# HG changeset patch
# User bgruening
# Date 1497877202 14400
# Node ID 7b48472d3fbb0922c3e6fdc2762131232a8900ef
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit c4057f9456151519de78ea9cc2f7c12c998ee31b
diff -r 000000000000 -r 7b48472d3fbb kinwalker.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/kinwalker.xml Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,134 @@
+
+ cotranscriptional folding of RNAs
+
+ kinwalker
+ macros.xml
+
+
+
+
+
+ seq.ident
+ &&
+ sed '1d' '$input_sequence' > input.seq
+ &&
+ kinwalker
+ $init_structure
+ $interrupt
+ ##$printfront
+
+ --barrier_heuristic $barrier_heuristic.used
+
+ #if $barrier_heuristic.used == "M"
+ --grouping $barrier_heuristic.grouping
+ --lookahead $barrier_heuristic.lookahead
+ #else if $barrier_heuristic.used == "B"
+ --maxkeep $barrier_heuristic.maxkeep
+ #end if
+
+ --dangle $dangle
+ --noLonelyPairs $noLonelyPairs
+ --transcribed $transcribed
+ --transcription_rate $transcription_rate
+ --windowsize $windowsize
+
+ < input.seq
+
+ > blah
+
+ &&
+ sed -n '2s/[\.\(\)]\+\s\+\(.\+\)$/ mfe: \1/p' blah > energy
+
+ &&
+ cat seq.ident energy > '$mfe_struct'
+
+ &&
+ sed -e '2s/^\([\.\(\)]\+\).*$/\1/' -ne '1,2p' blah >> '$mfe_struct'
+
+ &&
+ sed -e 's/[ \t]*$//' -ne '/TRAJ/,/Kinwal/ {/TRAJ/n;/Kinwal/!{s/\s/\t/gp}}' blah > '$trajectory'
+]]>
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+100), heuristic approaches have to be employed which explicitly construct a (re)folding path between the two structures. The saddle height is then estimated as the highest point along the path. The best known algorithm for approximating saddle heights between RNA conformations is the Morgan-Higgs heuristic, which tries to find a folding path from an origin secondary structure to a target secondary structure where the maximum height along the path is minimal. The heuristic models state transitions at base pair resolution.
+]]>
+
+**Input**
+
+RNA sequence in FASTA format
+
+**Output**
+
+RNA folding trajectory
+
+
+
+ 10.1016/j.jmb.2008.02.064
+
+
diff -r 000000000000 -r 7b48472d3fbb macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,27 @@
+
+
+
+ viennarna
+
+
+
+ 2.2.10
+
+ @EXECUTABLE@ --version
+
+
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+ 10.1186/1748-7188-6-26
+
+
+
diff -r 000000000000 -r 7b48472d3fbb rnafold_SHAPE.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnafold_SHAPE.py Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,45 @@
+### overcoming the problem of SHAPE data working with a single line.
+### creating multiple multiple files containg SHAPE data for a single sequence and running RNAfold for every
+### single sequence.
+
+import os
+import sys
+from os import system
+from Bio import SeqIO
+import re
+from subprocess import Popen, PIPE
+
+params_list = sys.argv[1:]
+param_list_no_shape = [s for s in params_list if not "--shape=" in s ]
+shape_file = [s for s in params_list if "--shape=" in s ]
+assert (len(shape_file) == 1)
+
+shape_file = shape_file[0]
+shape_file = shape_file.replace('--shape=', '')
+
+params_no_shape = " ".join(str(x) for x in param_list_no_shape)
+
+pattern = re.compile("^>.*$")
+id_line = ""
+with open(shape_file, 'r') as f:
+ content = f.read()
+ lines = content.split('\n')
+ for line in lines:
+ if pattern.match(line):
+ id_line = line.split()[0]
+ id_line = id_line[1:]
+ continue
+ else:
+ with open(id_line +'.tmp', "a") as clFile:
+ clFile.write(line + "\n")
+
+input_file = sys.stdin
+
+for record in SeqIO.parse(input_file, "fasta"):
+ seq = ">{}\n{}".format(record.id,record.seq)
+ cmd = " RNAfold --shape=" + record.id + '.tmp ' + params_no_shape
+ p = Popen(cmd , stdin=PIPE, shell=True, stdout=PIPE, stderr=PIPE)
+ out,err = p.communicate(seq.encode())
+ if err:
+ raise RuntimeError("Error in calling RNAfold\n{}\n{}\n".format(out, err))
+ print (out.decode('utf-8').strip())
diff -r 000000000000 -r 7b48472d3fbb test-data/kinfold_input.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kinfold_input.txt Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,1 @@
+ACUGAUCGUAGUCAC
diff -r 000000000000 -r 7b48472d3fbb test-data/mfe_struct_result.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mfe_struct_result.fasta Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,3 @@
+>test_seq mfe: -13.6
+ACAGGUUCGCCUGUGUUGCGAACCUGCGGGUUCG
+.(((((((((.......)))))))))........
diff -r 000000000000 -r 7b48472d3fbb test-data/rna2dfold_input1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rna2dfold_input1.txt Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,4 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
+.((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))..
