# HG changeset patch
# User rnateam
# Date 1484344156 18000
# Node ID e91e4f48875eed2d3b1e9bc8fd4e5b8679e53cf9
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 287021573c592fdb70fdbbc88943aa16a8740fc0
diff -r 000000000000 -r e91e4f48875e locarna.tar.bz2
Binary file locarna.tar.bz2 has changed
diff -r 000000000000 -r e91e4f48875e locarna_exparnap.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/locarna_exparnap.xml Fri Jan 13 16:49:16 2017 -0500
@@ -0,0 +1,274 @@
+
+
+ Pairwise Simultaneous Matching and Folding of RNAs (ExpaRNA-P)
+
+
+
+ macros.xml
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 'postscript' in outputs
+
+
+ 'postscript' in outputs
+
+
+ 'anchors-fasta' in outputs
+
+
+ 'anchors-pp' in outputs
+
+
+ 'anchors-pp' in outputs
+
+
+ 'clustal' in outputs
+
+
+ 'epm_list' in outputs
+
+
+ 'chained_epm_list' in outputs
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r e91e4f48875e macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Jan 13 16:49:16 2017 -0500
@@ -0,0 +1,322 @@
+
+ 1.9.0
+
+
+
+ locarna
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ## -------------------- 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
+
+
+
+ $stdout_verbosity
+
+ #if str($stdout_verbosity) != "--quiet":
+ > '$stdout'
+ #end if
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ stdout_verbosity != '--quiet'
+
+
+
+
+
+
+ 'clustal' in outputs
+
+
+ 'clustal_strict' in outputs
+
+
+ 'stockholm' in outputs
+
+
+ 'pp' in outputs
+
+
+ 'mlocarna_results' in outputs
+
+
+
+
+
+ 10.1371/journal.pcbi.0030065
+ 10.1261/rna.029041.111
+ 10.1093/bioinformatics/btv185
+ 10.1186/s12859-014-0404-0
+
+
+
+
+
+
+
diff -r 000000000000 -r e91e4f48875e test-data/archaea-default.stdout
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/archaea-default.stdout Fri Jan 13 16:49:16 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 e91e4f48875e test-data/archaea-probabilistic.aln
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/archaea-probabilistic.aln Fri Jan 13 16:49:16 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 e91e4f48875e test-data/archaea-ref.aln
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/archaea-ref.aln Fri Jan 13 16:49:16 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 e91e4f48875e 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 16:49:16 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 e91e4f48875e test-data/archaea.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/archaea.fa Fri Jan 13 16:49:16 2017 -0500
@@ -0,0 +1,14 @@
+>fruA
+CCUCGAGGGGAACCCGAAAGGGACCCGAGAGG
+>fdhA
+CGCCACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAGGUGGCG
+>vhuU
+AGCUCACAACCGAACCCAUUUGGGAGGUUGUGAGCU
+>hdrA
+GGCACCACUCGAAGGCUAAGCCAAAGUGGUGCU
+>vhuD
+GUUCUCUCGGGAACCCGUCAAGGGACCGAGAGAAC
+>selD
+UUACGAUGUGCCGAACCCUUUAAGGGAGGCACAUCGAAA
+>fwdB
+AUGUUGGAGGGGAACCCGUAAGGGACCCUCCAAGAU
diff -r 000000000000 -r e91e4f48875e test-data/archaea.tar.gz
Binary file test-data/archaea.tar.gz has changed
diff -r 000000000000 -r e91e4f48875e test-data/archaea_relplot.scr
