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changeset 6:61e51eabbb95 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit 36681a08c6e44c663169caaefd964781c43d0d29
author rnateam
date Wed, 20 Dec 2017 08:38:03 -0500
parents 16d733b920d8
children
files test-data/Anolis_caro_chrUn_GL343207.trna3_AlaAGC_dp.ps test-data/Anolis_caro_chrUn_GL343207.trna3_AlaAGC_ss.ps test-data/Anolis_caro_chrUn_GL343590.trna2_AlaAGC_dp.ps test-data/Anolis_caro_chrUn_GL343590.trna2_AlaAGC_ss.ps test-data/rnaalifold_input1.fa test-data/rnaduplex_input1.fa test-data/rnaduplex_result1.txt test-data/rnafold_input1.fa test-data/rnafold_input2.fa test-data/rnafold_result1.txt test-data/rnafold_result1_mea.txt test-data/rnafold_result1_pf.txt test-data/rnafold_result2.txt test-data/rnafold_result3.txt test-data/rnalfold_input1.fa test-data/rnalfold_result1.txt test-data/rnapaln_input1.fa test-data/rnapaln_result1.txt test-data/rnapdist_input1.fa test-data/rnapdist_result1.txt test-data/rnapkplex_input1.fa test-data/rnapkplex_result1.txt test-data/rnaplex_input1.fa test-data/rnaplex_result1.txt test-data/rnaplfold_input1.fa test-data/rnaplot_input1.fa test-data/rnasubopt_input1.fa test-data/rnasubopt_result1.txt test-data/rnaup_input1.fa test-data/rnaup_result1.txt test-data/sample_3_result.txt
diffstat 31 files changed, 1412 insertions(+), 80 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Anolis_caro_chrUn_GL343207.trna3_AlaAGC_dp.ps	Wed Dec 20 08:38:03 2017 -0500
@@ -0,0 +1,370 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Anolis_caro_chrUn_GL343207.trna3_AlaAGC_ss.ps	Wed Dec 20 08:38:03 2017 -0500
@@ -0,0 +1,231 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Anolis_caro_chrUn_GL343590.trna2_AlaAGC_dp.ps	Wed Dec 20 08:38:03 2017 -0500
@@ -0,0 +1,507 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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+[135.16680908 110.24712372]
+[150.04531860 112.15238953]
+[164.92382812 114.05766296]
+[179.80232239 115.96292877]
+[194.68083191 117.86819458]
+[206.04914856 107.13062286]
+[221.66270447 106.26418304]
+[234.14927673 115.67798615]
+[237.61306763 130.92712402]
+[230.41859436 144.81141663]
+[215.96286011 150.77513123]
+[201.07142639 146.00236511]
+[192.77557373 132.74670410]
+[177.89706421 130.84143066]
+[163.01855469 128.93617249]
+[148.14004517 127.03089905]
+[133.26153564 125.12563324]
+[122.21434021 135.27252197]
+[122.85095978 150.25900269]
+[123.48757935 165.24548340]
+[124.12419128 180.23197937]
+[124.76081085 195.21846008]
+[125.39743042 210.20494080]
+[134.64427185 223.74850464]
+[127.29573059 238.40902710]
+] def
+/pairs [
+[2 71]
+[3 70]
+[4 69]
+[5 68]
+[6 67]
+[7 66]
+[10 25]
+[11 24]
+[12 23]
+[13 22]
+[27 43]
+[28 42]
+[29 41]
+[30 40]
+[31 39]
+[49 65]
+[50 64]
+[51 63]
+[52 62]
+[53 61]
+] def
+
+init
+
+% switch off outline pairs or bases by removing these lines
+drawoutline
+drawpairs
+drawbases
+% show it
+showpage
+end
+%%EOF
--- a/test-data/rnaalifold_input1.fa	Thu Sep 28 16:27:10 2017 -0400
+++ b/test-data/rnaalifold_input1.fa	Wed Dec 20 08:38:03 2017 -0500
@@ -1,4 +1,4 @@
->Anolis_carolinensis_chrUn_GL34
+>Anolis_caro_chrUn_GL34
 TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA
->Anolis_carolinensis_chrUn_GL35
+>Anolis_caro_chrUn_GL35
 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
--- a/test-data/rnaduplex_input1.fa	Thu Sep 28 16:27:10 2017 -0400
+++ b/test-data/rnaduplex_input1.fa	Wed Dec 20 08:38:03 2017 -0500
@@ -1,4 +1,4 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_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
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
--- a/test-data/rnaduplex_result1.txt	Thu Sep 28 16:27:10 2017 -0400
+++ b/test-data/rnaduplex_result1.txt	Wed Dec 20 08:38:03 2017 -0500
@@ -1,3 +1,3 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC
->Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC
+>Anolis_caro_chrUn_GL343590.trna2-AlaAGC
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC
 .((((((..((......((((...((((..(((.((((((.......((((((..(..((((...(((((((.&)))))))..........))))..)..))))))..))))))..)))..)))).......)))).)))))))).   1,73  :   1,72  (-40.70)
--- a/test-data/rnafold_input1.fa	Thu Sep 28 16:27:10 2017 -0400
+++ b/test-data/rnafold_input1.fa	Wed Dec 20 08:38:03 2017 -0500
@@ -1,4 +1,4 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_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
+>Anolis_caro_chrUn_GL343207.trna3_AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
--- a/test-data/rnafold_input2.fa	Thu Sep 28 16:27:10 2017 -0400
+++ b/test-data/rnafold_input2.fa	Wed Dec 20 08:38:03 2017 -0500
@@ -1,4 +1,4 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_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
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
--- a/test-data/rnafold_result1.txt	Thu Sep 28 16:27:10 2017 -0400
+++ b/test-data/rnafold_result1.txt	Wed Dec 20 08:38:03 2017 -0500
@@ -1,14 +1,6 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-A
+>Anolis_caro_chrUn_GL343590.trna2_AlaAGC
 UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
 .((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. (-22.00)
-,((((((..((((........)))).(((((.......))))).....(((((.......))))))))),)), [-23.20]
-.((((((..((((........)))).(((((.......))))).....(((((.......))))))))).)). {-21.90 d=9.72}
-.((((((..((((........)))).(((((.......))))).....(((((.......))))))))).)). {-21.90 MEA=58.88}
- frequency of mfe structure in ensemble 0.142309; ensemble diversity 14.51 
->Anolis_carolinensis_chrUn_GL343207.trna3-A
+>Anolis_caro_chrUn_GL343207.trna3_AlaAGC
 GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA
 (((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). (-29.60)
-(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). [-29.88]
-(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). {-29.60 d=0.64}
-(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). {-29.60 MEA=71.81}
- frequency of mfe structure in ensemble 0.63265; ensemble diversity 1.15  
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnafold_result1_mea.txt	Wed Dec 20 08:38:03 2017 -0500
@@ -0,0 +1,14 @@
+>Anolis_caro_chrUn_GL343590.trna2_AlaAGC
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
+.((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. (-22.00)
+,((((((..((((........)))).(((((.......))))).....(((((.......))))))))),)), [-23.20]
+.((((((..((((........)))).(((((.......))))).....(((((.......))))))))).)). {-21.90 d=9.72}
+.((((((..((((........)))).(((((.......))))).....(((((.......))))))))).)). {-21.90 MEA=58.88}
+ frequency of mfe structure in ensemble 0.142309; ensemble diversity 14.51 
+>Anolis_caro_chrUn_GL343207.trna3_AlaAGC
+GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). (-29.60)
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). [-29.88]
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). {-29.60 d=0.64}
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). {-29.60 MEA=71.81}
+ frequency of mfe structure in ensemble 0.63265; ensemble diversity 1.15  
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnafold_result1_pf.txt	Wed Dec 20 08:38:03 2017 -0500
@@ -0,0 +1,12 @@
+>Anolis_caro_chrUn_GL343590.trna2_AlaAGC
+UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
+.((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. (-22.00)
+,((((((..((((........)))).(((((.......))))).....(((((.......))))))))),)), [-23.20]
+.((((((..((((........)))).(((((.......))))).....(((((.......))))))))).)). {-21.90 d=9.72}
+ frequency of mfe structure in ensemble 0.142309; ensemble diversity 14.51 
+>Anolis_caro_chrUn_GL343207.trna3_AlaAGC
+GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). (-29.60)
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). [-29.88]
+(((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). {-29.60 d=0.64}
+ frequency of mfe structure in ensemble 0.63265; ensemble diversity 1.15  
--- a/test-data/rnafold_result2.txt	Thu Sep 28 16:27:10 2017 -0400
+++ b/test-data/rnafold_result2.txt	Wed Dec 20 08:38:03 2017 -0500
@@ -1,14 +1,6 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-A
+>Anolis_caro_chrUn_GL343590.trna2-AlaAGC
 UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
 ..(((.....((((....((..(((....)))..))...)))).....(((((.......)))))....))). ( -3.37)
-.{((,..,..{(({.,{,.{,.(((....)))},.}},.}}}},,..,(((((.......)))))..,,})). [ -7.81]
-...........((...(.....(((....)))....)...))......(((((.......)))))........ {  2.85 d=11.83}
-.((........(((..(.....(((....)))....)..)))......(((((.......))))).....)). {  1.96 MEA=51.92}
- frequency of mfe structure in ensemble 0.00162209; ensemble diversity 17.27 
->Anolis_carolinensis_chrUn_GL343207.trna3-A
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC
 GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA
 (((((..((.(((.....((..(((....)))..))......))).))(((((.......)))))..))))). ( -5.02)
-(((((..,..{({...{,.{.,{((....))),..},,..,.}},.,,(((((.......))))).,))))). [ -9.30]
-(((((.................(((....)))................(((((.......)))))..))))). { -4.42 d=10.17}
-(((((......((.........(((....)))..........))....(((((.......)))))..))))). { -2.50 MEA=54.73}
- frequency of mfe structure in ensemble 0.00205781; ensemble diversity 15.91 
--- a/test-data/rnafold_result3.txt	Thu Sep 28 16:27:10 2017 -0400
+++ b/test-data/rnafold_result3.txt	Wed Dec 20 08:38:03 2017 -0500
@@ -1,7 +1,3 @@
 >Sequence
 UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
 .((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. (-22.00)
-,((((((..((((........)))).(((((.......))))).....(((((.......))))))))),)), [-23.20]
-.((((((..((((........)))).(((((.......))))).....(((((.......))))))))).)). {-21.90 d=9.72}
-.((((((..((((........)))).(((((.......))))).....(((((.......))))))))).)). {-21.90 MEA=58.88}
- frequency of mfe structure in ensemble 0.142309; ensemble diversity 14.51 
--- a/test-data/rnalfold_input1.fa	Thu Sep 28 16:27:10 2017 -0400
+++ b/test-data/rnalfold_input1.fa	Wed Dec 20 08:38:03 2017 -0500
@@ -1,4 +1,4 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_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
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
--- a/test-data/rnalfold_result1.txt	Thu Sep 28 16:27:10 2017 -0400
+++ b/test-data/rnalfold_result1.txt	Wed Dec 20 08:38:03 2017 -0500
@@ -1,4 +1,4 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
 .((((....)))).	( -0.10)	56
 .(((..((((....)))).))).	( -3.40)	51
 .(((((.......))))).	( -7.70)	48
@@ -13,7 +13,7 @@
 .((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).	(-22.00)	1
 UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
  (-22.00)
->Anolis_carolinensis_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 .(((..((((....)))).))).	( -3.40)	51
 .(((((.......))))).	( -9.20)	48
 .((((..(((((.......)))))..)))).	(-11.80)	42
--- a/test-data/rnapaln_input1.fa	Thu Sep 28 16:27:10 2017 -0400
+++ b/test-data/rnapaln_input1.fa	Wed Dec 20 08:38:03 2017 -0500
@@ -1,4 +1,4 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_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
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
--- a/test-data/rnapaln_result1.txt	Thu Sep 28 16:27:10 2017 -0400
+++ b/test-data/rnapaln_result1.txt	Wed Dec 20 08:38:03 2017 -0500
@@ -1,5 +1,5 @@
->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
+>Anolis_caro_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 68.8844
 UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA
