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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f447414150c19865e904d3914a68e2479fadddce
author bgruening
date Thu, 15 Dec 2016 18:18:52 -0500
parents
children
files NSPDK_candidateClusters.xml NSPDK_sparseVect.xml test-data/1.group.gspan.bz2 test-data/SVECTOR/data.svector test-data/SVECTOR/data.svector.1.fast_cluster test-data/SVECTOR/data.svector.1.fast_cluster_sim test-data/SVECTOR/data.svector.blacklist.1 test-data/data.fasta test-data/data.names test-data/data.svector.1
diffstat 9 files changed, 495 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NSPDK_candidateClusters.xml	Thu Dec 15 18:18:52 2016 -0500
@@ -0,0 +1,149 @@
+<tool id="NSPDK_candidateClust" name="NSPDK_candidateClusters" version="9.2">
+	<requirements>
+		<requirement type="package" version="0.1">graphclust-wrappers</requirement>
+		<requirement type="package" version="0.5">perl-array-utils</requirement>
+		<requirement type="package" version="9.2">nspdk</requirement>
+	</requirements>
+	<stdio>
+		<exit_code range="1:" />
+	</stdio>
+	<command>
+		<![CDATA[
+
+        mkdir -p SVECTOR &&
+
+        cp $data_svector SVECTOR/data.svector &&
+
+        'NSPDK_candidateClusters.pl'  '$data_fasta' '$data_names' $noCache $ensf $oc $usn $knn $nhf $nspdk_nhf_max $nspdk_nhf_step $GLOBAL_num_clusters $max_rad $max_dist_relations
+
+        #if  $iteration_num.iteration_num_selector:
+          $iteration_num.CI
+          '$blacklist'
+          '$final_partition_soft'
+          '$fast_cluster_last_round'
+          $iteration_num.GLOBAL_hit_blacklist_overlap
+
+        #else:
+          1
+
+        #end if
+
+]]>
+	</command>
+	<inputs>
+		<param type="data" name="data_svector" format="zip"  />
+		<param type="data" name="data_fasta" format="fasta" />
+		<param type="data" name="data_names" format="txt" />
+		<conditional name="iteration_num">
+			<param name="iteration_num_selector" type="boolean"  checked="no" label="Multiple iterations"  help="for single iteration- NO, for multiple-YES"/>
+			<when value="true">
+				<param name="CI" type="integer" value="2" size="5" label="Number of current iteration "/>
+				<param type="data" name="blacklist" format="txt" />
+				<param type="data" name="final_partition_soft" format="txt" />
+				<param type="data" name="fast_cluster_last_round" format="txt" />
+				<param name="GLOBAL_hit_blacklist_overlap" type="float" value="0.2" size="5" label="Blacklist hit overlap" />
+			</when>
+			<when value="false" >
+				<param name="CI" type="hidden" value="1" size="5" label="Number of current iteration "></param>
+			</when>
+		</conditional>
+		<param name="max_rad" type="integer" value="3" size="5" label="maximum radius " help="-R"/>
+		<param name="max_dist_relations" type="integer" value="3" size="5" label="maximum distance relations" help="-D"/>
+		<param name="noCache" truevalue="-no-cache" falsevalue="" checked="True" type="boolean"
+                label="Deactivate caching of kernel value computation  (-no-cache)" help="to minimize memory usage"/>
+		<param name="ensf" type="integer" value="5" size="5" label="eccess neighbour size factor" help="-ensf"/>
+		<param name="usn" truevalue="-usn" falsevalue="" checked="True" type="boolean"
+                label="Use shared neighbourhood to weight center density (-usn)" help="by default true"/>
+		<param name="oc" truevalue="-oc" falsevalue="" checked="True" type="boolean"
