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Changeset 0:6baa763b77ba (2017-10-20)

Next changeset 1:6e36667f1729 (2019-01-02)

Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv commit 3bc676ca60e837f8aca261d0b7860128b3474a5c

added:
cmv.xml
macros.xml
tRNA.pdf
test-data/Hammerhead_1.pdf
test-data/Hammerhead_3.pdf
test-data/Hammerhead_HH10.pdf
test-data/Hammerhead_HH9.cm
test-data/Hammerhead_HH9.pdf
test-data/Hammerhead_II.pdf
test-data/hammerheadClan.cm
test-data/hammerheadClan.hmm
test-data/input.cmcompare
test-data/input.hmmcompare
test-data/tRNA.hmm
test-data/tRNA.pdf

diff -r 000000000000 -r 6baa763b77ba cmv.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cmv.xml Fri Oct 20 04:26:28 2017 -0400

[

@@ -0,0 +1,61 @@
+<tool id="cmv" name="cmv" version="@VERSION@.1">
+  <description>
+    CMV is a tool for visualization of RNA family models, also known as covariance models (CM)
+  </description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+
+  <expand macro="requirements" />
+
+  <expand macro="stdio" />
+
+  <expand macro="version" />
+  <command><![CDATA[
+  CMV
+        @COMMON_ARGS@
+        -m $model_filepath
+  ]]></command>
+
+  <inputs>
+    <param name="model_filepath" type="data" format="cm" label="Input model"/>
+    <section name="common" title="Common parameters">
+      <expand macro="common_parameters" />
+    </section>
+  </inputs>
+
+  <outputs>
+    <expand macro="vis_output"/>
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="model_filepath" value="Hammerhead_HH9.cm" />
+      <param name="output_format" value="pdf" />
+      <param name="model_details" value="detailed" />
+      <param name="emission_layout" value="bar" />
+      <output_collection name="output_pdfs" type="list">
+        <element name="Hammerhead_HH9" file="Hammerhead_HH9.pdf" ftype="pdf" compare="sim_size" />
+      </output_collection>
+    </test>
+  </tests>
+  <help><![CDATA[
+  **CMV -- Visualisation of RNA family models**
+
+  **Input.**
+  Covariance Models in INFERNAL format.
+  Optionally a stockholm alignment for each input model can be provided.
+
+  **Output.**
+  Depending on the detail level, only nodes with index (minimal), nodes with node type and indices (simple)
+  or nodes with states, emission and transition probabilities are visualised. Nodes linked by input comparison data
+  between different families are highlighted with color labels.
+  File in pdf,svg,png,ps format.
+
+  For more information, see
+  .. __: https://github.com/eggzilla/cmv
+
+  ]]></help>
+  <expand macro="citations" />
+
+</tool>

diff -r 000000000000 -r 6baa763b77ba macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Oct 20 04:26:28 2017 -0400

[

@@ -0,0 +1,86 @@
+<macros>
+    <token name="@VERSION@">1.0.6</token>
+
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">cmv</requirement>
+        </requirements>
+    </xml>
+
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:" />
+        </stdio>
+    </xml>
+
+    <xml name="version">
+        <version_command>
+            <![CDATA[
+                HMMV --version
+            ]]>
+        </version_command>
+    </xml>
+
+    <xml name="common_parameters">
+        <param name="alignment_filepath" type="data" format="stockholm" label="Input stockholm alignment" optional="true"/>
+        <param name="output_format" type="select" label="Output format" help="pdf, svg, png, ps">
+            <option value="pdf">pdf</option>
+            <option value="svg">svg</option>
+            <option value="png">png</option>
+            <option value="ps">ps</option>
+        </param>
+        <param name="model_details" type="select" label="Specify visualization detail level." help="minimal,simple,detailed">
+            <option value="minimal">minimal</option>
+            <option value="simple">simple</option>
+            <option value="detailed">detailed</option>
+        </param>
+        <param name="emission_layout" type="select" label="Specify layout of emission probabilites." help="score,probability,bar">
+            <option value="score">score</option>
+            <option value="probability">probability</option>
+            <option value="bar">bar</option>
+        </param>
+        <param argument="-t" type="float" value="0.01" label="Transition probability threshold" help="Minimal value for a transition probability to be displayed (Default: 0.01)"/>
+        <param argument="-c" type="float" value="2" label="Image scaling factor" help="Set uniform scaling factor for image size (Default: 2)"/>
+        <param argument="-w" type="integer" value="100" label="Maximum image width" help="Set maximal width of result figure (Default: 100)" optional="true"/>
+        <param argument="-n" type="integer" value="50" label="Stockholm alignment entries"  help="Set cutoff for included stockholm alignment entries (Default: 50)" optional="true"/>
+    </xml>
+
+    <xml name="vis_output">
+        <collection name="output_pdfs" type="list" label="${tool.name} on ${on_string}: output.pdfs">
+            <discover_datasets pattern="(?P<designation>.*)\.pdf" format="pdf"/>
+            <filter>common['output_format'] == 'pdf'</filter>
+        </collection>
+        <collection name="output_svg" type="list" label="${tool.name} on ${on_string}: output.svgs">
+            <discover_datasets pattern="(?P<designation>.*)\.svg" format="svg"/>
+            <filter>common['output_format'] == 'svg'</filter>
+        </collection>
+        <collection name="output_png" type="list" label="${tool.name} on ${on_string}: output.pngs">
+            <discover_datasets pattern="(?P<designation>.*)\.png" format="png"/>
+            <filter>common['output_format'] == 'png'</filter>
+        </collection>
+        <collection name="output_ps" type="list" label="${tool.name} on ${on_string}: output.ps">
+            <discover_datasets pattern="(?P<designation>.*)\.ps" format="ps"/>
+            <filter>common['output_format'] == 'ps'</filter>
+        </collection>
+    </xml>
+
+    <token name="@COMMON_ARGS@">
+      -d $common.model_details
+      -e $common.emission_layout
+      -n $common.n
+      -w $common.w
+      -c $common.c
+      -t $common.t
+      -f $common.output_format
+      #if $common.alignment_filepath
+         -s $common.alignment_filepath
+      #end if
+    </token>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/nar/gkt329</citation>
+        </citations>
+    </xml>
+</macros>
+

