi) +>SNORD48 revised (2 extra bases on 5' end) x Kt-CD-box.AGU GGAGUGAUGAUGACCCCAGGUAACUCUUGAGUGUGUCGCUGAUGCCAUCACCGCAGCGCUCUGACC +((((((.((.((((((((((.....)))).).).)))).((((...))))...)).)))))).... ((...(((((..((..((((.....)))).))((((.((((((...))))..)).))))))))))) -1.84698486328 diff -r b7cf9b172cfe -r 4d16cf9414cf tool_dependencies.xml --- a/tool_dependencies.xml Wed Aug 03 04:54:40 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - diff -r b7cf9b172cfe -r 4d16cf9414cf utils_add-read-counts.xml --- a/utils_add-read-counts.xml Wed Aug 03 04:54:40 2016 -0400 +++ b/utils_add-read-counts.xml Fri Feb 24 04:18:22 2017 -0500 @@ -5,18 +5,10 @@ macros.xml - - python - numpy - pysam - htseq - segmentation-fold-utils - - + + - @VERSION_COMMAND_UTILS@ - - - \ No newline at end of file + diff -r b7cf9b172cfe -r 4d16cf9414cf utils_estimate-energy.xml --- a/utils_estimate-energy.xml Wed Aug 03 04:54:40 2016 -0400 +++ b/utils_estimate-energy.xml Fri Feb 24 04:18:22 2017 -0500 @@ -5,20 +5,10 @@ macros.xml - - python - numpy - pysam - htseq - segmentation-fold-utils - - segmentation-fold - - + + - echo $(@VERSION_COMMAND_SMF@)", "$(@VERSION_COMMAND_UTILS@) - - diff -r b7cf9b172cfe -r 4d16cf9414cf utils_extract-boxed-sequences.xml --- a/utils_extract-boxed-sequences.xml Wed Aug 03 04:54:40 2016 -0400 +++ b/utils_extract-boxed-sequences.xml Fri Feb 24 04:18:22 2017 -0500 @@ -5,18 +5,10 @@ macros.xml - - python - numpy - pysam - htseq - segmentation-fold-utils - - + + - @VERSION_COMMAND_UTILS@ - - macros.xml - - python - numpy - pysam - htseq - segmentation-fold-utils - - + + - @VERSION_COMMAND_UTILS@ - - macros.xml - - python - numpy - pysam - htseq - segmentation-fold-utils - - + + - @VERSION_COMMAND_UTILS@ - - macros.xml - - python - numpy - pysam - htseq - segmentation-fold-utils - + + - - - @VERSION_COMMAND_UTILS@ - - - + diff -r b7cf9b172cfe -r 4d16cf9414cf utils_fix-fasta-headers.xml --- a/utils_fix-fasta-headers.xml Wed Aug 03 04:54:40 2016 -0400 +++ b/utils_fix-fasta-headers.xml Fri Feb 24 04:18:22 2017 -0500 @@ -5,19 +5,10 @@ macros.xml - - python - numpy - pysam - htseq - segmentation-fold-utils - + + - - - @VERSION_COMMAND_UTILS@ - - + label="Fasta file with RNA-sequece" + argument="-f" /> @@ -40,12 +31,12 @@ - + - +