+                label=" flag to output clusters (-oc)" help="by default true"/>
+		<param name="knn" type="integer" value="20" size="5" label="Number of nearest neighbors" help="-knn num"/>
+		<param name="nhf" type="integer" value="500" size="5" label="Number of hash functions " help="-nhf num"/>
+		<param name="nspdk_nhf_max" type="integer" value="1000" size="5" label="Maximal number of hash functions " />
+		<param name="nspdk_nhf_step" type="integer" value="25" size="5" label="Size of step for increasing hash functions " help="The number of hash functions is increased by this value after each iteration."/>
+		<param name="GLOBAL_num_clusters" type="integer" value="100" size="5" label="Maxinum number of clusters " />
+	</inputs>
+	<outputs>
+		<data name="fast_cluster" format="txt" from_work_dir="SVECTOR/data.svector.1.fast_cluster" label="fast_cluster.1"  >
+			<filter> iteration_num['iteration_num_selector'] is False</filter>
+		</data>
+		<data name="fast_cluster_sim" format="txt" from_work_dir="SVECTOR/data.svector.1.fast_cluster_sim" label="fast_cluster_sim.1" >
+			<filter> iteration_num['iteration_num_selector'] is False </filter>
+		</data>
+		<data name="black_list" format="txt" from_work_dir="SVECTOR/data.svector.blacklist.1" label="blacklist.1" >
+			<filter> iteration_num['iteration_num_selector'] is False </filter>
+		</data>
+		<data name="fast_cluster_m" format="txt" from_work_dir="SVECTOR/data.svector.*.fast_cluster" label="fast_cluster.$iteration_num.CI"  >
+			<filter> iteration_num['iteration_num_selector'] is True</filter>
+		</data>
+		<data name="fast_cluster_sim_m" format="txt" from_work_dir="SVECTOR/data.svector.*.fast_cluster_sim" label="fast_cluster_sim.$iteration_num.CI" >
+			<filter> iteration_num['iteration_num_selector'] is True</filter>
+		</data>
+		<data name="black_list_m" format="txt" from_work_dir="SVECTOR/data.svector.blacklist.*" label="blacklist.$iteration_num.CI" >
+			<filter> iteration_num['iteration_num_selector'] is True</filter>
+		</data>
+	</outputs>
+	<tests>
+		<test>
+			<param name="data_fasta" value="data.fasta"/>
+			<param name="data_names" value="data.names"/>
+			<param name="data_svector" value="data.svector.1" ftype="zip"  />
+			<conditional name="iteration_num">
+				<param name="iteration_num_selector" value="false"/>
+			</conditional>
+			<param name="noCache" value="-no-cache"/>
+			<param name="ensf" value="5"/>
+			<param name="oc" value="-oc"/>
+			<param name="max_rad" value="3"/>
+			<param name="max_dist_relations" value="3"/>
+			<param name="usn" value="-usn"/>
+			<param name="knn" value="20"/>
+			<param name="nhf" value="500"/>
+			<param name="nspdk_nhf_max" value="1000"/>
+			<param name="nspdk_nhf_step" value="25"/>
+			<param name="GLOBAL_num_clusters" value="100"/>
+			<output name="fast_cluster" file="SVECTOR/data.svector.1.fast_cluster" />
+			<output name="fast_cluster_sim" file="SVECTOR/data.svector.1.fast_cluster_sim" />
+			<output name="black_list" file="SVECTOR/data.svector.blacklist.1" />
+		</test>
+	</tests>
+	<help>
+		<![CDATA[
+
+**What it does**
+
+Copmutes global feature index and returns top dense sets.
+The candidate clusters are chosen as the top ranking neighborhoods provided that the size of their overlap
+is below a specified threshold.
+For more information see *Fast neighborhood subgraph pairwise distance kernel* paper.