 ,((((((..((((........)))).(((((.......))))).....(((((.......))))))))),)),
--- a/test-data/rnapdist_input1.fa	Thu Sep 28 16:27:10 2017 -0400
+++ b/test-data/rnapdist_input1.fa	Wed Dec 20 08:38:03 2017 -0500
@@ -1,4 +1,4 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_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
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
--- a/test-data/rnapdist_result1.txt	Thu Sep 28 16:27:10 2017 -0400
+++ b/test-data/rnapdist_result1.txt	Wed Dec 20 08:38:03 2017 -0500
@@ -1,3 +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
+>Anolis_caro_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 8.66253
--- a/test-data/rnapkplex_input1.fa	Thu Sep 28 16:27:10 2017 -0400
+++ b/test-data/rnapkplex_input1.fa	Wed Dec 20 08:38:03 2017 -0500
@@ -1,4 +1,4 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_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
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
--- a/test-data/rnapkplex_result1.txt	Thu Sep 28 16:27:10 2017 -0400
+++ b/test-data/rnapkplex_result1.txt	Wed Dec 20 08:38:03 2017 -0500
@@ -1,6 +1,6 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_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
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA
 (((((((..((((..[[[.[[)))).(((((.]].]]]))))).....(((((.......)))))))))))). (-38.54)
--- a/test-data/rnaplex_input1.fa	Thu Sep 28 16:27:10 2017 -0400
+++ b/test-data/rnaplex_input1.fa	Wed Dec 20 08:38:03 2017 -0500
@@ -1,4 +1,4 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_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
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
--- a/test-data/rnaplex_result1.txt	Thu Sep 28 16:27:10 2017 -0400
+++ b/test-data/rnaplex_result1.txt	Wed Dec 20 08:38:03 2017 -0500
@@ -1,4 +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
+>Anolis_caro_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_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>
 
--- a/test-data/rnaplfold_input1.fa	Thu Sep 28 16:27:10 2017 -0400
+++ b/test-data/rnaplfold_input1.fa	Wed Dec 20 08:38:03 2017 -0500
@@ -1,4 +1,4 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_chrUn_GL343590.trna2-A (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
+>Anolis_caro_chrUn_GL343207.trna3-A (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
--- a/test-data/rnaplot_input1.fa	Thu Sep 28 16:27:10 2017 -0400
+++ b/test-data/rnaplot_input1.fa	Wed Dec 20 08:38:03 2017 -0500
@@ -1,4 +1,4 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_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
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
--- a/test-data/rnasubopt_input1.fa	Thu Sep 28 16:27:10 2017 -0400
+++ b/test-data/rnasubopt_input1.fa	Wed Dec 20 08:38:03 2017 -0500
@@ -1,4 +1,4 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_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
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
--- a/test-data/rnasubopt_result1.txt	Thu Sep 28 16:27:10 2017 -0400
+++ b/test-data/rnasubopt_result1.txt	Wed Dec 20 08:38:03 2017 -0500
@@ -1,7 +1,7 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-A [0]
+>Anolis_caro_chrUn_GL343590.trna2-AlaAGC [0]
 UGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUAGUGGGAUCGAUGCCCACAUUCUCCA -22.00   0.00
 (((((((..((((........)))).(((((.......))))).....(((((.......))))))))).))) -22.00
 .((((((..((((........)))).(((((.......))))).....(((((.......))))))))))).. -22.00
->Anolis_carolinensis_chrUn_GL343207.trna3-A [0]
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC [0]
 GGGGAAUUAGCUCAAAUGGUAGAGCGCUCGCUUAGCAUGCGAGAGGUAGCGGGAUUGAUGCCCGCAUUCUCCA -29.60   0.00
 (((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). -29.60
--- a/test-data/rnaup_input1.fa	Thu Sep 28 16:27:10 2017 -0400
