# HG changeset patch
# User rnateam
# Date 1484344111 18000
# Node ID c5f150d2686fadf8bfa21fbbf788ecde527bc758
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
diff -r 000000000000 -r c5f150d2686f locarna.tar.bz2
Binary file locarna.tar.bz2 has changed
diff -r 000000000000 -r c5f150d2686f locarna_pairwise_p.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/locarna_pairwise_p.xml Fri Jan 13 16:48:31 2017 -0500
@@ -0,0 +1,212 @@
+
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+ Partition Function and Probabilities from Pairwise Simultaneous Alignment and Folding of RNAs (LocARNA-P)
+
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+ macros.xml
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+ 'base_match_probs' in outputs
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+ 'arc_match_probs' in outputs
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diff -r 000000000000 -r c5f150d2686f macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Jan 13 16:48:31 2017 -0500
@@ -0,0 +1,322 @@
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+ 1.9.0
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+ locarna
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+ ## -------------------- scoring parameters
+ --indel $Scoring.indel
+ --indel-opening $Scoring.indel_opening
+ --struct-weight $Scoring.struct_weight
+ --tau $Scoring.tau
+
+ #if str($Scoring.sequence_score.sequence_score_selector) == "match"
+ --match $Scoring.sequence_score.match
+ --mismatch $Scoring.sequence_score.mismatch
+ #elif str($Scoring.sequence_score.sequence_score_selector) == "ribosum"
+ --use-ribosum true
+ #elif str($Scoring.sequence_score.sequence_score_selector) == "ribofit"
+ --ribofit true
+ #end if
+
+
+
+ ## -------------------- folding parameters
+ #if float($Folding.rnafold_temperature) != 37.0
+ --rnafold-temperature $Folding.rnafold_temperature
+ #end if
+
+
+
+ ## -------------------- heuristic parameters
+ -p $Heuristics.min_prob
+
+ #if str($Heuristics.max_diff_mode.max_diff_mode_selector) == "off"
+ --max-diff -1
+ #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff"
+ --max-diff $Heuristics.max_diff_mode.max_diff
+ #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff-at-am"
+ --max-diff -1
+ --max-diff-at-am $Heuristics.max_diff_mode.max_diff_at_am
+ #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff-aln"
+ --max-diff $Heuristics.max_diff_mode.max_diff
+ --max-diff-aln '$Heuristics.max_diff_mode.max_diff_aln'
+ $Heuristics.max_diff_mode.max_diff_relax
+ #end if
+
+ --max-diff-am $Heuristics.max_diff_am
+
+ #if float($Heuristics.max_bps_length_ratio) > 0.0
+ --max-bps-length-ratio $Heuristics.max_bps_length_ratio
+ #end if
+
+
+
+ ## -------------------- constraint parameters
+ $Constraints.lonely_pairs
+
+ #if $Constraints.maxBPspan != -1
+ --maxBPspan $Constraints.maxBPspan
+ #end if
+
+ $Constraints.ignore_constraints
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+
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+ $stdout_verbosity
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+ #if str($stdout_verbosity) != "--quiet":
+ > '$stdout'
+ #end if
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+ stdout_verbosity != '--quiet'
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+ 'clustal' in outputs
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+ 'clustal_strict' in outputs
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+ 'stockholm' in outputs
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+ 'pp' in outputs
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+ 'mlocarna_results' in outputs
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+ 10.1371/journal.pcbi.0030065
+ 10.1261/rna.029041.111
+ 10.1093/bioinformatics/btv185
+ 10.1186/s12859-014-0404-0
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diff -r 000000000000 -r c5f150d2686f test-data/archaea-default.stdout
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/archaea-default.stdout Fri Jan 13 16:48:31 2017 -0500
@@ -0,0 +1,18 @@
+mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA 1.9.0
+Copyright Sebastian Will
+
+Compute pair probs ...
+Compute pairwise alignments ...
+Perform progressive alignment ...