diff -r 000000000000 -r 6baa763b77ba tRNA.pdf

Binary file tRNA.pdf has changed

diff -r 000000000000 -r 6baa763b77ba test-data/Hammerhead_1.pdf

Binary file test-data/Hammerhead_1.pdf has changed

diff -r 000000000000 -r 6baa763b77ba test-data/Hammerhead_3.pdf

Binary file test-data/Hammerhead_3.pdf has changed

diff -r 000000000000 -r 6baa763b77ba test-data/Hammerhead_HH10.pdf

Binary file test-data/Hammerhead_HH10.pdf has changed

diff -r 000000000000 -r 6baa763b77ba test-data/Hammerhead_HH9.cm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Hammerhead_HH9.cm Fri Oct 20 04:26:28 2017 -0400

[

b'@@ -0,0 +1,598 @@\n+INFERNAL1/a [1.1 | October 2013]\n+NAME Hammerhead_HH9\n+ACC RF02275\n+STATES 240\n+NODES 65\n+CLEN 77\n+W 103\n+ALPH RNA\n+RF no\n+CONS yes\n+MAP yes\n+DATE Fri Feb 28 01:30:52 2014\n+COM [1] /nfs/production/xfam/rfam/software/bin/cmbuild -F CM SEED\n+COM [2] /nfs/production/xfam/rfam/software/bin/cmcalibrate --mpi CM\n+PBEGIN 0.05\n+PEND 0.05\n+WBETA 1e-07\n+QDBBETA1 1e-07\n+QDBBETA2 1e-15\n+N2OMEGA 1.52588e-05\n+N3OMEGA 1.52588e-05\n+ELSELF -0.08926734\n+NSEQ 33\n+EFFN 1.567017\n+CKSUM 796486396\n+NULL 0.000 0.000 0.000 0.000 \n+GA 52.00\n+TC 52.40\n+NC 51.90\n+EFP7GF -8.3103 0.71890\n+ECMLC 0.69960 -5.09380 2.60784 1600000 262533 0.004571\n+ECMGC 0.43156 -15.39797 -3.48915 1600000 68246 0.005861\n+ECMLI 0.73853 -2.62455 4.04692 1600000 165569 0.007248\n+ECMGI 0.51255 -9.59123 -0.17571 1600000 49879 0.008019\n+CM\n+ [ ROOT 0 ] - - - - - -\n+ S 0 -1 0 1 4 0 1 103 135 -6.791 -6.998 -0.308 -2.513 \n+ IL 1 1 2 1 4 4 30 105 138 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 \n+ IR 2 2 3 2 3 3 30 105 137 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+ [ MATL 1 ] 1 - u - - -\n+ ML 3 2 3 5 3 3 29 103 136 -7.602 -0.027 -6.257 -0.234 -0.123 -0.914 0.766 \n+ D 4 2 3 5 3 1 26 101 134 -7.290 -2.048 -0.412 \n+ IL 5 5 3 5 3 3 29 104 137 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+ [ MATL 2 ] 2 - u - - -\n+ ML 6 5 3 8 3 2 28 102 135 -7.645 -0.026 -6.299 -0.229 -0.080 -0.850 0.719 \n+ D 7 5 3 8 3 1 25 100 133 -7.141 -0.628 -1.532 \n+ IL 8 8 3 8 3 2 28 103 135 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+ [ MATL 3 ] 3 - g - - -\n+ ML 9 8 3 11 3 1 27 101 134 -8.220 -0.291 -2.481 0.177 -0.839 0.571 -0.278 \n+ D 10 8 3 11 3 0 24 99 132 -5.620 -0.734 -1.403 \n+ IL 11 11 3 11 3 2 28 101 134 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 \n+ [ MATR 4 ] - 84 - u - -\n+ MR 12 11 3 14 3 3 29 100 133 -7.954 -0.025 -6.271 0.090 -0.349 -0.887 0.687 \n+ D 13 11 3 14 3 0 22 97 130 -7.578 -2.756 -0.240 \n+ IR 14 14 3 14 3 2 28 100 133 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 \n+ [ MATR 5 ] - 83 - a - -\n+ MR 15 14 3 17 3 2 28 99 132 -7.954 -0.025 -6.271 0.182 -0.063 -0.261 0.103 \n+ D 16 14 3 17 3 0 22 97 130 -7.578 -1.489 -0.647 \n+ IR 17 17 3 17 3 2 27 99 132 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 \n+ [ MATR 6 ] - 82 - a - -\n+ MR 18 17 3 20 3 2 28 98 131 -8.058 -0.023 -6.376 0.400 -0.418 -0.083 -0.018 \n+ D 19 17 3 20'..b'1.46634 0.26236 1.09861 0.40547\n+ 56 2.86281 2.06764 2.51281 0.30739 63 U - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04130 3.90062 3.90062 1.46634 