+
+
+**Parameters**
+
++ **-knn** : <num nearest neighbors> (default: 10)
+
++ **-otknn** : flag to output true (i.e. implies full kernel matrix evaluation) k-nearest neighburs (default: 0)
+
++ **-oc** : flag to output clusters (default: 0)
+
++ **-nhf** : <num hash functions> for the Locality Sensitive Hashing function (default: 250)
+
++ **-ensf** : <eccess neighbour size factor> (default: 10) (0 to avoid trimming)
+
++ **-usn** : use shared neighbourhood to weight center density (default: 0)
+
+
+    ]]>
+	</help>
+	<citations>
+		<citation type="doi">10.1093/bioinformatics/bts224</citation>
+		<citation type="bibtex">@inproceedings{costa2010fast,
+        title={Fast neighborhood subgraph pairwise distance kernel},
+        author={Costa, Fabrizio and De Grave, Kurt},
+        booktitle={Proceedings of the 26th International Conference on Machine Learning},
+        pages={255--262},
+        year={2010},
+        organization={Omnipress}
+      }
+      </citation>
+	</citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NSPDK_sparseVect.xml	Thu Dec 15 18:18:52 2016 -0500
@@ -0,0 +1,66 @@
+<tool id="nspdk_sparse" name="NSPDK_sparseVect" version="9.2">
+	<requirements>
+			<requirement type="package" version="0.1">graphclust-wrappers</requirement>
+			<requirement type="package" version="9.2">nspdk</requirement>
+	</requirements>
+	<stdio>
+		<exit_code range="1:" />
+	</stdio>
+	<command>
+		<![CDATA[
+
+
+      'NSPDK_sparseVect.pl' '$data_fasta' '$gspan_file'  $max_rad $max_dist_relations
+
+]]>
+	</command>
+	<inputs>
+		<param type="data" name="gspan_file" format="searchgui_archive"  />
+		<param type="data" name="data_fasta" format="fasta" />
+		<param name="max_rad" type="integer" value="3" size="5" label="maximum radius " help="-R"/>
+		<param name="max_dist_relations" type="integer" value="3" size="5" label="maximum distance relations" help="-D"/>
+	</inputs>
+	<outputs>
+		<data name="data_svector" format="zip" from_work_dir="SVECTOR/data.svector" label="data_svector"/>
+	</outputs>
+	<tests>
+		<test>
+			<param name="data_fasta" value="data.fasta"/>
+			<param name="gspan_file" value="1.group.gspan.bz2" ftype="searchgui_archive"/>
+			<param name="max_rad" value="3"/>
+			<param name="max_dist_relations" value="3"/>
+			<output name="data_svector" file="SVECTOR/data.svector" ftype="zip" />
+		</test>
+	</tests>
+	<help>
+		<![CDATA[
+
+**What it does**
+
+Produces an explicit sparse feature encoding.
+Integer code for the invariant graph encoding is used as a feature indicator. In this way,
+the integer associated to each feature (i.e. each pair or neighborhood subgraphs of radius r whose
+roots are at distance d) can be interpreted as the feature key and the (normalized) count of occurrences as its value.
+This allows to obtain an explicit feature encoding for a given graph G as a sparse vector in ℝ^m (with a very high dimension m).