+
+
+
+vhuU AG-CUCACAACCGAACCC-AU------------UUGGGAGGUUGUGAGCU-
+fwdB AU-GUUGGAGGGGAACCC-GU------------AAGGGACCCUCCAAGAU-
+selD UUACGAUGUGCCGAACCCUUU------------AAGGGAGGCACAUCGAAA
+hdrA GG--CACCACUCGAAGGC--U------------AAGCCAAAGUGGUG-CU-
+vhuD GU--UCUCUCGGGAACCCGUC------------AAGGGACCGAGAGA-AC-
+fruA ---CCUCGAGGGGAACCC-GA------------AAGGGACCCGAGAGG---
+fdhA CG-CCACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAG-GUGGCG-
+
+alifold ((.(((((((((...(((.................))).))))))))))). (-31.59 = -20.01 + -11.58)
diff -r 000000000000 -r c5f150d2686f test-data/archaea-probabilistic.aln
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/archaea-probabilistic.aln Fri Jan 13 16:48:31 2017 -0500
@@ -0,0 +1,11 @@
+CLUSTAL W --- LocARNA 1.9.0
+
+
+
+selD UUACGAUGUGCCGAACCCUU------------UAAGGGAGGCACAUCGAAA
+vhuU AGC-UCACAACCGAACCCAU-------------UUGGGAGGUUGUGAG-CU
+fwdB AUG-UUGGAGGGGAACCCGU-------------AAGGGACCCUCCAAG-AU
+hdrA GGC-ACC-ACUCGAAGGCU--------------AAGCCAAAGU-GGUG-CU
+vhuD GUU-CUC-UCGGGAACCCGU------------CAAGGGACCGA-GAGA-AC
+fdhA CGC-CACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAG-GUGG-CG
+fruA CC-UCG--AGGGGAACCCGA-------------AAGGGACCC--GAGA-GG
diff -r 000000000000 -r c5f150d2686f test-data/archaea-ref.aln
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/archaea-ref.aln Fri Jan 13 16:48:31 2017 -0500
@@ -0,0 +1,9 @@
+CLUSTAL W --- LocARNA 1.9.0
+
+selD UUACGAUGUGCCGAACCCUU------------UAAGGGAGGCACAUCGAAA
+vhuU AGC-UCACAACCGAACCCAU-------------UUGGGAGGUUGUGAG-CU
+fwdB AUG-UUGGAGGGGAACCCGU-------------AAGGGACCCUCCAAG-AU
+hdrA GGC-ACC-ACUCGAAGGCU--------------AAGCCAAAGU-GGUG-CU
+vhuD GUU-CUC-UCGGGAACCCGU------------CAAGGGACCGA-GAGA-AC
+fdhA CGC-CACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAG-GUGG-CG
+fruA CC-UCG--AGGGGAACCCGA-------------AAGGGACCC--GAGA-GG
diff -r 000000000000 -r c5f150d2686f test-data/archaea-ref_result.aln
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/archaea-ref_result.aln Fri Jan 13 16:48:31 2017 -0500
@@ -0,0 +1,11 @@
+CLUSTAL W --- LocARNA 1.9.0
+
+
+
+vhuU AG-CUCACAACCGAACCC-AU------------UUGGGAGGUUGUGAGCU-
+fwdB AU-GUUGGAGGGGAACCC-GU------------AAGGGACCCUCCAAGAU-
+selD UUACGAUGUGCCGAACCCUUU------------AAGGGAGGCACAUCGAAA
+hdrA GG--CACCACUCGAAGGC--U------------AAGCCAAAGUGGUG-CU-
+vhuD GU--UCUCUCGGGAACCCGUC------------AAGGGACCGAGAGA-AC-
+fruA ---CCUCGAGGGGAACCC-GA------------AAGGGACCCGAGAGG---
+fdhA CG-CCACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAG-GUGGCG-
diff -r 000000000000 -r c5f150d2686f test-data/archaea.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/archaea.fa Fri Jan 13 16:48:31 2017 -0500
@@ -0,0 +1,14 @@
+>fruA
+CCUCGAGGGGAACCCGAAAGGGACCCGAGAGG
+>fdhA
+CGCCACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAGGUGGCG
+>vhuU
+AGCUCACAACCGAACCCAUUUGGGAGGUUGUGAGCU
+>hdrA
+GGCACCACUCGAAGGCUAAGCCAAAGUGGUGCU
+>vhuD
+GUUCUCUCGGGAACCCGUCAAGGGACCGAGAGAAC
+>selD
+UUACGAUGUGCCGAACCCUUUAAGGGAGGCACAUCGAAA
+>fwdB
+AUGUUGGAGGGGAACCCGUAAGGGACCCUCCAAGAU
diff -r 000000000000 -r c5f150d2686f test-data/archaea.tar.gz
Binary file test-data/archaea.tar.gz has changed
diff -r 000000000000 -r c5f150d2686f test-data/archaea_relplot.scr
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/archaea_relplot.scr Fri Jan 13 16:48:31 2017 -0500
@@ -0,0 +1,137 @@