0.26236 1.09861 0.40547\n+ 57 2.34004 3.07136 0.22061 2.89516 64 G - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04130 3.90062 3.90062 1.46634 0.26236 1.09861 0.40547\n+ 58 2.76328 0.48300 2.45809 1.45077 65 C - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04130 3.90062 3.90062 1.46634 0.26236 1.09861 0.40547\n+ 59 0.37592 2.83207 1.69132 2.65672 66 A - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04130 3.90062 3.90062 1.46634 0.26236 1.09861 0.40547\n+ 60 2.34367 3.07620 0.21949 2.90108 67 G - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04130 3.90062 3.90062 1.46634 0.26236 1.09861 0.40547\n+ 61 2.55429 2.52778 3.06936 0.22820 68 U - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04130 3.90062 3.90062 1.46634 0.26236 1.09861 0.40547\n+ 62 0.16531 3.17973 2.90967 2.87749 69 A - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04130 3.90062 3.90062 1.46634 0.26236 1.09861 0.40547\n+ 63 2.14420 0.55656 2.71929 1.41166 70 C - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04130 3.90062 3.90062 1.46634 0.26236 1.09861 0.40547\n+ 64 2.39469 1.59253 1.87945 0.59291 71 U - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04130 3.90062 3.90062 1.46634 0.26236 1.09861 0.40547\n+ 65 2.53045 2.97714 0.20945 2.84031 72 G - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04130 3.90062 3.90062 1.46634 0.26236 1.09861 0.40547\n+ 66 2.33999 3.07129 0.22063 2.89508 73 G - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04130 3.90062 3.90062 1.46634 0.26236 1.09861 0.40547\n+ 67 3.20820 0.25953 2.92763 2.00521 74 C - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04130 3.90062 3.90062 1.46634 0.26236 1.09861 0.40547\n+ 68 1.98104 1.14215 1.62238 1.06273 75 u - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04130 3.90062 3.90062 1.46634 0.26236 1.09861 0.40547\n+ 69 1.61663 2.00825 1.87483 0.66586 76 U - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.19731 3.90062 1.83991 1.46634 0.26236 1.09861 0.40547\n+ 70 0.81558 2.17566 1.32970 1.71742 77 a - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04811 3.75142 3.75142 1.46634 0.26236 2.28762 0.10704\n+ 71 0.81612 1.82472 1.79275 1.46927 78 a - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04811 3.75142 3.75142 1.46634 0.26236 2.28762 0.10704\n+ 72 1.34010 1.90825 1.16493 1.28051 79 g - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04811 3.75142 3.75142 1.46634 0.26236 2.28762 0.10704\n+ 73 0.90336 1.74956 1.59163 1.52624 80 a - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04811 3.75142 3.75142 1.46634 0.26236 2.28762 0.10704\n+ 74 1.18139 1.49660 1.80689 1.18714 81 a - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04811 3.75142 3.75142 1.46634 0.26236 2.28762 0.10704\n+ 75 1.10246 1.68127 1.41247 1.43435 82 a - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.15306 3.75142 2.13335 1.46634 0.26236 2.28762 0.10704\n+ 76 1.27283 1.40257 1.54710 1.34272 83 a - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.05329 3.65165 3.65165 1.46634 0.26236 2.63151 0.07469\n+ 77 1.34601 1.64433 2.07238 0.86584 84 u - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.49277 0.94400 * 0.13173 2.09216 0.00000 *\n+//\n'