+.((((((..(((..........))).(((((.......))))).....(((((.......)))))))))))..
diff -r 000000000000 -r 7b48472d3fbb test-data/rna2dfold_result1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rna2dfold_result1.txt Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,6 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
+.((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. (-22.00)
+.((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. (-22.00) [
+.((((((..(((..........))).(((((.......))))).....(((((.......))))))))))).. (-17.30) ][
+k l en structure
diff -r 000000000000 -r 7b48472d3fbb test-data/rnaaliduplex_input1.clustal
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaaliduplex_input1.clustal Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,7 @@
+CLUSTAL 2.1 multiple sequence alignment
+
+
+Anolis_carolinensis_chrUn_GL34 TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+Anolis_carolinensis_chrUn_GL35 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
+ ************************************** ************** ******* *********
+
diff -r 000000000000 -r 7b48472d3fbb test-data/rnaaliduplex_result1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaaliduplex_result1.txt Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,1 @@
+(((((((..(.......((((..(..((((((..((((((.......((((((..(..(((((..(((((((.&)))))))..).......))))..)..))))))..)))))).......))))))..)..)))))..))))))). 1,73 : 1,73 (-40.30)
diff -r 000000000000 -r 7b48472d3fbb test-data/rnaalifold_input1.clustal
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaalifold_input1.clustal Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,7 @@
+CLUSTAL 2.1 multiple sequence alignment
+
+
+Anolis_carolinensis_chrUn_GL34 TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+Anolis_carolinensis_chrUn_GL35 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
+ ************************************** ************** ******* *********
+
diff -r 000000000000 -r 7b48472d3fbb test-data/rnaalifold_result1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaalifold_result1.txt Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,2 @@
+GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUCGAUGCCCACAUUCUCCA
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). (-26.45 = -26.20 + -0.25)
diff -r 000000000000 -r 7b48472d3fbb test-data/rnacofold_input1.fas
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnacofold_input1.fas Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,2 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA&UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
diff -r 000000000000 -r 7b48472d3fbb test-data/rnacofold_result1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnacofold_result1.txt Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,3 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-A
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA&UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
+.((((((..((((........)))).(((((.......))))).....(((((((((((.(((((((((((..&.))))))..((((........)))).(((((.......))))).....))))))))))).))))))))))).. (-55.90)
diff -r 000000000000 -r 7b48472d3fbb test-data/rnadistance_input1.dbn
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnadistance_input1.dbn Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,2 @@
+.((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))..
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))).
diff -r 000000000000 -r 7b48472d3fbb test-data/rnadistance_result1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnadistance_result1.txt Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,1 @@
+f: 4
diff -r 000000000000 -r 7b48472d3fbb test-data/rnaduplex_input1.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaduplex_input1.fa Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,4 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55
+TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15
+GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r 000000000000 -r 7b48472d3fbb test-data/rnaduplex_result1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaduplex_result1.txt Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,3 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC
+.((((((..((......((((...((((..(((.((((((.......((((((..(..((((...(((((((.&)))))))..........))))..)..))))))..))))))..)))..)))).......)))).)))))))). 1,73 : 1,72 (-40.70)
diff -r 000000000000 -r 7b48472d3fbb test-data/rnaeval_input1.dbn
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaeval_input1.dbn Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,3 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
+.((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))..
