Repository 'viennarna_rnafold'
hg clone https://toolshed.g2.bx.psu.edu/repos/rnateam/viennarna_rnafold

Changeset 2:84aad99aca1f (2017-05-16)
Previous changeset 1:f87325531be8 (2016-12-21) Next changeset 3:fcf2463f85c1 (2017-05-29)
Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n'
modified:
macros.xml
rnafold.xml
added:
rnafold_SHAPE.py
test-data/sample_3.fa
test-data/sample_3.react
test-data/sample_3_result.txt
b
diff -r f87325531be8 -r 84aad99aca1f macros.xml
--- a/macros.xml Wed Dec 21 17:33:12 2016 -0500
+++ b/macros.xml Tue May 16 16:30:38 2017 -0400
b
@@ -2,6 +2,7 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="2.2.10">viennarna</requirement>
+            <yield/>
         </requirements>
     </xml>
     <token name="@VERSION@">2.2.10</token>
b
diff -r f87325531be8 -r 84aad99aca1f rnafold.xml
--- a/rnafold.xml Wed Dec 21 17:33:12 2016 -0500
+++ b/rnafold.xml Tue May 16 16:30:38 2017 -0400
[
b'@@ -1,23 +1,31 @@\n-<tool id="viennarna_rnafold" name="@EXECUTABLE@" version="@VERSION@.0">\n+<tool id="viennarna_rnafold" name="@EXECUTABLE@" version="@VERSION@.1">\n     <description>Calculate minimum free energy secondary structures and partition function of RNAs</description>\n     <macros>\n         <token name="@EXECUTABLE@">RNAfold</token>\n         <import>macros.xml</import>\n     </macros>\n-    <expand macro="requirements" />\n+    <expand macro="requirements">\n+\t    <requirement type="package" version="1.65">biopython</requirement>\n+    </expand>\n     <expand macro="stdio" />\n     <expand macro="version_command" />\n     <command>\n  <![CDATA[\n     #if str($input_source.select_fasta) == "false"\n         #if str($input_source.input_sequence).lstrip()[0] == ">"\n-            echo "${input_source.input_sequence}" > "input.fasta" &&\n+            echo \'${input_source.input_sequence}\' > "input.fasta" &&\n         #else\n             echo ">Sequence"                      >  "input.fasta" &&\n-            echo "${input_source.input_sequence}" >> "input.fasta" &&\n+            echo \'${input_source.input_sequence}\' >> "input.fasta" &&\n         #end if\n-    #end if    \n-    RNAfold\n+    #end if\n+\n+    #if str($constraints.shapeOption.shapeSelector) == "isUsed"\n+      python  \'$__tool_directory__/rnafold_SHAPE.py\'\n+    #else\n+      RNAfold\n+    #end if\n+\n     -T $temperature\n     --dangles=$dangling\n     #if $layout_type ==0\n@@ -33,7 +41,7 @@\n         #if $measelect.pfScale <> 1.07\n             --pfScale=$measelect.pfScale\n         #end if\n-    #end if   \n+    #end if\n     $advancedOptions.noconversion\n     $advancedOptions.gquad\n     $advancedOptions.nolp\n@@ -49,7 +57,7 @@\n     #end if\n     #if $advancedOptions.betaScale <> 1.0\n         --betaScale=$advancedOptions.betaScale\n-    #end if\t\n+    #end if\n     #if $constraints.maxBPspan <> -1\n         --maxBPspan=$constraints.maxBPspan\n     #end if\n@@ -69,7 +77,7 @@\n             --shapeMethod=$s\n         #else if str($constraints.shapeOption.shapeMethod.methodSelector) == "Z"\n             #set $s="Zb"+str($constraints.shapeOption.shapeMethod.b)\n-            --shapeMethod=$s\t\t\t\n+            --shapeMethod=$s\n             #if str($constraints.shapeOption.shapeMethod.shapeConversion.conversionSelector) == "C"\n                 #set $c="C"+str($constraints.shapeOption.shapeMethod.shapeConversion.c)\n                 --shapeConversion=$c\n@@ -90,8 +98,8 @@\n     #end if\n     #if $constraints.motif\n         --motif=\'$constraints.motif\'\n-    #end if\t\n-    < \n+    #end if\n+    <\n     #if str($input_source.select_fasta) == "false"\n         "input.fasta"\n     #else\n@@ -120,11 +128,11 @@\n             <option value="1">1: unpaired bases participate in one dangling end only</option>\n             <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>\n             <option value="3">3: allow coaxial stacking</option>\n-        </param>        \n+        </param>\n         <param name="layout_type" type="select" label="Layout algorithm" argument="--layout_type" >\n             <option value="1" selected="true">Default: Naview layout</option>\n             <option value="0">Simple radial layout</option>\n-        </param>        \n+        </param>\n         <conditional name="measelect">\n             <param name="mea" type="select" label="Calculate Maximum Expected accuracy" argument="--MEA">\n                 <option value="no">No</option>\n@@ -138,7 +146,7 @@\n                 <param name="pf" type="boolean" checked="false" truevalue="--partfunc" falsevalue="" label="Calculate Partition Function" help="--partfunc"/>\n                 <param argument="--pfScale" type="float" value="1.07" label="Scaling factor" help="In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows). The default is 1.07, useful values are 1.0 to 1.2. Occasionally needed for long sequences."/>\n             </when>\n-        </conditional>\t \n+        </conditional'..b' <param name="id_digits" \n-                type="integer" value="4" min="1" max="18" \n-                label="The number of digits of the counter in automatically generated sequence IDs" \n-                help="When sequences IDs are automatically generated, they receive an increasing number, starting with 1. This number will always be left\xe2\x88\x92padded by leading zeros, such that the number takes up a certain width. Using this parameter, the width can be specified to the users need. We allow numbers in the range [1:18]." \n+            <param name="id_digits"\n+                type="integer" value="4" min="1" max="18"\n+                label="The number of digits of the counter in automatically generated sequence IDs"\n+                help="When sequences IDs are automatically generated, they receive an increasing number, starting with 1. This number will always be left\xe2\x88\x92padded by leading zeros, such that the number takes up a certain width. Using this parameter, the width can be specified to the users need. We allow numbers in the range [1:18]."