+
+**Parameters**
+
++	**-R** <max radius> (default: 1)
++	**-D** <max distance relations> (default: 4)
+
+
+    ]]>
+	</help>
+	<citations>
+		<citation type="doi">10.1093/bioinformatics/bts224</citation>
+		<citation type="bibtex">@inproceedings{costa2010fast,
+      title={Fast neighborhood subgraph pairwise distance kernel},
+      author={Costa, Fabrizio and De Grave, Kurt},
+      booktitle={Proceedings of the 26th International Conference on Machine Learning},
+      pages={255--262},
+      year={2010},
+      organization={Omnipress}
+    }
+	</citation>
+	</citations>
+</tool>
Binary file test-data/1.group.gspan.bz2 has changed
Binary file test-data/SVECTOR/data.svector has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SVECTOR/data.svector.1.fast_cluster	Thu Dec 15 18:18:52 2016 -0500
@@ -0,0 +1,2 @@
+46 35 28 17 37 33 30 18 16 9 31 7 23 51 32 15 54 53 52 10 76 21 19 12 24 2 5 36 50 26 22 11 13 60 4 58 1 74 72 77 3 20 45 61 82 73 56 68 75 85 88 14 57 55 84 70 80 62 87 63 91 78 40 79 69 29 89 92 6 83 48 27 64 67 81 39 65 59 43 86 66 42 71 34 44 49 90 25 38 8 41 47 
+87 80 84 81 55 79 82 85 78 88 75 86 72 39 56 89 57 1 59 3 76 66 73 12 26 29 14 67 13 42 91 2 61 28 6 20 74 63 77 25 70 37 60 18 53 54 52 50 47 49 38 15 92 5 64 22 90 43 40 11 65 36 34 17 7 83 27 19 58 44 71 21 68 24 30 51 69 10 48 8 4 46 33 41 45 16 23 35 9 62 31 32 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SVECTOR/data.svector.1.fast_cluster_sim	Thu Dec 15 18:18:52 2016 -0500
@@ -0,0 +1,2 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/data.fasta	Thu Dec 15 18:18:52 2016 -0500
@@ -0,0 +1,184 @@
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+>4 SEQ4#1#73#+ ORIGID RF00005_rep.0_M15347.1/1040-968_4 ORIGHEAD RF00005_rep.0
+GGCUCCAUAGCUCAGGGGUUAGAGCACUGGUCUUGUAAACCAGGGGUCGCGAGUUCAAUUCUCGCUGGGGCUU
+>5 SEQ5#1#72#+ ORIGID RF00005_rep.10_X58792.1/174-245_5 ORIGHEAD RF00005_rep.10
+GGUCCCAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUGGGACCU
+>6 SEQ6#1#66#+ ORIGID RF00005_rep.11_AF346992.1/15890-15955_6 ORIGHEAD RF00005_rep.11
+GUCCUUGUAGUAUAAACUAAUACACCAGUCUUGUAAACCGGAGAUGAAAACCUUUUUCCAAGGACA
+>7 SEQ7#1#83#+ ORIGID RF00005_rep.12_AC108081.2/59868-59786_7 ORIGHEAD RF00005_rep.12
+GUCAGGAUGGCCGAGCGGUCUAAGGCGCUGCGUUCAGGUCGCAGUCUCCCCUGGAGGCGUGGGUUCGAAUCCCACUUCUGACA