diff -r 000000000000 -r 6baa763b77ba test-data/Hammerhead_HH9.pdf

Binary file test-data/Hammerhead_HH9.pdf has changed

diff -r 000000000000 -r 6baa763b77ba test-data/Hammerhead_II.pdf

Binary file test-data/Hammerhead_II.pdf has changed

diff -r 000000000000 -r 6baa763b77ba test-data/hammerheadClan.cm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hammerheadClan.cm Fri Oct 20 04:26:28 2017 -0400

[

b'@@ -0,0 +1,1447 @@\n+INFERNAL1/a [1.1 | October 2013]\n+NAME Hammerhead_HH10\n+ACC RF02277\n+STATES 384\n+NODES 97\n+CLEN 125\n+W 144\n+ALPH RNA\n+RF no\n+CONS yes\n+MAP yes\n+DATE Thu Feb 20 19:56:21 2014\n+COM [1] /nfs/production/xfam/rfam/software/bin/cmbuild -F CM SEED\n+COM [2] /nfs/production/xfam/rfam/software/bin/cmcalibrate --mpi CM\n+PBEGIN 0.05\n+PEND 0.05\n+WBETA 1e-07\n+QDBBETA1 1e-07\n+QDBBETA2 1e-15\n+N2OMEGA 1.52588e-05\n+N3OMEGA 1.52588e-05\n+ELSELF -0.08926734\n+NSEQ 18\n+EFFN 0.962402\n+CKSUM 3402290674\n+NULL 0.000 0.000 0.000 0.000 \n+GA 75.00\n+TC 83.00\n+NC 68.00\n+EFP7GF -5.2222 0.71834\n+ECMLC 0.67226 -5.99835 2.14435 1600000 286094 0.004194\n+ECMGC 0.39225 -16.80988 -7.07053 1600000 18247 0.021921\n+ECMLI 0.60414 -4.80295 3.82929 1600000 220830 0.005434\n+ECMGI 0.45551 -9.18438 -0.78188 1600000 18377 0.021766\n+CM\n+ [ ROOT 0 ] - - - - - -\n+ S 0 -1 0 1 4 1 1 144 166 -6.485 -6.692 -0.074 -5.106 \n+ IL 1 1 2 1 4 27 71 148 169 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 \n+ IR 2 2 3 2 3 27 70 147 169 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+ [ MATL 1 ] 1 - u - - -\n+ ML 3 2 3 5 3 27 70 144 166 -7.540 -0.028 -6.194 0.306 -0.505 -0.844 0.587 \n+ D 4 2 3 5 3 22 65 143 164 -6.174 -1.687 -0.566 \n+ IL 5 5 3 5 3 26 69 146 168 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+ [ MATL 2 ] 2 - a - - -\n+ ML 6 5 3 8 3 26 69 143 165 -7.540 -0.028 -6.194 0.988 -1.096 -0.227 -0.526 \n+ D 7 5 3 8 3 21 64 142 163 -6.174 -1.687 -0.566 \n+ IL 8 8 3 8 3 25 68 145 166 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+ [ MATL 3 ] 3 - a - - -\n+ ML 9 8 3 11 3 25 68 142 164 -7.540 -0.028 -6.194 0.990 -0.979 -0.488 -0.332 \n+ D 10 8 3 11 3 20 63 141 162 -6.174 -1.687 -0.566 \n+ IL 11 11 3 11 3 25 68 144 165 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+ [ MATL 4 ] 4 - a - - -\n+ ML 12 11 3 14 3 24 67 141 163 -7.540 -0.028 -6.194 0.838 -0.660 -0.654 -0.083 \n+ D 13 11 3 14 3 20 62 140 161 -6.174 -1.687 -0.566 \n+ IL 14 14 3 14 3 24 67 143 164 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+ [ MATL 5 ] 5 - A - - -\n+ ML 15 14 3 17 3 24 66 140 162 -7.540 -0.028 -6.194 1.114 -1.046 -0.756 -0.397 \n+ D 16 14 3 17 3 19 62 139 160 -6.174 -1.687 -0.566 \n+ IL 17 17 3 17 3 23 66 142 163 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+ [ MATL 6 ] 6 - A - - -\n+ ML 18 17 3 20 3 23 65 139 161 -7.540 -0.028 -6.194 1.323 -1.350 -0.895 -0.815 \n+ D 19 17 3 '..b'0.25318 1.49756 1.09861 0.40547\n+ 46 2.48566 0.89872 0.99191 1.97494 58 c - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547\n+ 47 2.13617 2.43801 0.28287 3.19563 59 G - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547\n+ 48 3.31779 4.38460 0.06727 4.11340 60 G - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547\n+ 49 1.85426 1.37282 1.50755 0.99808 61 u - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547\n+ 50 0.88929 1.78542 1.68621 1.44347 62 a - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547\n+ 51 5.05323 0.02311 5.39549 4.42941 63 C - - ,\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547\n+ 52 4.78480 4.48556 5.35375 0.02466 64 U - - ,\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547\n+ 53 4.64450 5.75634 0.01873 5.15426 65 G - - ,\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547\n+ 54 0.01670 5.42928 5.02297 5.18612 66 A - - ,\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547\n+ 55 3.60942 1.24185 4.20502 0.40173 67 U - - ,\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547\n+ 56 4.64450 5.75634 0.01873 5.15426 68 G - - ,\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547\n+ 57 0.01670 5.42928 5.02297 5.18612 69 A - - ,\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.35908 1.22331 4.90265 0.51588 0.90876 1.09861 0.40547\n+ 58 3.52173 4.67249 0.05344 4.33237 72 G - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547\n+ 59 3.70014 0.13807 3.35799 2.66739 73 C - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547\n+ 60 0.01670 5.42928 5.02297 5.18612 74 A - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547\n+ 61 2.96959 5.02019 0.07051 4.59033 75 G - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547\n+ 62 1.71038 0.26874 4.29103 3.19012 76 C - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547\n+ 63 2.32511 0.45172 2.74721 1.60152 77 C - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547\n+ 64 0.84725 1.54111 1.47935 2.04422 78 a - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547\n+ 65 0.32766 2.21587 2.36388 2.57341 79 A - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547\n+ 66 0.64240 2.02512 1.25557 2.86334 80 A - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01497 4.90265 4.90265 1.46634 0.26236 1.09861 0.40547\n+ 67 1.22218 1.51879 1.04805 1.99647 81 g - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00751 4.89520 * 1.46634 0.26236 0.00000 *\n+//\n'