\n                 argument="--id-digits"/>\n-            <param name="id_start" \n-                type="integer" value="1" min="0" \n-                label="First number in automatically generated sequence IDs" \n-                help="When sequence IDs are automatically generated, they receive an increasing number, usually starting with 1. Using this parameter, the first number can be specified to the users requirements. Note: negative numbers are not allowed. Note: Setting this parameter implies continuous sequence IDs, i.e. it activates the \xe2\x88\x92\xe2\x88\x92continuous\xe2\x88\x92ids flag.." \n+            <param name="id_start"\n+                type="integer" value="1" min="0"\n+                label="First number in automatically generated sequence IDs"\n+                help="When sequence IDs are automatically generated, they receive an increasing number, usually starting with 1. Using this parameter, the first number can be specified to the users requirements. Note: negative numbers are not allowed. Note: Setting this parameter implies continuous sequence IDs, i.e. it activates the \xe2\x88\x92\xe2\x88\x92continuous\xe2\x88\x92ids flag.."\n                 argument="--id-start"/>\n-        </section>        \n+        </section>\n     </inputs>\n     <outputs>\n         <data format="dbn" name="tabular_file"/>\n@@ -292,19 +300,26 @@\n             <param name="fasta_input" value="rnafold_input1.fa"/>\n             <output name="out_file1" file="rnafold_result1.txt"/>\n         </test>\n-        \n         <test>\n             <param name="select_fasta" value="true" />\n             <param name="fasta_input" value="rnafold_input2.fa"/>\n             <param name="temperature" value="75"/>\n             <output name="out_file1" file="rnafold_result2.txt"/>\n         </test>\n-        \n         <test>\n             <param name="select_fasta" value="false" />\n             <param name="input_sequence" value="TGGGAATTAGCTCAAATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTAGTGGGATCGATGCCCACATTCTCCA"/>\n             <output name="out_file1" file="rnafold_result3.txt"/>\n         </test>\n+        <test>\n+            <param name="select_fasta" value="true" />\n+            <param name="fasta_input" value="sample_3.fa"/>\n+            <conditional name="shapeOption">\n+              <param name="shapeSelector" value="isUsed"/>\n+            </conditional>\n+            <param name="shapeFile" value="sample_3.react"/>\n+            <output name="out_file1" file="sample_3_result.txt"/>\n+        </test>\n     </tests>\n     <help>\n <![CDATA[\n@@ -343,7 +358,7 @@\n \n - several possible postscript images bundled together in a tar file\n     - secondary structure for each sequence in the input file\n-    - if partition function is calculated (--MEA or --partfunc is set) then also the pairing probabilty matrix is generated for each sequence \n+    - if partition function is calculated (--MEA or --partfunc is set) then also the pairing probabilty matrix is generated for each sequence\n \n ]]>\n     </help>\n'
b
diff -r f87325531be8 -r 84aad99aca1f rnafold_SHAPE.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnafold_SHAPE.py Tue May 16 16:30:38 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())
b
diff -r f87325531be8 -r 84aad99aca1f test-data/sample_3.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_3.fa Tue May 16 16:30:38 2017 -0400
b
@@ -0,0 +1,6 @@
+>SECIS_1 test