+>8 SEQ8#1#70#+ ORIGID RF00005_rep.13_AC067849.6/4771-4840_8 ORIGHEAD RF00005_rep.13
+CACUGUAAAGCUAACUUAGCAUUAACCUUUUAAGUUAAAGAUUAAGAGAACCAACACCUCUUUACAGUGA
+>9 SEQ9#1#73#+ ORIGID RF00005_rep.14_AL021808.2/65570-65498_9 ORIGHEAD RF00005_rep.14
+GCUUCUGUAGUGUAGUGGUUAUCACGUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAAACCGGGCAGAAGCA
+>10 SEQ10#1#73#+ ORIGID RF00005_rep.15_AC008443.10/42590-42518_10 ORIGHEAD RF00005_rep.15
+GCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCG
+>11 SEQ11#1#82#+ ORIGID RF00005_rep.16_AL133551.13/12355-12436_11 ORIGHEAD RF00005_rep.16
+GCAGCGAUGGCCGAGUGGUUAAGGCGUUGGACUUGAAAUCCAAUGGGGUCUCCCCGCGCAGGUUCGAACCCUGCUCGCUGCG
+>12 SEQ12#1#82#+ ORIGID RF00005_rep.17_AL021918.1/54817-54736_12 ORIGHEAD RF00005_rep.17
+GUAGUCGUGGCCGAGUGGUUAAGGCGAUGGACUUGAAAUCCAUUGGGGUUUCCCCGCGCAGGUUCGAAUCCUGUCGGCUACG
+>13 SEQ13#1#82#+ ORIGID RF00005_rep.18_AL021918.1/81116-81197_13 ORIGHEAD RF00005_rep.18
+GUAGUCGUGGCCGAGUGGUUAAGGCGAUGGACUAGAAAUCCAUUGGGGUUUCCCCACGCAGGUUCGAAUCCUGCCGACUACG
+>14 SEQ14#1#73#+ ORIGID RF00005_rep.19_AF134583.1/1816-1744_14 ORIGHEAD RF00005_rep.19
+UAGAUUGAAGCCAGUUGAUUAGGGUGCUUAGCUGUUAACUAAGUGUUUGUGGGUUUAAGUCCCAUUGGUCUAG
+>15 SEQ15#1#73#+ ORIGID RF00005_rep.1_AC005329.1/7043-6971_15 ORIGHEAD RF00005_rep.1
+GCCGAAAUAGCUCAGUUGGGAGAGCGUUAGACUGAAGAUCUAAAGGUCCCUGGUUCGAUCCCGGGUUUCGGCA
+>16 SEQ16#1#72#+ ORIGID RF00005_rep.20_AL671879.2/100356-100285_16 ORIGHEAD RF00005_rep.20
+GGGGAUGUAGCUCAGUGGUAGAGCGCAUGCUUCGCAUGUAUGAGGCCCCGGGUUCGAUCCCCGGCAUCUCCA
+>17 SEQ17#1#71#+ ORIGID RF00005_rep.21_AL355149.13/15278-15208_17 ORIGHEAD RF00005_rep.21
+GCAUUGGUGGUUCAGUGGUAGAAUUCUCGCCUCCCACGCGGGAGACCCGGGUUCAAUUCCCGGCCAAUGCA
+>18 SEQ18#1#72#+ ORIGID RF00005_rep.22_AL590385.23/26487-26416_18 ORIGHEAD RF00005_rep.22
+GCGUUGGUGGUAUAGUGGUGAGCAUAGCUGCCUUCCAAGCAGUUGACCCGGGUUCGAUUCCCGGCCAACGCA
+>19 SEQ19#1#82#+ ORIGID RF00005_rep.23_M16479.1/42-123_19 ORIGHEAD RF00005_rep.23
+GGUGGGGUUCCCGAGCGGCCAAAGGGAGCAGACUCUAAAUCUGCCGUCAUCGACUUCGAAGGUUCGAAUCCUUCCCCCACCA
+>20 SEQ20#1#72#+ ORIGID RF00005_rep.24_AC004941.2/32735-32806_20 ORIGHEAD RF00005_rep.24
+GGGGGUAUAGCUCAGGGGUAGAGCAUUUGACUGCAGAUCAAGAGGUCCCUGGUUCAAAUCCAGGUGCCCCCU
+>21 SEQ21#1#74#+ ORIGID RF00005_rep.25_AC006449.19/196857-196784_21 ORIGHEAD RF00005_rep.25
+GUCUCUGUGGCGCAAUCGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGCCCACCCAGGGACG
+>22 SEQ22#1#72#+ ORIGID RF00005_rep.26_AF346999.1/4402-4331_22 ORIGHEAD RF00005_rep.26
+UAGGAUGGGGUGUGAUAGGUGGCACGGAGAAUUUUGGAUUCUCAGGGAUGGGUUCGAUUCUCAUAGUCCUAG
+>23 SEQ23#1#74#+ ORIGID RF00005_rep.27_AL352978.6/119697-119770_23 ORIGHEAD RF00005_rep.27
+GGCCGGUUAGCUCAGUUGGUUAGAGCGUGGUGCUAAUAACGCCAAGGUCGCGGGUUCGAUCCCCGUACGGGCCA
+>24 SEQ24#1#73#+ ORIGID RF00005_rep.28_X04779.1/1-73_24 ORIGHEAD RF00005_rep.28
+CCUUCGAUAGCUCAGCUGGUAGAGCGGAGGACUGUAGAUCCUUAGGUCGCUGGUUCGAUUCCGGCUCGAAGGA
+>25 SEQ25#1#69#+ ORIGID RF00005_rep.29_AF381996.2/4265-4333_25 ORIGHEAD RF00005_rep.29
+AGAAAUAUGUCUGAUAAAAGAGUUACUUUGAUAGAGUAAAUAAUAGGAGCUUAAACCCCCUUAUUUCUA
+>26 SEQ26#1#72#+ ORIGID RF00005_rep.2_AL662865.4/12206-12135_26 ORIGHEAD RF00005_rep.2
+GGUUCCAUGGUGUAAUGGUUAGCACUCUGGACUCUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUGGAACCU
+>27 SEQ27#1#69#+ ORIGID RF00005_rep.30_AL132988.4/95773-95841_27 ORIGHEAD RF00005_rep.30
+AAGGGCUUAGCUUAAUUAAAGUGGCUGAUUUGCGUUCAGUUGAUGCAGAGUGGGGUUUUGCAGUCCUUA
+>28 SEQ28#1#71#+ ORIGID RF00005_rep.31_AC092686.3/29631-29561_28 ORIGHEAD RF00005_rep.31
+GCAUUGGUGGUUCAGUGGUAGAAUUCUCGCCUGCCACGCGGGAGGCCCGGGUUCGAUUCCCGGCCAAUGCA
+>29 SEQ29#1#66#+ ORIGID RF00005_rep.32_AF347015.1/5892-5827_29 ORIGHEAD RF00005_rep.32
+GGUAAAAUGGCUGAGUGAAGCAUUGGACUGUAAAUCUAAAGACAGGGGUUAGGCCUCUUUUUACCA
+>30 SEQ30#1#72#+ ORIGID RF00005_rep.33_AC018638.5/4694-4623_30 ORIGHEAD RF00005_rep.33
+GGCUCGUUGGUCUAGGGGUAUGAUUCUCGCUUAGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGACGAGCCC
+>31 SEQ31#1#73#+ ORIGID RF00005_rep.34_AC008443.10/43006-42934_31 ORIGHEAD RF00005_rep.34
+GUUUCCGUAGUGUAGUGGUUAUCACGUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAAACCGGGCGGAAACA
+>32 SEQ32#1#73#+ ORIGID RF00005_rep.35_AC005783.1/27398-27326_32 ORIGHEAD RF00005_rep.35
+GUUUCCGUAGUGUAGCGGUUAUCACAUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAUCCCGGGCGGAAACA
+>33 SEQ33#1#72#+ ORIGID RF00005_rep.36_AC007298.17/145366-145295_33 ORIGHEAD RF00005_rep.36
+UCCUCGUUAGUAUAGUGGUGAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCGAUUCCCCGACGGGGAG
+>34 SEQ34#1#68#+ ORIGID RF00005_rep.37_AF347001.1/16015-15948_34 ORIGHEAD RF00005_rep.37