diff -r 000000000000 -r 6baa763b77ba test-data/hammerheadClan.hmm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hammerheadClan.hmm Fri Oct 20 04:26:28 2017 -0400

[

b'@@ -0,0 +1,362 @@\n+HMMER3/f [i1.1 | October 2013]\n+NAME Hammerhead_1\n+ACC RF00163\n+LENG 46\n+MAXL 1024\n+ALPH RNA\n+RF no\n+MM no\n+CONS yes\n+CS yes\n+MAP yes\n+DATE Mon Apr 7 16:26:36 2014\n+COM [1] /nfs/production/xfam/rfam/software/bin/cmbuild -F CM SEED\n+NSEQ 29\n+EFFN 29.000000\n+CKSUM 822789652\n+STATS LOCAL MSV -7.2434 0.72420\n+STATS LOCAL VITERBI -8.0368 0.72420\n+STATS LOCAL FORWARD -3.9333 0.72420\n+HMM A C G U \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 1.23160 1.40725 1.36162 1.57448\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00643 5.74300 5.74300 1.46634 0.26236 0.00000 *\n+ 1 1.05150 0.79288 2.10623 2.57240 1 c - - (\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00643 5.74300 5.74300 1.46634 0.26236 1.09861 0.40547\n+ 2 3.57334 2.35748 2.81121 0.20194 2 U - - (\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00643 5.74300 5.74300 1.46634 0.26236 1.09861 0.40547\n+ 3 2.13788 0.94667 3.09051 0.80165 3 u - - (\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.05509 5.74300 2.98777 1.46634 0.26236 1.09861 0.40547\n+ 4 4.19719 0.98552 3.95023 0.52346 4 U - - (\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00675 5.69466 5.69466 1.46634 0.26236 0.11973 2.18181\n+ 5 1.10187 0.99383 2.32825 1.60881 5 c - - (\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00643 5.74300 5.74300 1.46634 0.26236 1.09861 0.40547\n+ 6 1.81855 1.02498 1.03243 2.09726 6 c - - (\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00643 5.74300 5.74300 1.46634 0.26236 1.09861 0.40547\n+ 7 2.32168 0.15763 4.96854 3.19967 7 C - - ,\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00643 5.74300 5.74300 1.46634 0.26236 1.09861 0.40547\n+ 8 2.51100 2.68275 4.56816 0.17428 8 U - - ,\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00643 5.74300 5.74300 1.46634 0.26236 1.09861 0.40547\n+ 9 5.32753 6.52376 0.00925 5.84922 9 G - - ,\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00643 5.74300 5.74300 1.46634 0.26236 1.09861 0.40547\n+ 10 0.03510 5.34451 5.30287 3.69926 10 A - - ,\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00643 5.74300 5.74300 1.46634 0.26236 1.09861 0.40547\n+ 11 0.78913 1.06413 2.18044 2.43336 11 a - - ,\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00643 5.74300 5.74300 1.46634 0.26236 1.09861 0.40547\n+ 12 5.05359 3.99671 0.02921 5.51634 12 G - - ,\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00643 5.74300 5.74300 1.46634 0.26236 1.09861 0.40547\n+ 13 0.12729 3.90906 4.06325 2.49775 13 A - - ,\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00643 5.74300 5.74300 1.46634 0.26236 1.09861 0.40547\n+ 14 3.40084 5.71124 0.04079 5.70842 14 G - - <\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00643 5.74300 5.74300 1.46634 0.26236 1.09861 0.40547\n+ 15 0.87362 3.64062 4.79136 0.60144 15 U - - <\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00643 5.74300 5.74300 1.46634 0.26236 1.09861 0.40547\n+ 16 5.35572 0.12161 3.01897 2.79792 16 C - - <\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00643 5.74300 5.74300 1.46634 0.26236 1.09861 0.40547\n+ 17 5.34129 0.65767 0.83205 3.17017 17 C - - <\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03409 5.74300 3.49639 1.46634 0.26236 1.09861 0.40547\n+ 18 0.83459 0.84384 3.21993 2.34406 18 a - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00661 5.71553 5.71553 1.46634 0.26236 0.19187 1.74534\n+ 19 0.08607 3.46116 3.24250 4.'