diff -r 000000000000 -r 7b48472d3fbb test-data/rnaeval_result1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaeval_result1.txt Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,3 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
+.((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. (-22.00)
diff -r 000000000000 -r 7b48472d3fbb test-data/rnafold_input1.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnafold_input1.fa Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,4 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55
+TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15
+GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r 000000000000 -r 7b48472d3fbb test-data/rnafold_input2.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnafold_input2.fa Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,4 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55
+TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15
+GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r 000000000000 -r 7b48472d3fbb test-data/rnafold_result1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnafold_result1.txt Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,6 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-A
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
+.((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. (-22.00)
+>Anolis_carolinensis_chrUn_GL343207.trna3-A
+GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). (-29.60)
diff -r 000000000000 -r 7b48472d3fbb test-data/rnafold_result2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnafold_result2.txt Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,6 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-A
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
+..(((.....((((....((..(((....)))..))...)))).....(((((.......)))))....))). ( -3.37)
+>Anolis_carolinensis_chrUn_GL343207.trna3-A
+GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA
+(((((..((.(((.....((..(((....)))..))......))).))(((((.......)))))..))))). ( -5.02)
diff -r 000000000000 -r 7b48472d3fbb test-data/rnafold_result3.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnafold_result3.txt Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,3 @@
+>Sequence
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
+.((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. (-22.00)
diff -r 000000000000 -r 7b48472d3fbb test-data/rnaheat_input1.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaheat_input1.fa Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,2 @@
+> comment 1
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
diff -r 000000000000 -r 7b48472d3fbb test-data/rnaheat_result1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaheat_result1.txt Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,102 @@
+> comment 1
+0 0.0407267
+1 0.0435052
+2 0.0470227
+3 0.0505646
+4 0.0553391
+5 0.0603894
+6 0.0662047
+7 0.0718158
+8 0.0782007
+9 0.0863514
+10 0.0950516
+11 0.10505
+12 0.115613
+13 0.128245
+14 0.141712
+15 0.157281
+16 0.17497
+17 0.195056
+18 0.216799
+19 0.241743
+20 0.270432
+21 0.302132
+22 0.337644
+23 0.377263
+24 0.421546
+25 0.470799
+26 0.525589
+27 0.587016
+28 0.653829
+29 0.726606
+30 0.806458
+31 0.892656
+32 0.984857
+33 1.08272
+34 1.18601
+35 1.29332
+36 1.40305
+37 1.51467
+38 1.62618
+39 1.73524
+40 1.84032
+41 1.9407
+42 2.03385
+43 2.11859
+44 2.19443
+45 2.26182
+46 2.31999
+47 2.36969
+48 2.41182
+49 2.44826
+50 2.47967
+51 2.50769
+52 2.534
+53 2.55942
+54 2.5851
+55 2.61217
+56 2.64151
+57 2.67329
+58 2.70759
+59 2.74465
+60 2.78458
+61 2.8279
+62 2.8742
+63 2.92425
+64 2.97698
+65 3.03283
+66 3.09163
+67 3.15591
+68 3.23033
+69 3.3067
+70 3.38122
+71 3.45791
+72 3.54606
+73 3.63843
+74 3.73392
+75 3.83847
+76 3.94646
+77 4.05462
+78 4.16571
+79 4.28366
+80 4.39944
+81 4.50863
+82 4.61035
+83 4.70186
+84 4.78345
+85 4.85204
+86 4.90509
+87 4.9392
+88 4.95425
+89 4.95214
+90 4.93688