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/archaea_relplot.scr Fri Jan 13 16:49:16 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 e91e4f48875e test-data/ferritin_human.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ferritin_human.fa Fri Jan 13 16:49:16 2017 -0500
@@ -0,0 +1,2 @@
+> human ferritin
+CCAGACGUUCUUCGCCGAGAGUCGUCGGGGUUUCCUGCUUCAACAGUGCUUGGACGGAACCCGGCGCUCGUUCCCCACCCCGGCCGGCCGCCCAUAGCCAGCCCUCCGUCACCUCUUCACCGCACCCUCGGACUGCCCCAAGGCCCCCGCCGCCGCUCCAGCGCCGCGCAGCCACCGCCGCCGCCGCCGCCUCUCCUUAGUCGCCGCC
diff -r 000000000000 -r e91e4f48875e test-data/ferritin_mouse.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ferritin_mouse.fa Fri Jan 13 16:49:16 2017 -0500
@@ -0,0 +1,2 @@
+> mouse ferritin
+CAGACGUUCUCGCCCAGAGUCGCCGCGGUUUCCUGCUUCAACAGUGCUUGAACGGAACCCGGUGCUCGACCCCUCCGACCCCCGCCGGCCGCUUCGAGCCUGAGCCCUUUGCAACUUCGUCGUUCCGCCGCUCCAGCGUCGCCACCGCGCCUCGCCCCGCCGCCACC
diff -r 000000000000 -r e91e4f48875e 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 16:49:16 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 e91e4f48875e 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 16:49:16 2017 -0500
@@ -0,0 +1,3 @@
+ACA59 GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGGCCCAUGGGUGACCCUGGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUAACAAUACUUACUCUCGUUGGUGAUAAGGAACA
+#A1 .............................................................AAAAAA...............................................................................BBB
+#A2 .............................................................123456...............................................................................123
diff -r 000000000000 -r e91e4f48875e 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 16:49:16 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 e91e4f48875e 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 16:49:16 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 e91e4f48875e test-data/haca.snoRNA.aln
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/haca.snoRNA.aln Fri Jan 13 16:49:16 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 e91e4f48875e test-data/haca.snoRNA.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/haca.snoRNA.fa Fri Jan 13 16:49:16 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 e91e4f48875e 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 16:49:16 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 e91e4f48875e 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 16:49:16 2017 -0500
@@ -0,0 +1,2 @@
+>D10744
+GGAAAAUUGAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGGUGAGUUCGAAUCUCACAUUUUCCG
diff -r 000000000000 -r e91e4f48875e 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 16:49:16 2017 -0500
@@ -0,0 +1,2 @@
+>AF008220
+GGAGGAUUAGCUCAGCUGGGAGAGCAUCUGCCUUACAAGCAGAGGGUCGGCGGUUCGAGCCCGUCAUCCUCCA
diff -r 000000000000 -r e91e4f48875e test-data/tRNA_2.aln
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA_2.aln Fri Jan 13 16:49:16 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 e91e4f48875e test-data/tRNA_2.amprobs