..b'1.46634 0.26236 1.09861 0.40547\n+ 37 2.03553 1.14366 0.89607 1.94793 40 g - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00437 6.12818 6.12818 1.46634 0.26236 1.09861 0.40547\n+ 38 1.57384 4.50180 5.08139 0.25431 41 U - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.29218 6.12818 1.38157 1.46634 0.26236 1.09861 0.40547\n+ 39 3.09844 5.93445 0.05360 5.42125 42 G - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00582 5.84183 5.84183 1.46634 0.26236 4.76382 0.00857\n+ 40 0.57139 2.99642 0.98909 4.31405 43 A - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.49939 1.05274 3.12088 3.14323 0.04410 4.76382 0.00857\n+ 41 1.04364 1.08329 1.31484 3.19837 68 a - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00608 5.79974 5.79974 1.46634 0.26236 2.04285 0.13887\n+ 42 0.02310 5.57631 5.42805 4.22311 69 A - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00579 5.84716 5.84716 1.46634 0.26236 0.12551 2.13749\n+ 43 1.40381 1.25554 2.81848 0.89228 70 u - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00448 6.10255 6.10255 1.46634 0.26236 2.68142 0.07092\n+ 44 0.38958 5.50418 1.15768 5.43206 71 A - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00448 6.10255 6.10255 1.46634 0.26236 0.14726 1.98827\n+ 45 0.78318 1.63842 1.13792 3.56564 72 a - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00437 6.12818 6.12818 1.46634 0.26236 1.09861 0.40547\n+ 46 2.67107 5.67654 0.08033 5.38484 73 G - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00437 6.12818 6.12818 1.46634 0.26236 1.09861 0.40547\n+ 47 0.74767 1.36240 1.39759 3.75960 74 a - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00437 6.12818 6.12818 1.46634 0.26236 1.09861 0.40547\n+ 48 6.09436 0.02609 5.94200 3.86953 75 C - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00437 6.12818 6.12818 1.46634 0.26236 1.09861 0.40547\n+ 49 4.27804 6.30999 0.02714 4.50238 76 G - - ,\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00437 6.12818 6.12818 1.46634 0.26236 1.09861 0.40547\n+ 50 0.01709 6.15625 4.41390 5.90874 77 A - - ,\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00437 6.12818 6.12818 1.46634 0.26236 1.09861 0.40547\n+ 51 0.00581 6.55643 6.07425 6.18037 78 A - - ,\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00451 6.09683 6.09683 1.46634 0.26236 1.09861 0.40547\n+ 52 0.01022 6.29796 5.35703 5.62188 79 A - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00451 6.09683 6.09683 1.46634 0.26236 1.09861 0.40547\n+ 53 4.82883 0.06808 5.14616 2.95661 80 C - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00451 6.09683 6.09683 1.46634 0.26236 1.09861 0.40547\n+ 54 2.05206 3.60982 2.04635 0.33510 81 U - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00451 6.09683 6.09683 1.46634 0.26236 1.09861 0.40547\n+ 55 4.17624 1.44976 0.70955 1.35420 82 g - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02546 6.09683 3.77729 1.46634 0.26236 1.09861 0.40547\n+ 56 1.57713 2.34364 1.12299 0.98846 83 u - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00461 6.07598 6.07598 1.46634 0.26236 2.49906 0.08573\n+ 57 0.91090 3.50943 2.33812 0.75202 84 u - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.36397 6.07598 1.19472 1.46634 0.26236 2.49906 0.08573\n+ 58 2.20011 1.23892 0.74080 2.09739 85 g - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00330 5.71531 * 1.46634 0.26236 0.00000 *\n+//\n'