+AUUUUAUCCAUGAAAGUGUUUCCUCUAAACCUAUGUGGAGGAACACCUGAUGUCCAGGAAAAU
+>6S_1 test1
+GAAACCCUAAUGUAUUCGAUAUAGUUCCUGAUAUUUUUGAACCGAACAAUUUUUUAUACCUAGGGAGCUUGGAGUUCCGGCGCGGCGCACAUGCCUUCACACGAGGAAGUGCAAACCGUUAGACAGAGCACCCACCUGCUUUAAUUGAGAGCGGGUUCAAAGGAAGGGAAUCCUAAACGGUACGAUUGGGGUUUCU
+>6S_2
+UUGUCCCUGCCGUGCUCGUGACUUGGCCAUACAUUCUCUGAACCUAUGUCUUACGGCAUAUGGGUUGCGGGAGUGUAGAGCUGGAGUGAUCGUCUACUCGUAGACGAACCCGAUGCUCUUCGGAUCGCGACCACCUUGAACCUCAGGGUUCGAGAUGCCGGCCUUGACGGCACAGGCGGGGCAUC
b
diff -r f87325531be8 -r 84aad99aca1f test-data/sample_3.react
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_3.react Tue May 16 16:30:38 2017 -0400
b
@@ -0,0 +1,447 @@
+>SECIS_1
+1 0.0657466222
+2 0.1280448842
+3 0.2786665403
+4 0.1391216354
+5 0.0272299574
+6 0.1717063095
+7 0.488732281
+8 3.3015172695
+9 0.414494604
+10 0.1957445189
+11 0.4670328791
+12 0.1943420556
+13 0.2099109521
+14 0.5846784488
+15 0.1296563697
+16 0.0359267698
+17 0.0438238841
+18 1.6364597431
+19 1.72206594665E-17
+20 0.0099928394
+21 0.0475042774
+22 0.0065948845
+23 0.0574522715
+24 0.2126102485
+25 1.2006488448
+26 0.6040825271
+27 0.4114049219
+28 1.1514597937
+29 1.216707413
+30 0.0186005737
+31 0.0841609069
+32 0.086771667
+33 1.1672973211
+34 0.8144419625
+35 0.2583987716
+36 0.0182542709
+37 0.0875979754
+38 0.094456587
+39 0.5206337515
+40 0.000517531
+41 0.0253820905
+42 0.2076338063
+43 0.0087295599
+44 0.0129264641
+45 0.0127365182
+46 0.1193338151
+47 0.0186183812
+48 0.3581141112
+49 0.0941009884
+50 0.2050905673
+51 0.0209195644
+52 0.6030952711
+53 5.2129588113
+54 0.1747678483
+55 1.2231479801
+56 0.4978854319
+57 0.5711590135
+58 0.2793524314
+59 0.0037936012
+60 0.2158137729
+61 0.5646393912
+62 0.6229186627
+63 0.0193621982
+>6S_1
+1 0.1158690877
+2 0.0774028501
+3 0.2349947573
+4 1.72206594665E-17
+5 0.0926174169
+6 0.0505177415
+7 0.0457131819
+8 0.0194615986
+9 2.1495069267
+10 0.0409639397
+11 0.2185631969
+12 0.1776745985
+13 0.0086422926
+14 0.0241577615
+15 0.0092855631
+16 0.3453240509
+17 0.1535840586
+18 0.0180643958
+19 0.1188776616
+20 0.3091581196
+21 0.3748109806
+22 0.6187506508
+23 0.3511511383
+24 0.6512026704
+25 0.3096370415
+26 0.5283368492
+27 0.7500060952
+28 0.0352720444
+29 0.3776026196
+30 0.3489100484
+31 1.3035405919
+32 0.1023638167
+33 0.133082988
+34 0.0024118398
+35 0.0281166587
+36 0.2818828676
+37 0.1316060603
+38 0.1813992598
+39 0.0047490217
+40 0.0204058553
+41 0.0675891142
+42 0.045119933
+43 0.0266727645
+44 0.0673921107
+45 0.0085752561
+46 0.495476266
+47 0.8224799434
+48 0.5574272341
+49 0.2431151153
+50 0.256015696
+51 0.0386339787
+52 0.6618567864
+53 0.0707284393
+54 1.1215284869
+55 0.0463423016
+56 0.3338809513
+57 0.3987796157
+58 1.1046527917
+59 0.6156154318
+60 0.1179259769
+61 2.0333569471
+62 0.1224421595
+63 0.0266055429
+64 0.0298356423
+65 0.3004015135
+66 2.1966900004
+67 0.0222153137
+68 0.0095300422
+69 0.0503009918
+70 0.0418994997
+71 0.0384566069
+72 2.6211662666
+73 0.1704872628
+74 0.8386436572
+75 0.6961218859
+76 0.1995308419
+77 0.0552442152
+78 0.1937915065
+79 0.1239592493
+80 0.0782601391
+81 0.0138965117
+82 0.0231978646
+83 0.0150709773
+84 0.4084290821
+85 0.0792668417
+86 1.0630476211