+91 4.91166
+92 4.87691
+93 4.8314
+94 4.78561
+95 4.75271
+96 4.71866
+97 4.66056
+98 4.57671
+99 4.48395
+100 4.39006
diff -r 000000000000 -r 7b48472d3fbb test-data/rnainverse_input1.clu
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnainverse_input1.clu Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,2 @@
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))).
+gggccccnnaauunnnnnnnnaauunGGGGcnnnnnnnAAAAAnnnnnuuuuannnnnnnuaaaaggggcccn
diff -r 000000000000 -r 7b48472d3fbb test-data/rnalalifold_input1.clustal
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnalalifold_input1.clustal Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,7 @@
+CLUSTAL 2.1 multiple sequence alignment
+
+
+Anolis_carolinensis_chrUn_GL34 TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+Anolis_carolinensis_chrUn_GL35 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
+ ************************************** ************** ******* *********
+
diff -r 000000000000 -r 7b48472d3fbb test-data/rnalalifold_result1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnalalifold_result1.txt Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,4 @@
+(((.(((((.(((((.......)))))..)).(((((.......)))))..)))))) (-19.05) 17 - 73
+((((........)))). ( -5.10) 10 - 26
+GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUCGAUGCCCACAUUCUCCA
+
diff -r 000000000000 -r 7b48472d3fbb test-data/rnalfold_input1.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnalfold_input1.fa Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,4 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55
+TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15
+GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r 000000000000 -r 7b48472d3fbb test-data/rnalfold_result1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnalfold_result1.txt Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,28 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55
+.((((....)))). ( -0.10) 56
+.(((..((((....)))).))). ( -3.40) 51
+.(((((.......))))). ( -7.70) 48
+.((((..(((((.......)))))..)))). (-10.30) 42
+.(((((...(((((.......))))).))))). (-11.50) 40
+.((.(((((...(((((.......))))).))))))) (-12.10) 37
+.(((((.......))))). ( -5.80) 26
+.((.(((((.......)))))..)). ( -6.70) 23
+.((((....)))). ( -3.20) 21
+.((.((((....)))).)). ( -4.70) 18
+.((((........)))). ( -5.30) 9
+.((((((..((((........)))).(((((.......))))).....(((((.......))))))))))). (-22.00) 1
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
+ (-22.00)
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15
+.(((..((((....)))).))). ( -3.40) 51
+.(((((.......))))). ( -9.20) 48
+.((((..(((((.......)))))..)))). (-11.80) 42
+.(((((...(((((.......))))).))))). (-13.30) 40
+.((.(((((...(((((.......))))).))))))) (-13.60) 37
+.(((((.......))))). ( -7.70) 26
+.((.(((((.......)))))..)). ( -8.60) 23
+.(((.(((((.(((((.......)))))..)).(((((.......)))))..)))))) (-20.00) 16
+.((((........)))). ( -5.30) 9
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). (-29.60) 1
+GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA
+ (-29.60)
diff -r 000000000000 -r 7b48472d3fbb test-data/rnapaln_input1.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnapaln_input1.fa Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,4 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55
+TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15
+GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r 000000000000 -r 7b48472d3fbb test-data/rnapaln_input1.fas
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnapaln_input1.fas Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,1 @@
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA&UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
diff -r 000000000000 -r 7b48472d3fbb test-data/rnapaln_result1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnapaln_result1.txt Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,7 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15