+pdf("/tmp/tmp5yxSuG/files/000/dataset_2.dat",width=12,height=4,version="1.4")
+
+rel <- read.table("mlocarna_results/results/result.bmreliability");
+seqrel <- rel[[2]]
+strrel <- rel[[3]]
+
+if ("" != "") {
+ seq <- ""
+ seq <- strsplit(seq,split="")
+ tab <- unlist(seq)!="-"
+
+ seqrel<-seqrel[tab]
+ strrel<-strrel[tab]
+}
+
+len<-length(seqrel)
+
+if (0) {
+ seqrel<-seqrel[len:1]
+ strrel<-strrel[len:1]
+}
+
+
+
+if (1) {
+ seqrel <- seqrel/1.0
+}
+
+
+totalrel <- seqrel+strrel;
+
+anno_space<-0.075
+
+maxy <- max(c(1,totalrel))+anno_space*(0+1);
+
+
+firstpos <- 1
+lastpos <- 1+len-1
+
+if (0) {
+ the_xlim <- c(lastpos,firstpos)
+} else {
+ the_xlim <- c(firstpos,lastpos)
+}
+
+# set margin
+# b, l, t, r
+par(mar=c(6,2.5,1,1))
+
+# open plot (and draw threshold)
+plot(c(0),c(0),type="l",
+ xlab="",ylab="",
+ xlim=the_xlim,ylim=c(0,maxy),
+ yaxp=c(0,1,2))
+
+## title inside of plot
+legend("topleft","",bty="n")
+
+
+# total reliability
+polygon(c(firstpos,firstpos:lastpos,lastpos),c(0,totalrel,0),col=rgb(0.8,0.8,0.9,0.5),lwd=2,border=FALSE)
+lines(firstpos:lastpos,totalrel,col="blue",lwd=2)
+
+# plot structure reliability
+polygon(c(firstpos,firstpos:lastpos,lastpos),c(0,strrel,0),col=rgb(0.3,0.3,0.5,0.8),lwd=1,border=FALSE)
+
+
+## draw other signals
+signals<-c();
+signal_sizes<-c();
+
+signal_starts <- 1:0
+
+signal_starts[1]<-1;
+if (0>1) {
+ for (i in 2:0) {
+ signal_starts[i]<-signal_starts[i-1]+signal_sizes[i-1]*2+1;
+ }
+}
+
+colors <- c(
+ rgb(0.6,0.1,0.1,0.9),
+ rgb(0.6,0.6,0.1,0.9),
+ rgb(0.1,0.6,0.6,0.9),
+ rgb(0.6,0.1,0.6,0.9)
+);
+colors<-c(colors,colors);
+
+if (0>0) {
+
+ for (i in 1:0) {
+ orientation <- signals[signal_starts[i]+signal_sizes[i]*2];
+ sig_y <- maxy-i*anno_space;
+
+ for (j in 0:(signal_sizes[i]-1)) {
+
+ sig_x <- c(signals[signal_starts[i]+j*2],signals[signal_starts[i]+j*2+1]);
+
+ ## draw arrows
+ if (orientation!=0) {
+ the_code <- 1+(orientation+1)/2;
+ arrows(sig_x[1],sig_y,sig_x[2],sig_y,lwd=4,col=colors[i],code=the_code,angle=20,length=0.15);
+ } else {
+ lines(sig_x,c(sig_y,sig_y),lwd=4,col=colors[i]);
+ }
+ }
+ }
+}
+
+#draw inferred on-signal
+hit_color <- rgb(0.1,0.6,0.1,0.9)
+
+if (0!=1) {
+
+ on <- c(0,4,33,44,49);
+ off <- c(3,20,43,48,51);
+
+ if (length(on)>0) {
+ for (i in 1:length(on)) {
+ lines(c(1+on[i],1+off[i]-1),c(maxy,maxy),lwd=7,col=hit_color);
+ }
+ }
+
+ ### draw on/off values
+ if (0) {
+ lines(c(1,1+len),c(0.0355791,0.0355791),lty=2,lwd=1)
+ lines(c(1,1+len),c(0.702675,0.702675),lty=2,lwd=1)
+ }
+}
+
+
+signal_names<-c();
+
+if (length(signal_names)>0 || (0!=1)) {
+ legend("bottom",c("LocARNA",signal_names),lwd=7,col=c(hit_color,colors),horiz=TRUE,inset=-0.4);
+ # ,xpd=TRUE
+}
diff -r 000000000000 -r c5f150d2686f test-data/ferritin_human.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ferritin_human.fa Fri Jan 13 16:48:31 2017 -0500
@@ -0,0 +1,2 @@
+> human ferritin
+CCAGACGUUCUUCGCCGAGAGUCGUCGGGGUUUCCUGCUUCAACAGUGCUUGGACGGAACCCGGCGCUCGUUCCCCACCCCGGCCGGCCGCCCAUAGCCAGCCCUCCGUCACCUCUUCACCGCACCCUCGGACUGCCCCAAGGCCCCCGCCGCCGCUCCAGCGCCGCGCAGCCACCGCCGCCGCCGCCGCCUCUCCUUAGUCGCCGCC
diff -r 000000000000 -r c5f150d2686f test-data/ferritin_mouse.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ferritin_mouse.fa Fri Jan 13 16:48:31 2017 -0500
@@ -0,0 +1,2 @@
+> mouse ferritin