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA_2.amprobs Fri Jan 13 16:49:16 2017 -0500
@@ -0,0 +1,108 @@
+64 69 54 59 0.079977
+63 70 53 60 0.0158884
+63 71 53 61 0.0915855
+62 72 52 62 0.203921
+61 73 51 63 0.202155
+60 74 50 64 0.175676
+59 75 49 65 0.0815626
+39 44 33 38 0.0114647
+39 46 33 37 0.0168669
+38 47 33 38 0.0303705
+37 48 32 39 0.0111801
+37 48 31 39 0.0434528
+36 42 34 38 0.0105213
+36 42 33 37 0.0442772
+36 42 33 38 0.0150469
+36 49 30 40 0.0445378
+35 40 33 37 0.0438048
+35 40 33 38 0.0131652
+35 43 33 37 0.0482007
+35 43 33 38 0.0524118
+35 43 32 39 0.0124841
+35 44 33 38 0.0456243
+35 44 32 39 0.0111628
+35 46 33 37 0.0220704
+35 50 29 41 0.016731
+34 44 33 38 0.0275446
+34 44 32 39 0.0318614
+34 44 31 39 0.0265932
+34 45 32 39 0.0344691
+33 42 31 39 0.123358
+33 47 31 39 0.0238501
+33 48 31 39 0.207448
+33 48 30 40 0.0278532
+33 49 32 39 0.0279853
+33 49 30 40 0.0365409
+32 36 33 37 0.0659838
+32 37 33 38 0.0229925
+32 40 31 39 0.01072
+32 43 30 40 0.102105
+32 45 31 39 0.0127413
+32 45 30 40 0.0472967
+32 46 30 40 0.0814206
+32 50 29 41 0.012395
+31 38 32 39 0.0108954
+31 44 29 41 0.0212986
+31 46 29 41 0.0101171
+31 50 30 40 0.105751
+31 50 29 41 0.490312
+31 50 28 42 0.0414615
+30 38 31 39 0.10883
+30 51 29 41 0.110433
+30 51 28 42 0.628654
+30 51 27 43 0.0377824
+29 39 30 40 0.119173
+29 52 28 42 0.130101
+29 52 27 43 0.657133
+28 40 29 41 0.103713
+28 53 27 43 0.113664
+28 53 25 45 0.0385623
+27 41 28 42 0.114432
+27 54 25 45 0.651098
+26 42 27 43 0.107977
+26 55 25 45 0.119566
+26 55 23 47 0.0239947
+26 56 25 46 0.011099
+26 56 24 47 0.147548
+26 56 23 47 0.0142523
+25 57 24 47 0.0172058
+25 57 22 48 0.0238997
+24 49 25 45 0.0155194
+24 57 23 47 0.0913467
+24 57 22 48 0.640114
+23 58 22 48 0.121828
+21 60 19 51 0.071982
+20 60 18 51 0.512044
+18 63 16 53 0.410891
+17 56 18 51 0.0172516
+17 64 15 54 0.505795
+17 65 15 55 0.0373483
+16 57 17 52 0.025034
+16 65 14 55 0.456198
+15 58 16 53 0.0181784
+15 67 13 57 0.463917
+14 19 13 18 0.0159303
+14 59 15 54 0.0239939
+14 68 12 58 0.536735
+13 60 14 55 0.0191717
+12 16 11 15 0.0116456
+12 21 13 22 0.0351601
+11 17 10 16 0.0359852
+11 22 12 23 0.0512024
+11 69 11 59 0.534042
+10 14 11 15 0.0213866
+10 23 11 24 0.0659783
+10 70 10 60 0.389747
+10 72 10 62 0.247777
+9 18 9 17 0.0444132
+9 73 8 63 0.0119982
+8 19 8 18 0.0421045
+8 74 9 64 0.0471423
+8 76 8 66 0.0271918
+7 76 7 66 0.821868
+6 77 6 67 0.869036
+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 e91e4f48875e test-data/tRNA_2.bmprobs
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA_2.bmprobs Fri Jan 13 16:49:16 2017 -0500
@@ -0,0 +1,172 @@
+1 1 0.247253
+2 2 0.247252
+3 3 0.127121
+4 4 0.0367335
+5 5 0.0369676
+6 6 0.129988
+7 7 0.156077
+8 8 0.835935
+8 9 0.012729
+9 8 0.010632
+9 9 0.727258
+9 10 0.0549287
+10 9 0.04195
+10 10 0.0853335
+10 11 0.0115868
+11 10 0.0364601
+11 11 0.112239
+12 10 0.011935
+12 11 0.0436248
+12 12 0.0614308
+13 11 0.0645154
+13 12 0.028434
+14 12 0.133445
+14 13 0.0169358
+15 13 0.260167
+15 14 0.0172799
+15 16 0.0124747
+16 14 0.271834
+16 15 0.0178714
+16 17 0.0141486
+17 15 0.185722
+17 16 0.0202801