+87 0.2524739666
+88 0.0229636507
+89 0.1153934877
+90 0.2693801005
+91 0.0071337145
+92 1.0279231796
+93 0.0574241281
+94 0.103312087
+95 0.2100864561
+96 0.0252070712
+97 0.6067864142
+98 0.0607860625
+99 0.5416948523
+100 0.7090251541
+101 2.0470096713
+102 0.0368697578
+103 0.1221648319
+104 0.0484836208
+105 0.7188621431
+106 0.2405585888
+107 0.1071170724
+108 0.6859305671
+109 0.0997679124
+110 0.0342400356
+111 0.0201635
+112 0.4527960874
+113 0.7018417748
+114 0.2561295384
+115 0.2788440973
+116 0.2437240042
+117 0.0984135237
+118 0.1146045041
+119 0.2116296362
+120 0.0360702095
+121 0.2006613525
+122 0.0635994434
+123 0.8384420629
+124 0.3546527057
+125 0.014380068
+126 0.0041004554
+127 0.2404132813
+128 0.0016204246
+129 0.016365643
+130 0.0025333389
+131 0.0207130798
+132 0.2199275512
+133 0.2973627433
+134 1.7680018464
+135 0.3120917444
+136 0.854288287
+137 0.4309335923
+138 2.3003988746
+139 0.047166557
+140 0.7391255635
+141 0.1357653755
+142 0.4672659386
+143 0.3601080698
+144 0.9111911856
+145 0.7435427597
+146 0.3353115579
+147 1.0513358906
+148 0.1406855309
+149 0.3543459659
+150 0.0561408821
+151 0.563013834
+152 0.1549691284
+153 0.7460309808
+154 0.0486849156
+155 0.1080587915
+156 0.0699642772
+157 0.4423435657
+158 0.0171555252
+159 0.0064557797
+160 0.4739275466
+161 0.2617128164
+162 0.0879369647
+163 0.0062762841
+164 0.1060085461
+165 0.0971932081
+166 0.3139785044
+167 0.0771649003
+168 0.0753029618
+169 0.5676607679
+170 0.9836368904
+171 0.6193661835
+172 0.3890022353
+173 0.3304911731
+174 0.9354752573
+175 2.5683088408
+176 0.6777050636
+177 0.0195000778
+178 0.0532349161
+179 0.0993391181
+180 0.0667310411
+181 0.0123690861
+182 0.0165201319
+183 0.2056431695
+184 0.0114477122
+185 0.1684423923
+186 0.6236165725
+187 0.2533573459
+188 7.4644850979
+189 1.72206594665E-17
+190 0.0510513818
+191 0.071993023
+192 0.093087642
+193 0.026770297
+194 0.1003921418
+195 0.731799564
+196 0.3882654324
+>6S_2
+1 5.135077189
+2 0.0137794619
+3 0.0198585136
+4 0.0394762621
+5 0.1032256038
+6 0.0124879331
+7 0.050343991
+8 0.0266906427
+9 0.0867862234
+10 0.0250443701
+11 0.1241682715
+12 0.0888505404
+13 1.72206594665E-17
+14 0.0443782398
+15 0.0331749933
+16 1.190843321
+17 0.0083605324
+18 0.1025127456
+19 0.0318835351
+20 0.6764653014
+21 1.6659553696
+22 0.0532195755
+23 0.1306535914
+24 3.2368938797
+25 0.2999875752
+26 0.1771608894
+27 0.0735275063
+28 1.1463641343
+29 0.3436951718
+30 0.6339043401
+31 0.8229568123
+32 0.0567986298
+33 0.3413998482
+34 0.1291037675
+35 0.561127074
+36 0.0076983354
+37 0.147000237
+38 0.0214390185
+39 0.5304305785
+40 0.0785507542
+41 0.0483731004
+42 0.0976091996
+43 1.2125480978
+44 0.1865263845
+45 0.6312459899
+46 0.1817958047
+47 2.8617198725
+48 0.2055922577
+49 1.3068827801
+50 0.2629492567
+51 0.8571308379
+52 0.2726647331
+53 1.129084224
+54 0.275119436
+55 0.5874419445
+56 0.3657294569
+57 0.2500734975
+58 1.0443534711
+59 4.5331285532
+60 0.2551985691
+61 0.1800315837
+62 1.2079574507
+63 0.1377332438
+64 0.034281766
+65 0.0098202871
+66 0.9938878178
+67 0.0331980613
+68 0.2884058117
+69 0.1471099733
+70 0.0250835628
+71 0.0040433138
+72 2.1207460501