diff -r 000000000000 -r 6baa763b77ba test-data/input.cmcompare
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.cmcompare Fri Oct 20 04:26:28 2017 -0400

[

@@ -0,0 +1,1 @@
+Hammerhead_HH10 Hammerhead_II -2.968 -0.922 GCGCCCCCGCGGGCGC ((((((....)))))) ((((((....)))))) [26,27,28,29,30,31,32,33,34,35,36] [25,26,27,28,29,30,31,32,33,34,35,36,37,38,39]

diff -r 000000000000 -r 6baa763b77ba test-data/input.hmmcompare
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.hmmcompare Fri Oct 20 04:26:28 2017 -0400

[

@@ -0,0 +1,1 @@
+Hammerhead_1 Hammerhead_3 6.168 5.244 GUCCCAGUAAUAGGAC [17,18,19,20,21,22,23,23,24,25,26,27,28] [36,37,38,39,40,41,42,43,44,45,46,47,48]

diff -r 000000000000 -r 6baa763b77ba test-data/tRNA.hmm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA.hmm Fri Oct 20 04:26:28 2017 -0400

[

b'@@ -0,0 +1,238 @@\n+HMMER3/f [i1.1 | October 2013]\n+NAME tRNA\n+ACC RF00005\n+LENG 71\n+MAXL 253\n+ALPH RNA\n+RF no\n+MM no\n+CONS yes\n+CS yes\n+MAP yes\n+DATE Tue Mar 18 15:30:04 2014\n+COM [1] /nfs/production/xfam/rfam/software/bin/cmbuild -F CM SEED\n+NSEQ 954\n+EFFN 559.992432\n+CKSUM 1403477983\n+STATS LOCAL MSV -9.0828 0.73401\n+STATS LOCAL VITERBI -9.6771 0.73401\n+STATS LOCAL FORWARD -2.6167 0.73401\n+HMM A C G U \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 1.34376 1.54626 1.34829 1.32272\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01089 9.16555 4.53501 1.46634 0.26236 0.00000 *\n+ 1 1.77738 2.48413 0.40741 2.49918 1 G - - (\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00021 9.15487 9.15487 1.46634 0.26236 0.01931 3.95671\n+ 2 1.70723 1.28195 0.88318 2.05828 2 g - - (\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00021 9.16555 9.16555 1.46634 0.26236 1.09861 0.40547\n+ 3 1.16771 1.50075 1.31207 1.62608 3 a - - (\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00021 9.16555 9.16555 1.46634 0.26236 1.09861 0.40547\n+ 4 1.45971 1.75541 0.94997 1.56969 4 g - - (\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00021 9.16555 9.16555 1.46634 0.26236 1.09861 0.40547\n+ 5 0.99705 1.64839 1.41564 1.63013 5 a - - (\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00021 9.16555 9.16555 1.46634 0.26236 1.09861 0.40547\n+ 6 1.62605 1.74147 1.35530 0.99381 6 u - - (\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00021 9.16555 9.16555 1.46634 0.26236 1.09861 0.40547\n+ 7 0.91594 3.16623 1.01357 1.63590 7 a - - (\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00021 9.16555 9.16555 1.46634 0.26236 1.09861 0.40547\n+ 8 2.66516 4.88171 3.01992 0.13465 8 U - - ,\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03342 3.68933 4.84310 0.00835 4.78975 1.09861 0.40547\n+ 9 0.58939 3.25595 1.00776 3.17602 10 A - - ,\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02924 3.55044 9.15774 0.00733 4.92001 0.02619 3.65549\n+ 10 2.41169 2.38509 0.28093 2.76190 12 G - - <\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00021 9.16555 9.16555 1.46634 0.26236 1.09861 0.40547\n+ 11 3.26023 0.54810 2.54667 1.18668 13 C - - <\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00021 9.16555 9.16555 1.46634 0.26236 1.09861 0.40547\n+ 12 2.15431 1.47701 1.82444 0.70443 14 u - - <\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00021 9.16555 9.16555 1.46634 0.26236 1.09861 0.40547\n+ 13 1.60140 1.50019 1.39889 1.11344 15 u - - <\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00210 9.16555 6.21942 1.46634 0.26236 1.09861 0.40547\n+ 14 0.13193 5.26257 3.22617 2.54198 16 A - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00916 9.16366 4.70900 1.46634 0.26236 3.04606 0.04871\n+ 15 0.89567 3.14554 0.79030 2.35479 17 g - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.17992 9.15472 1.80452 1.46634 0.26236 4.66400 0.00947\n+ 16 1.81826 1.59646 3.52093 0.50169 18 U - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.48849 1.02501 