+CAGACGUUCUCGCCCAGAGUCGCCGCGGUUUCCUGCUUCAACAGUGCUUGAACGGAACCCGGUGCUCGACCCCUCCGACCCCCGCCGGCCGCUUCGAGCCUGAGCCCUUUGCAACUUCGUCGUUCCGCCGCUCCAGCGUCGCCACCGCGCCUCGCCCCGCCGCCACC
diff -r 000000000000 -r c5f150d2686f test-data/haca.snoRNA-1.aln
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/haca.snoRNA-1.aln Fri Jan 13 16:48:31 2017 -0500
@@ -0,0 +1,5 @@
+ACA7 ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGGAGGGAAAGCAAGCCUGGCAGAGGCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCGAUUGGAAGACACUCUGCGACA
+ACA30 UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAAC---CC-UUG--AUUGUAUUCUUGCCCUGGG---AUUAUACCAGUGGCAACUGUCACUCAAUGGGACA
+ACA5 UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGC--CCAGAAGGCUGCCACAGAAACAC--UGUGACUCAUGG-----GCCCUGUUCCUGUGUCCCAGGCUCAGGGAUAAAUUUGGUUACAGACA
+#A1 ................................................................AAAAAA...................................................................BBB
+#A2 ................................................................123456...................................................................123
diff -r 000000000000 -r c5f150d2686f test-data/haca.snoRNA-2.aln
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/haca.snoRNA-2.aln Fri Jan 13 16:48:31 2017 -0500
@@ -0,0 +1,3 @@
+ACA59 GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGGCCCAUGGGUGACCCUGGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUAACAAUACUUACUCUCGUUGGUGAUAAGGAACA
+#A1 .............................................................AAAAAA...............................................................................BBB
+#A2 .............................................................123456...............................................................................123
diff -r 000000000000 -r c5f150d2686f test-data/haca.snoRNA-c.aln
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/haca.snoRNA-c.aln Fri Jan 13 16:48:31 2017 -0500
@@ -0,0 +1,22 @@
+CLUSTAL W --- LocARNA 1.9.0
+
+ACA7 ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGG
+ACA30 UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGU
+ACA5 UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGC--CCAGAAGGC
+ACA59 GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGG-CCCAUG--GGUGACCCU
+#A1 ............................................................
+#A2 ............................................................
+
+ACA7 AGGGAAAGCAAGCCUGGCAGAG-GCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCG
+ACA30 GCUGAGAGAAAAC---CC-UUG---AUUGUAUUCUUGCCCUGGG---AUUAUACCAGUGG
+ACA5 UGCCACAGAAACAC--UGUGAC-UCAUGG-----GCCCUGUUCCUGUGUCCCAGGCUCAG
+ACA59 GGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA
+#A1 ....AAAAAA..................................................
+#A2 ....123456..................................................
+
+ACA7 AUUGGA--AGA---CACU-CUGCG-----ACA
+ACA30 CAACUG--UCA---CUCA-AUGGG-----ACA
+ACA5 GGAUAA--AUU---UGGU-UACAG-----ACA
+ACA59 ACAAUACUUACUCUCGUUGGUGAUAAGGAACA
+#A1 .............................BBB
+#A2 .............................123
diff -r 000000000000 -r c5f150d2686f test-data/haca.snoRNA-default.stdout
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/haca.snoRNA-default.stdout Fri Jan 13 16:48:31 2017 -0500
@@ -0,0 +1,33 @@
+mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA 1.9.0
+Copyright Sebastian Will
+
+Compute pair probs ...