+17 18 0.0184277
+18 16 0.300704
+18 17 0.0355582
+18 19 0.0165149
+19 17 0.700705
+19 18 0.0610097
+19 20 0.0138794
+20 18 0.193762
+20 19 0.11731
+20 21 0.012503
+21 19 0.633061
+21 20 0.119843
+22 20 0.625797
+22 21 0.127468
+23 20 0.0117929
+23 21 0.621337
+23 22 0.0118595
+23 24 0.0104834
+24 21 0.0184503
+24 22 0.0481581
+24 23 0.0441549
+24 25 0.0420745
+25 23 0.68405
+25 24 0.0269372
+25 26 0.0420693
+26 24 0.53624
+27 25 0.0346266
+27 26 0.120675
+28 26 0.681355
+28 27 0.0199945
+28 29 0.0196255
+29 27 0.0227404
+30 28 0.0396584
+30 29 0.0227396
+30 31 0.0165441
+31 29 0.121498
+31 32 0.114327
+32 30 0.351807
+32 31 0.0703916
+32 33 0.0332191
+33 31 0.0980398
+33 32 0.0266787
+33 34 0.0331979
+34 31 0.0122885
+34 32 0.400684
+34 33 0.0116529
+34 35 0.0331958
+35 32 0.0101403
+35 33 0.22599
+35 36 0.0332106
+36 33 0.0136772
+36 34 0.156117
+36 37 0.0332566
+37 34 0.0427905
+37 35 0.113127
+37 38 0.0933967
+38 35 0.0723242
+38 36 0.0618818
+39 34 0.0149807
+39 36 0.0997152
+39 37 0.0299675
+40 34 0.0108419
+40 35 0.01547
+40 37 0.111326
+40 38 0.0203761
+40 41 0.0196142
+41 35 0.0159003
+41 36 0.0127203
+41 38 0.149756
+42 34 0.0119499
+42 36 0.0189085
+42 37 0.010129
+42 39 0.0145996
+43 34 0.010789
+43 35 0.013731
+43 37 0.0170711
+43 38 0.0146016
+43 44 0.0354944
+44 35 0.0181452
+44 36 0.0122707
+44 38 0.0248855
+44 39 0.0183418
+44 45 0.0336616
+45 36 0.0423026
+45 39 0.0300877
+45 40 0.013096
+45 46 0.0286025
+46 37 0.0702926
+46 38 0.0130327
+46 40 0.0113529
+47 38 0.119444
+48 39 0.0264015
+48 40 0.0166626
+49 39 0.0133557
+49 40 0.309884
+50 41 0.109972
+51 41 0.0223073
+51 42 0.0365047
+52 43 0.0228365
+53 43 0.02009
+53 44 0.683193
+54 44 0.121387
+54 45 0.035521
+55 46 0.681952
+56 46 0.0343041
+56 47 0.536468
+56 48 0.0112514
+57 47 0.0531432
+57 48 0.0486503
+58 48 0.0521922
+58 49 0.632028
+59 49 0.117956
+59 50 0.628217
+60 50 0.0252284
+60 51 0.104879
+61 51 0.0460576
+61 52 0.573747
+62 52 0.165836
+62 53 0.0472354
+63 53 0.382375
+64 54 0.2672
+65 55 0.320519
+66 56 0.818192
+67 57 0.355528
+68 58 0.282881
+69 59 0.27801
+70 60 0.464549
+71 61 0.857675
+72 62 0.497193
+73 63 0.7313
+74 64 0.734773
+75 65 0.881053
+76 66 0.139472
+77 67 0.130956
+78 68 0.0370464
+79 69 0.0367371
+80 70 0.127122
+81 71 0.247251
+82 72 0.247251
+83 73 0.999955
diff -r 000000000000 -r e91e4f48875e test-data/tRNA_2.epms
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA_2.epms Fri Jan 13 16:49:16 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 e91e4f48875e test-data/tRNA_5.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA_5.fa Fri Jan 13 16:49:16 2017 -0500
@@ -0,0 +1,10 @@
+>D10744
+GGAAAAUUGAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGGUGAGUUCGAAUCUCACAUUUUCCG
+>AF008220
+GGAGGAUUAGCUCAGCUGGGAGAGCAUCUGCCUUACAAGCAGAGGGUCGGCGGUUCGAGCCCGUCAUCCUCCA
+>Z11880
+GCCUUCCUAGCUCAGUGGUAGAGCGCACGGCUUUUAACCGUGUGGUCGUGGGUUCGAUCCCCACGGAAGGCG
+>X02172
+GCCUUUAUAGCUUAGUGGUAAAGCGAUAAACUGAAGAUUUAUUUACAUGUAGUUCGAUUCUCAUUAAGGGCA
+>M68929
+GCGGAUAUAACUUAGGGGUUAAAGUUGCAGAUUGUGGCUCUGAAAACACGGGUUCGAAUCCCGUUAUUCGCC