+68.8844
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
+,((((((..((((........)))).(((((.......))))).....(((((.......))))))))),)),
+GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))).
diff -r 000000000000 -r 7b48472d3fbb test-data/rnapdist_input1.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnapdist_input1.fa Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,4 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55
+TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15
+GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r 000000000000 -r 7b48472d3fbb test-data/rnapdist_result1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnapdist_result1.txt Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,3 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15
+8.66253
diff -r 000000000000 -r 7b48472d3fbb test-data/rnapkplex_input1.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnapkplex_input1.fa Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,4 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55
+TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15
+GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r 000000000000 -r 7b48472d3fbb test-data/rnapkplex_result1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnapkplex_result1.txt Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,6 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
+.((((((..((((........)))).(((((.......))))).[[[.(((((]]]....))))))))))).. (-31.90)
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15
+GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA
+(((((((..((((..[[[.[[)))).(((((.]].]]]))))).....(((((.......)))))))))))). (-38.54)
diff -r 000000000000 -r 7b48472d3fbb test-data/rnaplex_input1.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaplex_input1.fa Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,4 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55
+TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15
+GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r 000000000000 -r 7b48472d3fbb test-data/rnaplex_result1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaplex_result1.txt Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,4 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15
+.((((((..((......((((...((((..(((.((((((.......((((((..(..((((...(((((((.&)))))))..........))))..)..))))))..))))))..)))..)))).......)))).)))))))). 1,73 : 1,72 (-40.70) i:72,j:1 <-41.26>
+
diff -r 000000000000 -r 7b48472d3fbb test-data/rnaplfold_input1.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaplfold_input1.fa Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,4 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55
+TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15
+GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r 000000000000 -r 7b48472d3fbb test-data/rnaplfold_result1.ps
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaplfold_result1.ps Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,242 @@
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diff -r 000000000000 -r 7b48472d3fbb test-data/rnaplfold_result2.ps
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaplfold_result2.ps Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,212 @@
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+%%Pages: 1
+%%EndComments
+
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diff -r 000000000000 -r 7b48472d3fbb test-data/rnaplot_input1.dbn
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaplot_input1.dbn Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,3 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
+.((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. (-21.90)
diff -r 000000000000 -r 7b48472d3fbb test-data/rnaplot_input1.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaplot_input1.fa Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,4 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55
+TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15
+GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r 000000000000 -r 7b48472d3fbb test-data/rnasnoop_input1a.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnasnoop_input1a.fa Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,2 @@
+>homo
+CGCGACCUCAGAUCAGACGUGGCGACCCGCUGAAUUUAAGCAUAUUAGUCAGCGGAGGAAAAGAAACUAACCAGGAUUCCCUCAGUAACGGCGAGUGAACAGGGAAGAGCCCAGCGCCGAAUCCCCGCCCCGCGGGGCGCGGGACAUGUGGCGUACGGAAGACCCGCUCCCCGGCGCCGCUCGUGGGGGGCCCAAGUCCUUCUGAUCGAGGCCCAGCCCGUGGACGGUGUGAGGCCGGUAGCGGCCGGCGCGCGCCCGGGUCUUCCCGGAGUCGGGUUGCUUGGGAAUGCAGCCCAAAGCGGGUGGUAAACUCCAUCUAAGGCUAAAUACCGGCACGAGACCGAUAGUCAACAAGUACCGUAAGGGAAAGUUGAAAAGAACUUUGAAGAGAGAGUUCAAGAGGGCGUGAAACCGUUAAGAGGUAAACGGGUGGGGUCCGCGCAGUCCGCCCGGAGGAUUCAACCCGGCGGCGGGUCCGGCCGUGUCGGCGGCCCGGCGGAUCUUUCCCGCCCCCCGUUCCUCCCGACCCCUCCACCCGCCCUCCCUUCCCCCGCCGCCCCUCCUCCUCCUCCCCGGAGGGGGCGGGCUCCGGCGGGUGCGGGGGUGGGCGGGCGGGGCCGGGGGUGGGGUCGGCGGGGGACCGUCCCCCGACCGGCGACCGGCCGCCGCCGGGCGCAUUUCCACCGCGGCGGUGCGCCGCGACCGGCUCCGGGACGGCUGGGAAGGCCCGGCGGGGAAGGUGGCUCGGGGGGCCCCGUCCGUCCGUCCGUCCUCCUCCUCCCCCGUCUCCGCCCCCCGGCCCCGCGUCCUCCCUCGGGAGGGCGCGCGGGUCGGGGCGGCGGCGGCGGCGGCGGUGGCGGCGGCGGCGGGGGCGGCGGGACCGAAACCCCCCCCGAGUGUUACAGCCCCCCCGGCAGCAGCACUCGCCGAAUCCCGGGGCCGAGGGAGCGAGACCCGUCGCCGCGCUCUCCCCCCUCCCGGCGCCCACCCCCGCGGGGAAUCCCCCGCGAGGGGGGUCUCCCCCGCGGGGGCGCGCCGGCGUCUCCUCGUGGGGGGGCCGGGCCACCCCUCCCACGGCGCGACCGCUCUCCCACCCCUCCUCCCCGCGCCCCCGCCCCGGCGACGGGGGGGGUGCCGCGCGCGGGUCGGGGGGCGGGGCGGACUGUCCCCAGUGCGCCCCGGGCGGGUCGCGCCGUCGGGCCCGGGGGAGGUUCUCUCGGGGCCACGCGCGCGUCCCCCGAAGAGGGGGACGGCGGAGCGAGCGCACGGGGUCGGCGGCGACGUCGGCUACCCACCCGACCCGUCUUGAAACACGGACCAAGGAGUCUAACACGUGCGCGAGUCGGGGGCUCGCACGAAAGCCGCCGUGGCGCAAUGAAGGUGAAGGCCGGCGCGCUCGCCGGCCGAGGUGGGAUCCCGAGGCCUCUCCAGUCCGCCGAGGGCGCACCACCGGCCCGUCUCGCCCGCCGCGCCGGGGAGGUGGAGCACGAGCGCACGUGUUAGGACCCGAAAGAUGGUGAACUAUGCCUGGGCAGGGCGAAGCCAGAGGAAACUCUGGUGGAGGUCCGUAGCGGUCCUGACGUGCAAAUCGGUCGUCCGACCUGGGUAUAGGGGCGAAAGACUAAUCGAACCAUCUAGUAGCUGGUUCCCUCCGAAGUUUCCCUCAGGAUAGCUGGCGCUCUCGCAGACCCGACGCACCCCCGCCACGCAGUUUUAUCCGGUAAAGCGAAUGAUUAGAGGUCUUGGGGCCGAAACGAUCUCAACCUAUUCUCAAACUUUAAAUGGGUAAGAAGCCCGGCUCGCUGGCGUGGAGCCGGGCGUGGAAUGCGAGUGCCUAGUGGGCCACUUUUGGUAAGCAGAACUGGCGCUGCGGGAUGAACCGAACGCCGGGUUAAGGCGCCCGAUGCCGACGCUCAUCAGACCCCAGAAAAGGUGUUGGUUGAUAUAGACAGCAGGACGGUGGCCAUGGAAGUCGGAAUCCGCUAAGGAGUGUGUAACAACUCACCUGCCGAAUCAACUAGCCCUGAAAAUGGAUGGCGCUGGAGCGUCGGGCCCAUACCCGGCCGUCGCCGGCAGUCGAGAGUGGACGGGAGCGGCGGGGGCGGCGCGCGCGCGCGCGCGUGUGGUGUGCGUCGGAGGGCGGCGGCGGCGGCGGCGGCGGGGGUGUGGGGUCCUUCCCCCGCCCCCCCCCCCACGCCUCCUCCCCUCCUCCCGCCCACGCCCCGCUCCCCGCCCCCGGAGCCCCGCGGACGCUACGCCGCGACGAGUAGGAGGGCCGCUGCGGUGAGCCUUGAAGCCUAGGGCGCGGGCCCGGGUGGAGCCGCCGCAGGUGCAGAUCUUGGUGGUAGUAGCAAAUAUUCAAACGAGAACUUUGAAGGCCGAAGUGGAGAAGGGUUCCAUGUGAACAGCAGUUGAACAUGGGUCAGUCGGUCCUGAGAGAUGGGCGAGCGCCGUUCCGAAGGGACGGGCGAUGGCCUCCGUUGCCCUCGGCCGAUCGAAAGGGAGUCGGGUUCAGAUCCCCGAAUCCGGAGUGGCGGAGAUGGGCGCCGCGAGGCGUCCAGUGCGGUAACGCGACCGAUCCCGGAGAAGCCGGCGGGAGCCCCGGGGAGAGUUCUCUUUUCUUUGUGAAGGGCAGGGCGCCCUGGAAUGGGUUCGCCCCGAGAGAGGGGCCCGUGCCUUGGAAAGCGUCGCGGUUCCGGCGGCGUCCGGUGAGCUCUCGCUGGCCCUUGAAAAUCCGGGGGAGAGGGUGUAAAUCUCGCGCCGGGCCGUACCCAUAUCCGCAGCAGGUCUCCAAGGUGAACAGCCUCUGGCAUGUUGGAACAAUGUAGGUAAGGGAAGUCGGCAAGCCGGAUCCGUAACUUCGGGAUAAGGAUUGGCUCUAAGGGCUGGGUCGGUCGGGCUGGGGCGCGAAGCGGGGCUGGGCGCGCGCCGCGGCUGGACGAGGCGCGCGCCCCCCCCACGCCCGGGGCACCCCCCUCGCGGCCCUCCCCCGCCCCACCCGCGCGCGCCGCUCGCUCCCUCCCCACCCCGCGCCCUCUCUCUCUCUCUCUCCCCCGCUCCCCGUCCUCCCCCCUCCCCGGGGGAGCGCCGCGUGGGGGCGCGGCGGGGGGAGAAGGGUCGGGGCGGCAGGGGCCGCGCGGCGGCCGCCGGGGCGGCCGGCGGGGGCAGGUCCCCGCGAGGGGGGCCCCGGGGACCCGGGGGGCCGGCGGCGGCGCGGACUCUGGACGCGAGCCGGGCCCUUCCCGUGGAUCGCCCCAGCUGCGGCGGGCGUCGCGGCCGCCCCCGGGGAGCCCGGCGGCGGCGCGGCGCGCCCCCCACCCCCACCCCACGUCUCGGUCGCGCGCGCGUCCGCUGGGGGCGGGAGCGGUCGGGCGGCGGCGGUCGGCGGGCGGCGGGGCGGGGCGGUUCGUCCCCCCGCCCUACCCCCCCGGCCCCGUCCGCCCCCCGUUCCCCCCUCCUCCUCGGCGCGCGGCGGCGGCGGCGGCAGGCGGCGGAGGGGCCGCGGGCCGGUCCCCCCCGCCGGGUCCGCCCCCGGGGCCGCGGUUCCGCGCGCGCCUCGCCUCGGCCGGCGCCUAGCAGCCGACUUAGAACUGGUGCGGACCAGGGGAAUCCGACUGUUUAAUUAAAACAAAGCAUCGCGAAGGCCCGCGGCGGGUGUUGACGCGAUGUGAUUUCUGCCCAGUGCUCUGAAUGUCAAAGUGAAGAAAUUCAAUGAAGCGCGGGUAAACGGCGGGAGUAACUAUGACUCUCUUAAGGUAGCCAAAUGCCUCGUCAUCUAAUUAGUGACGCGCAUGAAUGGAUGAACGAGAUUCCCACUGUCCCUACCUACUAUCCAGCGAAACCACAGCCAAGGGAACGGGCUUGGCGGAAUCAGCGGGGAAAGAAGACCCUGUUGAGCUUGACUCUAGUCUGGCACGGUGAAGAGACAUGAGAGGUGUAGAAUAAGUGGGAGGCCCCCGGCGCCCCCCCGGUGUCCCCGCGAGGGGCCCGGGGCGGGGUCCGCGGCCCUGCGGGCCGCCGGUGAAAUACCACUACUCUGAUCGUUUUUUCACUGACCCGGUGAGGCGGGGGGGCGAGCCCGAGGGGCUCUCGCUUCUGGCGCCAAGCGCCCGCCCGGCCGGGCGCGACCCGCUCCGGGGACAGUGCCAGGUGGGGAGUUUGACUGGGGCGGUACACCUGUCAAACGGUAACGCAGGUGUCCUAAGGCGAGCUCAGGGAGGACAGAAACCUCCCGUGGAGCAGAAGGGCAAAAGCUCGCUUGAUCUUGAUUUUCAGUACGAAUACAGACCGUGAAAGCGGGGCCUCACGAUCCUUCUGACCUUUUGGGUUUUAAGCAGGAGGUGUCAGAAAAGUUACCACAGGGAUAACUGGCUUGUGGCGGCCAAGCGUUCAUAGCGACGUCGCUUUUUGAUCCUUCGAUGUCGGCUCUUCCUAUCAUUGUGAAGCAGAAUUCGCCAAGCGUUGGAUUGUUCACCCACUAAUAGGGAACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUACUGAUGAUGUGUUGUUGCCAUGGUAAUCCUGCUCAGUACGAGAGGAACCGCAGGUUCAGACAUUUGGUGUAUGUGCUUGGCUGAGGAGCCAAUGGGGCGAAGCUACCAUCUGUGGGAUUAUGACUGAACGCCUCUAAGUCAGAAUCCCGCCCAGGCGAACGAUACGGCAGCGCCGCGGAGCCUCGGUUGGCCUCGGAUAGCCGGUCCCCCGCCUGUCCCCGCCGGCGGGCCGCCCCCCCCUCCACGCGCCCCGCCGCGGGAGGGCGCGUGCCCCGCCGCGCGCCGGGACCGGGGUCCGGUGCGGAGUGCCCUUCGUCCUGGGAAACGGGGCGCGGCCGGAAAGGCGGCCGCCCCCUCGCCCGUCACGCACCGCACGUUCGUGGGGAACCUGGCGCUAAACCAUUCGUAGACGACCUGCUUCUGGGUCGGGGUUUCGUACGUAGCAGAGCAGCUCCCUCGCUGCGAUCUAUUGAAAGUCAGCCCUCGACACAAGGGUUUGUC
diff -r 000000000000 -r 7b48472d3fbb test-data/rnasnoop_input1b.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnasnoop_input1b.fa Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,2 @@
+>ACA51
+AACCTACCCCATATACACCTCAGCTCAGGCCCTGTGCCTGGTCTGTATTGTGAATGGGGGAACATAG
diff -r 000000000000 -r 7b48472d3fbb test-data/rnasnoop_result1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnasnoop_result1.txt Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,4 @@
+>ACA51
+>homo
+<<<<<.<<<<.|.<<.<<<&...(((>>>.>>.((((...............................))))..>>>>.>>>>>))) 4468,4486;4479 : 8,65 (-35.60 = -16.10 + -7.60 + -12.40 + -3.60 + 4.1 ) (-23.60)
+UGUUCACCCACUAAUAGGG&AACCUACCCCAUAUACACCUCAGCUCAGGCCCUGUGCCUGGUCUGUAUUGUGAAUGGGGGAACAUAG
diff -r 000000000000 -r 7b48472d3fbb test-data/rnasubopt_input1.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnasubopt_input1.fa Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,4 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55
+TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15
+GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r 000000000000 -r 7b48472d3fbb test-data/rnasubopt_result1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnasubopt_result1.txt Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,7 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-A [0]
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA -22.00 0.00
+(((((((..((((........)))).(((((.......))))).....(((((.......))))))))).))) -22.00
+.((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. -22.00
+>Anolis_carolinensis_chrUn_GL343207.trna3-A [0]
+GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA -29.60 0.00
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). -29.60
diff -r 000000000000 -r 7b48472d3fbb test-data/rnaup_input1.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaup_input1.fa Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,4 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872) Ala (AGC) 73 bp Sc: 49.55
+TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698) Ala (AGC) 73 bp Sc: 56.15
+GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
diff -r 000000000000 -r 7b48472d3fbb test-data/rnaup_result1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaup_result1.txt Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,6 @@
+>Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC
+ 55, 58 (0.019) for u= 4
+RNAup output in file: Anolis_carolinensis_chrUn_GL343590.trna2-A_u1.out