+Compute pairwise alignments ...
+Perform progressive alignment ...
+
+
+
+ACA7 ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUUCGGAA-AGGG
+ACA30 UGGCACUUUCACAG--UUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGU
+ACA5 UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGCCCAGAA--GGC
+ACA59 GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGG-CCCAUGGGUGAC--CCU
+#A1 ............................................................
+#A2 ............................................................
+
+ACA7 AGGGAAAGCAAGCCUGGCAGAG-GCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCG
+ACA30 GCUGAGAGAAAAC---CC-UUG---AUUGUAUUCUUGCCCUGGG---AUUAUACCAGUGG
+ACA5 UGCCACAGAAACAC--UGUGAC-UCAUGG-----GCCCUGUUCCUGUGUCCCAGGCUCAG
+ACA59 GGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA
+#A1 ....AAAAAA..................................................
+#A2 ....123456..................................................
+
+ACA7 AUUGGA--AGA---CACU-CUGCG-----ACA
+ACA30 CAACUG--UCA---CUCA-AUGGG-----ACA
+ACA5 GGAUAA--AUU---UGGU-UACAG-----ACA
+ACA59 ACAAUACUUACUCUCGUUGGUGAUAAGGAACA
+#A1 .............................BBB
+#A2 .............................123
+
+alifold .((((((((........((((.(((((((......))))))).))))......))..)))
+ ))).............((((((.....((.....((((((((((((.....)))))))))
+ )))......)).....)).))))......... (-61.69 = -33.85 + -27.84)
diff -r 000000000000 -r c5f150d2686f test-data/haca.snoRNA.aln
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/haca.snoRNA.aln Fri Jan 13 16:48:31 2017 -0500
@@ -0,0 +1,16 @@
+CLUSTAL W --- LocARNA 1.9.0
+
+ACA7 ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGG
+ACA30 UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGU
+ACA5 UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGC--CCAGAAGGC
+ACA59 GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGG-CCCAUG--GGUGACCCU
+
+ACA7 AGGGAAAGCAAGCCUGGCAGAG-GCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCG
+ACA30 GCUGAGAGAAAAC---CC-UUG---AUUGUAUUCUUGCCCUGGG---AUUAUACCAGUGG
+ACA5 UGCCACAGAAACAC--UGUGAC-UCAUGG-----GCCCUGUUCCUGUGUCCCAGGCUCAG
+ACA59 GGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA
+
+ACA7 AUUGGA--AGA---CACU-CUGCG-----ACA
+ACA30 CAACUG--UCA---CUCA-AUGGG-----ACA
+ACA5 GGAUAA--AUU---UGGU-UACAG-----ACA
+ACA59 ACAAUACUUACUCUCGUUGGUGAUAAGGAACA
diff -r 000000000000 -r c5f150d2686f test-data/haca.snoRNA.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/haca.snoRNA.fa Fri Jan 13 16:48:31 2017 -0500
@@ -0,0 +1,21 @@
+>ACA59
+GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGGCCCAUGGGUGACCCUGGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUAACAAUACUUACUCUCGUUGGUGAUAAGGAACA
+.............................................................xxxxxx...............................................................................xxx #S
+.............................................................AAAAAA...............................................................................BBB #1
+.............................................................123456...............................................................................123 #2
+
+>ACA7
+ACCUCCUGGGAUCGCAUCUGGAGAGUGCCUAGUAUUCUGCCAGCUUCGGAAAGGGAGGGAAAGCAAGCCUGGCAGAGGCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCGAUUGGAAGACACUCUGCGACA
+...........................................................xxxxxx...................................................................xxx #S
+...........................................................AAAAAA...................................................................BBB #1
+...........................................................123456...................................................................123 #2
+>ACA5
+UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGCCCAGAAGGCUGCCACAGAAACACUGUGACUCAUGGGCCCUGUUCCUGUGUCCCAGGCUCAGGGAUAAAUUUGGUUACAGACA
+..............................................................xxxxxx............................................................xxx #S