3.58788 0.29781 1.35652 0.17366 1.83622\n+ 17 2.18421 3.21803 0.23359 2.88757 22 G - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01313 9.11400 4.34765 1.46634 0.26236 6.18099 0.00207\n+ 18 2.72437 3.05446 0.23471 2.33861 23 G - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.16612 9.10109 1.87766 1.46634 0.26236 6.39686 0.00167\n+ 19 2.54081 1.97700 3.62026 0.27980 '..b'0.01345 4.31515 1.09861 0.40547\n+ 50 1.54892 3.64681 0.35215 2.84261 90 G - - <\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.05447 9.16317 2.93921 1.46634 0.26236 3.24748 0.03965\n+ 51 2.91904 3.69075 0.10557 3.85142 91 G - - <\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01926 9.10892 3.96541 1.46634 0.26236 0.47025 0.98042\n+ 52 2.58713 3.30063 4.12158 0.13733 92 U - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01335 4.33098 9.12642 0.01645 4.11544 0.02336 3.76823\n+ 53 2.73380 3.55136 3.10063 0.14929 94 U - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00117 9.16487 6.84764 1.46634 0.26236 0.23519 1.56264\n+ 54 1.91909 0.28976 3.93473 2.46202 95 C - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00089 9.16459 7.15486 1.46634 0.26236 2.49712 0.08591\n+ 55 0.86370 3.18439 0.73315 2.87167 96 g - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02538 3.85434 5.55452 0.00986 4.62431 0.11370 2.23049\n+ 56 0.10751 3.36842 3.61643 3.20375 98 A - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02690 9.16179 3.63288 1.46634 0.26236 3.66212 0.02601\n+ 57 0.67201 2.24039 1.88732 1.46350 99 A - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.10924 3.26538 2.72866 0.25713 1.48400 3.15055 0.04377\n+ 58 3.03220 2.08118 4.58750 0.20232 102 U - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02872 9.06899 3.56869 1.46634 0.26236 0.44699 1.02041\n+ 59 3.62885 0.09251 4.76246 2.93245 103 C - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00022 9.10519 9.10519 1.46634 0.26236 0.04490 3.12561\n+ 60 2.82384 0.36562 3.60560 1.51557 104 C - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00021 9.16317 9.16317 1.46634 0.26236 0.08093 2.55433\n+ 61 1.98165 0.93537 2.03138 1.08305 105 c - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00021 9.16555 9.16555 1.46634 0.26236 1.09861 0.40547\n+ 62 1.41052 1.88381 1.22158 1.17374 106 u - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01727 4.07376 9.16555 0.01225 4.40843 1.09861 0.40547\n+ 63 2.92352 0.85192 2.12328 0.91624 108 c - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01067 4.63067 7.04730 0.02132 3.85875 1.09861 0.40547\n+ 64 1.64302 1.08197 3.15743 0.85533 110 u - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00021 9.16479 9.16479 1.46634 0.26236 0.21550 1.64060\n+ 65 1.19333 1.55287 1.48082 1.35596 111 a - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00021 9.16555 9.16555 1.46634 0.26236 1.09861 0.40547\n+ 66 1.77201 1.52940 1.50476 0.93835 112 u - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00021 9.16555 9.16555 1.46634 0.26236 1.09861 0.40547\n+ 67 1.68524 1.08580 1.59640 1.29337 113 c - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00021 9.16555 9.16555 1.46634 0.26236 1.09861 0.40547\n+ 68 1.70095 1.44882 1.44666 1.05760 114 u - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00021 9.16555 9.16555 1.46634 0.26236 1.09861 0.40547\n+ 69 2.07909 0.95836 1.28069 1.54370 115 c - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00021 9.16555 9.16555 1.46634 0.26236 1.09861 0.40547\n+ 70 2.48394 0.54896 2.55295 1.34252 116 C - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02417 9.16555 3.73919 1.46634 0.26236 1.09861 0.40547\n+ 71 0.68084 2.78597 1.26674 1.89452 118 A - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00011 9.14149 * 1.46634 0.26236 0.00000 *\n+//\n'

diff -r 000000000000 -r 6baa763b77ba test-data/tRNA.pdf

Binary file test-data/tRNA.pdf has changed