+>Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC
+ 16, 19 (0.004) for u= 4
+RNAup output in file: Anolis_carolinensis_chrUn_GL343207.trna3-A_u1.out
diff -r 000000000000 -r 7b48472d3fbb test-data/sample_3.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_3.fa Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,6 @@
+>SECIS_1 test
+AUUUUAUCCAUGAAAGUGUUUCCUCUAAACCUAUGUGGAGGAACACCUGAUGUCCAGGAAAAU
+>6S_1 test1
+GAAACCCUAAUGUAUUCGAUAUAGUUCCUGAUAUUUUUGAACCGAACAAUUUUUUAUACCUAGGGAGCUUGGAGUUCCGGCGCGGCGCACAUGCCUUCACACGAGGAAGUGCAAACCGUUAGACAGAGCACCCACCUGCUUUAAUUGAGAGCGGGUUCAAAGGAAGGGAAUCCUAAACGGUACGAUUGGGGUUUCU
+>6S_2
+UUGUCCCUGCCGUGCUCGUGACUUGGCCAUACAUUCUCUGAACCUAUGUCUUACGGCAUAUGGGUUGCGGGAGUGUAGAGCUGGAGUGAUCGUCUACUCGUAGACGAACCCGAUGCUCUUCGGAUCGCGACCACCUUGAACCUCAGGGUUCGAGAUGCCGGCCUUGACGGCACAGGCGGGGCAUC
diff -r 000000000000 -r 7b48472d3fbb test-data/sample_3.react
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_3.react Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,447 @@
+>SECIS_1
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+2 0.1280448842
+3 0.2786665403
+4 0.1391216354
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+18 1.6364597431
+19 1.72206594665E-17
+20 0.0099928394
+21 0.0475042774
+22 0.0065948845
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+1 0.1158690877
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+6 0.0505177415
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+1 5.135077189
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+4 0.0394762621
+5 0.1032256038
+6 0.0124879331
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+13 1.72206594665E-17
+14 0.0443782398
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+24 3.2368938797
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\ No newline at end of file
diff -r 000000000000 -r 7b48472d3fbb test-data/sample_3_result.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_3_result.txt Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,9 @@
+>SECIS_1
+AUUUUAUCCAUGAAAGUGUUUCCUCUAAACCUAUGUGGAGGAACACCUGAUGUCCAGGAAAAU
+.((((...(((.(..(((.((((((((........))))))))))).).))).....)))).. (-27.97)
+>6S_1
+GAAACCCUAAUGUAUUCGAUAUAGUUCCUGAUAUUUUUGAACCGAACAAUUUUUUAUACCUAGGGAGCUUGGAGUUCCGGCGCGGCGCACAUGCCUUCACACGAGGAAGUGCAAACCGUUAGACAGAGCACCCACCUGCUUUAAUUGAGAGCGGGUUCAAAGGAAGGGAAUCCUAAACGGUACGAUUGGGGUUUCU
+(((((((...(((((.((.....((((((....((((((((((...................(((.((((.....((.((((.(..((((.(.((((.....))))).))))...))))).))..)))).)))....(((((.....))))).))))))))))..))))))......)))))))....))))))). (-110.38)
+>6S_2
+UUGUCCCUGCCGUGCUCGUGACUUGGCCAUACAUUCUCUGAACCUAUGUCUUACGGCAUAUGGGUUGCGGGAGUGUAGAGCUGGAGUGAUCGUCUACUCGUAGACGAACCCGAUGCUCUUCGGAUCGCGACCACCUUGAACCUCAGGGUUCGAGAUGCCGGCCUUGACGGCACAGGCGGGGCAUC
+.((.(((((((((((.(((.(...((((...((.((((.((((((..(((....))).....((((((((...((.(((((.((.((..((((((......))))))))))...))))).))..)))))))).............))))))))))))..)))).).))))))).))))))))).. (-129.27)
diff -r 000000000000 -r 7b48472d3fbb test-data/test_sequence_input.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_sequence_input.fasta Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,2 @@
+>test_seq
+ACAGGUUCGCCUGUGUUGCGAACCUGCGGGUUCG
diff -r 000000000000 -r 7b48472d3fbb test-data/trajectory_result.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trajectory_result.tabular Mon Jun 19 09:00:02 2017 -0400
@@ -0,0 +1,10 @@
+..(((....))) -0.4 0.0550686 3.9 6.46108 12
+.((((....)))) -3 0.0600001 5.96046e-09 6.46108 13
+(((((....))))) -4.7 0.065 0 6.46108 14
+(((((....)))))..((((....)))) -5.3 0.135069 3.9 6.46108 28
+(((((....))))).(((((....))))) -5.8 0.14 1.90735e-07 6.46108 29
+(((((....))))).......(((....)))... -6.9 0.17246 6.7 7.46108 34
+(((((....)))))......((((....)))).. -7.8 0.17246 9.53674e-08 7.46108 34
+(((((....))))).....(((((....))))). -10.7 0.17246 1.90735e-07 7.46108 34
+(((((....)))))....((((((....)))))) -13.1 0.17246 -1.90735e-07 7.46108 34
+.(((((((((.......)))))))))........ -13.6 123.457 12.5 13 34
]