+++ b/test-data/rnaup_input1.fa	Wed Dec 20 08:38:03 2017 -0500
@@ -1,4 +1,4 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC (218800-218872)  Ala (AGC) 73 bp  Sc: 49.55
+>Anolis_caro_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
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC (1513626-1513698)  Ala (AGC) 73 bp  Sc: 56.15
 GGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGCGAGAGGTAGCGGGATTGATGCCCGCATTCTCCA
--- a/test-data/rnaup_result1.txt	Thu Sep 28 16:27:10 2017 -0400
+++ b/test-data/rnaup_result1.txt	Wed Dec 20 08:38:03 2017 -0500
@@ -1,6 +1,6 @@
->Anolis_carolinensis_chrUn_GL343590.trna2-AlaAGC
+>Anolis_caro_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
+RNAup output in file: Anolis_caro_chrUn_GL343590.trna2-AlaAGC_u1.out
+>Anolis_caro_chrUn_GL343207.trna3-AlaAGC
   16,  19 	 (0.004) 	 for u=  4
-RNAup output in file: Anolis_carolinensis_chrUn_GL343207.trna3-A_u1.out
+RNAup output in file: Anolis_caro_chrUn_GL343207.trna3-AlaAGC_u1.out
--- a/test-data/sample_3_result.txt	Thu Sep 28 16:27:10 2017 -0400
+++ b/test-data/sample_3_result.txt	Wed Dec 20 08:38:03 2017 -0500
@@ -1,21 +1,9 @@
 >SECIS_1
 AUUUUAUCCAUGAAAGUGUUUCCUCUAAACCUAUGUGGAGGAACACCUGAUGUCCAGGAAAAU
 .((((...(((.(..(((.((((((((........))))))))))).).))).....)))).. (-27.97)
-.((((...(((.{..(((.((((((((........))))))))))).}.))).....)))}.. [-29.13]
-..(((...(((....(((.((((((((........)))))))))))...))).....)))... {-26.59 d=5.82}
-.((((...(((.(..(((.((((((((........))))))))))).).))).....)))).. {-27.97 MEA=54.87}
- frequency of mfe structure in ensemble 0.151171; ensemble diversity 8.50
 >6S_1
 GAAACCCUAAUGUAUUCGAUAUAGUUCCUGAUAUUUUUGAACCGAACAAUUUUUUAUACCUAGGGAGCUUGGAGUUCCGGCGCGGCGCACAUGCCUUCACACGAGGAAGUGCAAACCGUUAGACAGAGCACCCACCUGCUUUAAUUGAGAGCGGGUUCAAAGGAAGGGAAUCCUAAACGGUACGAUUGGGGUUUCU
 (((((((...(((((.((.....((((((....((((((((((...................(((.((((.....((.((((.(..((((.(.((((.....))))).))))...))))).))..)))).)))....(((((.....))))).))))))))))..))))))......)))))))....))))))). (-110.38)
-(((((((,,{(((((,((.....{(((((....(((((((((({{{....,},.........(((.((((.....((.((((.(..((((.{.((((.....)))),.))))...))))).))}.)))).)))....(((((.....))))).))))))))))..))))),......))))))).}.,))))))). [-115.12]
-(((((((..((((((.((......(((((....((((((((((...................(((.((((.....((.((((.(..((((...((((.....))))..))))...))))).))..)))).)))....(((((.....))))).))))))))))..))))).......))))))).)..))))))). {-109.37 d=10.73}
-(((((((..((((((.((......(((((....((((((((((...................(((.((((.....((.((((.(..((((...((((.....))))..))))...))))).))..)))).)))....(((((.....))))).))))))))))..))))).......))))))).)..))))))). {-109.37 MEA=177.59}
- frequency of mfe structure in ensemble 0.000456946; ensemble diversity 17.02
 >6S_2
 UUGUCCCUGCCGUGCUCGUGACUUGGCCAUACAUUCUCUGAACCUAUGUCUUACGGCAUAUGGGUUGCGGGAGUGUAGAGCUGGAGUGAUCGUCUACUCGUAGACGAACCCGAUGCUCUUCGGAUCGCGACCACCUUGAACCUCAGGGUUCGAGAUGCCGGCCUUGACGGCACAGGCGGGGCAUC
 .((.(((((((((((.(((.(...((((...((.((((.((((((..(((....))).....((((((((...((.(((((.((.((..((((((......))))))))))...))))).))..)))))))).............))))))))))))..)))).).))))))).))))))))).. (-129.27)
-.((,(((((((((((.(((.{...((((...,,.((((.((((((..(((....))).....((((((((...{(.(((((.((.((..((((((,....,))))))))))...))))).)}..)))))))).....,,...,,.)))))))))),}..)))).}.))))))).))))))))).. [-132.48]
-.((.(((((((((((.(((.(...((((......((((.((((((..(((....))).....((((((((...((.(((((.((.((..((((((......))))))))))...))))).))..)))))))).............))))))))))....)))).).))))))).))))))))).. {-129.23 d=10.34}
-.((.(((((((((((.(((.(...((((...(..((((.((((((..(((....))).....((((((((...((.(((((.((.((..((((((......))))))))))...))))).))..)))))))).............)))))))))).)..)))).).))))))).))))))))).. {-128.23 MEA=168.16}
- frequency of mfe structure in ensemble 0.00547171; ensemble diversity 14.91