+73 0.7413016698
+74 0.2856087978
+75 0.1043896327
+76 2.5426831833
+77 0.024753755
+78 0.0197741979
+79 0.0256614712
+80 0.0931195919
+81 0.2341548619
+82 0.9442989
+83 0.6902004027
+84 0.2615426874
+85 0.1968596889
+86 0.1317761893
+87 0.3101105886
+88 0.3109082689
+89 0.6036478733
+90 0.1383132052
+91 1.72206594665E-17
+92 1.3701244222
+93 0.0259262955
+94 0.0427849321
+95 0.0059202715
+96 0.4620195968
+97 1.1627066739
+98 0.1193652803
+99 0.5039174355
+100 0.7685843498
+101 3.3504451177
+102 0.0156110762
+103 0.0405202895
+104 0.0448853051
+105 0.1130352336
+106 0.0128895533
+107 0.0140152443
+108 0.8487385272
+109 0.5411302314
+110 0.1921994675
+111 0.0804367301
+112 2.1393979849
+113 0.657192459
+114 0.9680746376
+115 0.0181673032
+116 0.1293355582
+117 0.0385348779
+118 0.0599847607
+119 0.0286153267
+120 0.0529816257
+121 0.0738905329
+122 1.9826160191
+123 0.6850277412
+124 0.0240149916
+125 0.1003714264
+126 0.0282377438
+127 0.016091267
+128 0.0654324545
+129 1.3672926211
+130 0.3123897874
+131 0.0125997931
+132 0.0326682275
+133 0.8141700098
+134 2.7208263459
+135 0.9376426669
+136 0.2104407859
+137 0.9213456642
+138 0.9496557623
+139 0.0158974709
+140 1.0394051723
+141 3.395502997
+142 0.2786545217
+143 0.0944673368
+144 0.1658691067
+145 1.5138095878
+146 0.2388473327
+147 0.0071582802
+148 0.0399196127
+149 0.0269685694
+150 0.0343298406
+151 0.0260244978
+152 0.1131275763
+153 0.0217325853
+154 0.1015784545
+155 0.0991349861
+156 1.4195713543
+157 0.5085589945
+158 0.1250938659
+159 0.788081555
+160 0.1135816768
+161 0.0633806979
+162 2.7826494
+163 1.8003487205
+164 0.7686439584
+165 0.0397996113
+166 0.8340757785
+167 0.0060961894
+168 0.0003936337
+169 0.0179660084
+170 0.033466093
+171 0.0469772809
+172 0.1070226766
+173 0.3447929483
+174 0.8559366126
+175 0.1279778477
+176 0.2188243998
+177 0.0449863446
+178 0.0382790499
+179 0.0022221768
+180 0.0311889472
+181 0.0257878168
+182 0.0172539125
+183 0.2710934097
+184 0.0914500662
+185 0.208503114
\ No newline at end of file
b
diff -r f87325531be8 -r 84aad99aca1f test-data/sample_3_result.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_3_result.txt Tue May 16 16:30:38 2017 -0400
b
@@ -0,0 +1,9 @@
+>SECIS_1
+AUUUUAUCCAUGAAAGUGUUUCCUCUAAACCUAUGUGGAGGAACACCUGAUGUCCAGGAAAAU
+.((((...(((.(..(((.((((((((........))))))))))).).))).....)))).. (-27.97)
+>6S_1
+GAAACCCUAAUGUAUUCGAUAUAGUUCCUGAUAUUUUUGAACCGAACAAUUUUUUAUACCUAGGGAGCUUGGAGUUCCGGCGCGGCGCACAUGCCUUCACACGAGGAAGUGCAAACCGUUAGACAGAGCACCCACCUGCUUUAAUUGAGAGCGGGUUCAAAGGAAGGGAAUCCUAAACGGUACGAUUGGGGUUUCU
+(((((((...(((((.((.....((((((....((((((((((...................(((.((((.....((.((((.(..((((.(.((((.....))))).))))...))))).))..)))).)))....(((((.....))))).))))))))))..))))))......)))))))....))))))). (-110.38)
+>6S_2
+UUGUCCCUGCCGUGCUCGUGACUUGGCCAUACAUUCUCUGAACCUAUGUCUUACGGCAUAUGGGUUGCGGGAGUGUAGAGCUGGAGUGAUCGUCUACUCGUAGACGAACCCGAUGCUCUUCGGAUCGCGACCACCUUGAACCUCAGGGUUCGAGAUGCCGGCCUUGACGGCACAGGCGGGGCAUC
+.((.(((((((((((.(((.(...((((...((.((((.((((((..(((....))).....((((((((...((.(((((.((.((..((((((......))))))))))...))))).))..)))))))).............))))))))))))..)))).).))))))).))))))))).. (-129.27)