+..............................................................AAAAAA............................................................BBB #1
+..............................................................123456............................................................123 #2
+>ACA30
+UGGCACUUUCACAGUUCCUUCCCCAGGCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAACCCUUGAUUGUAUUCUUGCCCUGGGAUUAUACCAGUGGCAACUGUCACUCAAUGGGACA
+..........................................................xxxxxx..........................................................xxx #S
+..........................................................AAAAAA..........................................................BBB #1
+..........................................................123456..........................................................123 #2
diff -r 000000000000 -r c5f150d2686f test-data/haca.snoRNA_anchor.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/haca.snoRNA_anchor.bed Fri Jan 13 16:48:31 2017 -0500
@@ -0,0 +1,8 @@
+ACA59 61 67 ANANNA
+ACA7 59 65 ANANNA
+ACA5 62 68 ANANNA
+ACA30 58 64 ANANNA
+ACA59 146 149 ACA
+ACA7 132 135 ACA
+ACA5 128 131 ACA
+ACA30 122 125 ACA
diff -r 000000000000 -r c5f150d2686f test-data/tRNA_2-1.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA_2-1.fa Fri Jan 13 16:48:31 2017 -0500
@@ -0,0 +1,2 @@
+>D10744
+GGAAAAUUGAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGGUGAGUUCGAAUCUCACAUUUUCCG
diff -r 000000000000 -r c5f150d2686f test-data/tRNA_2-2.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA_2-2.fa Fri Jan 13 16:48:31 2017 -0500
@@ -0,0 +1,2 @@
+>AF008220
+GGAGGAUUAGCUCAGCUGGGAGAGCAUCUGCCUUACAAGCAGAGGGUCGGCGGUUCGAGCCCGUCAUCCUCCA
diff -r 000000000000 -r c5f150d2686f test-data/tRNA_2.aln
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA_2.aln Fri Jan 13 16:48:31 2017 -0500
@@ -0,0 +1,7 @@
+CLUSTAL W --- LocARNA 1.9.0 --- Score: 2875
+
+D10744 GGAAAAUU-GAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGG
+AF008220 GGAGGAUUAGCUCAGCUGGGAGAGCAUCUGCCUUACAAGCAGAGGG-----------UCG
+
+D10744 UGAGUUCGAAUCUCACAUUUUCCG
+AF008220 GCGGUUCGAGCCCGUCAUCCUCCA
diff -r 000000000000 -r c5f150d2686f test-data/tRNA_2.amprobs
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA_2.amprobs Fri Jan 13 16:48:31 2017 -0500
@@ -0,0 +1,108 @@
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+33 42 31 39 0.123358
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+5 78 5 68 0.962952
+4 79 4 69 0.963261
+3 80 3 70 0.872876
+2 81 2 71 0.752745
+1 82 1 72 0.752744
diff -r 000000000000 -r c5f150d2686f test-data/tRNA_2.bmprobs
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA_2.bmprobs Fri Jan 13 16:48:31 2017 -0500
@@ -0,0 +1,172 @@
+1 1 0.247253
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+3 3 0.127121
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+72 62 0.497193
+73 63 0.7313
+74 64 0.734773
+75 65 0.881053
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+81 71 0.247251
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+83 73 0.999955
diff -r 000000000000 -r c5f150d2686f test-data/tRNA_2.epms
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA_2.epms Fri Jan 13 16:48:31 2017 -0500
@@ -0,0 +1,4 @@
+epm_id score structure positions
+0 3583 ((())) 1:4 2:5 3:6 80:67 81:68 82:69
+1 3593 ((())) 1:1 2:2 3:3 80:70 81:71 82:72
+
diff -r 000000000000 -r c5f150d2686f test-data/tRNA_5.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA_5.fa Fri Jan 13 16:48:31 2017 -0500
@@ -0,0 +1,10 @@
+>D10744
+GGAAAAUUGAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGGUGAGUUCGAAUCUCACAUUUUCCG
+>AF008220
+GGAGGAUUAGCUCAGCUGGGAGAGCAUCUGCCUUACAAGCAGAGGGUCGGCGGUUCGAGCCCGUCAUCCUCCA
+>Z11880
+GCCUUCCUAGCUCAGUGGUAGAGCGCACGGCUUUUAACCGUGUGGUCGUGGGUUCGAUCCCCACGGAAGGCG
+>X02172
+GCCUUUAUAGCUUAGUGGUAAAGCGAUAAACUGAAGAUUUAUUUACAUGUAGUUCGAUUCUCAUUAAGGGCA
+>M68929
+GCGGAUAUAACUUAGGGGUUAAAGUUGCAGAUUGUGGCUCUGAAAACACGGGUUCGAAUCCCGUUAUUCGCC