+CAGAGAAUAGUUUAAAUUAGAAUCUUAGCUUUGGGUGCUAAUGGUGGAGUUAAAGACUUUUUCUCUGA
+>35 SEQ35#1#72#+ ORIGID RF00005_rep.38_J00309.1/356-427_35 ORIGHEAD RF00005_rep.38
+UCCCUGGUGGUCUAGUGGCUAGGAUUCGGCGCUUUCACCGCCGCGCCCCGGGUUCGAUUCCCGGCCAGGAAU
+>36 SEQ36#1#73#+ ORIGID RF00005_rep.39_AL031229.2/40502-40430_36 ORIGHEAD RF00005_rep.39
+GUUUCCGUAGUGUAGUGGUUAUCACGUUCGCCUAACACGCGAAAGGUCCCUGGAUCAAAACCAGGCGGAAACA
+>37 SEQ37#1#82#+ ORIGID RF00005_rep.3_Z54587.1/126-45_37 ORIGHEAD RF00005_rep.3
+GGUAGCGUGGCCGAGCGGUCUAAGGCGCUGGAUUUAGGCUCCAGUCUCUUCGGAGGCGUGGGUUCGAAUCCCACCGCUGCCA
+>38 SEQ38#1#65#+ ORIGID RF00005_rep.40_AF382013.1/10403-10467_38 ORIGHEAD RF00005_rep.40
+UGGUAUAUAGUUUAAACAAAACGAAUGAUUUCGACUCAUUAAAUUAUGAUAAUCAUAUUUACCAA
+>39 SEQ39#1#69#+ ORIGID RF00005_rep.41_AC093311.2/140036-139968_39 ORIGHEAD RF00005_rep.41
+GUUCUUGUAGUUGAAAUACAACGAUGGUUUUUCAUAUCAUUGGUCGUGGUUGUAGUCCGUGCGAGAAUA
+>40 SEQ40#1#66#+ ORIGID RF00005_rep.42_AF347015.1/5827-5762_40 ORIGHEAD RF00005_rep.42
+AGCUCCGAGGUGAUUUUCAUAUUGAAUUGCAAAUUCGAAGAAGCAGCUUCAAACCUGCCGGGGCUU
+>41 SEQ41#1#68#+ ORIGID RF00005_rep.43_L23320.1/77-10_41 ORIGHEAD RF00005_rep.43
+ACUCUUUUAGUAUAAAUAGUACCGUUAACUUCCAAUUAACUAGUUUUGACAACAUUCAAAAAAGAGUA
+>42 SEQ42#1#69#+ ORIGID RF00005_rep.44_AC008670.6/83597-83665_42 ORIGHEAD RF00005_rep.44
+GUAAAUAUAGUUUAACCAAAACAUCAGAUUGUGAAUCUGACAACAGAGGCUCACGACCCCUUAUUUACC
+>43 SEQ43#1#71#+ ORIGID RF00005_rep.45_AF382005.1/581-651_43 ORIGHEAD RF00005_rep.45
+GUUUAUGUAGCUUACCUCCUCAAAGCAAUACACUGAAAAUGUUUAGACGGGCUCACAUCACCCCAUAAACA
+>44 SEQ44#1#69#+ ORIGID RF00005_rep.46_AF347015.1/1604-1672_44 ORIGHEAD RF00005_rep.46
+CAGAGUGUAGCUUAACACAAAGCACCCAACUUACACUUAGGAGAUUUCAACUUAACUUGACCGCUCUGA
+>45 SEQ45#1#72#+ ORIGID RF00005_rep.4_Z98744.2/66305-66234_45 ORIGHEAD RF00005_rep.4
+AGCAGAGUGGCGCAGCGGAAGCGUGCUGGGCCCAUAACCCAGAGGUCGAUGGAUCGAAACCAUCCUCUGCUA
+>46 SEQ46#1#72#+ ORIGID RF00005_rep.5_AL590385.23/26129-26058_46 ORIGHEAD RF00005_rep.5
+UCCCUGGUGGUCUAGUGGUUAGGAUUCGGCGCUCUCACCGCCGCGGCCCGGGUUCGAUUCCCGGUCAGGGAA
+>47 SEQ47#1#68#+ ORIGID RF00005_rep.6_X93334.1/6942-7009_47 ORIGHEAD RF00005_rep.6
+AAGGUAUUAGAAAAACCAUUUCAUAACUUUGUCAAAGUUAAAUUAUAGGCUAAAUCCUAUAUAUCUUA
+>48 SEQ48#1#71#+ ORIGID RF00005_rep.7_AF347005.1/12268-12338_48 ORIGHEAD RF00005_rep.7
+ACUUUUAAAGGAUAACAGCUAUCCAUUGGUCUUAGGCCCCAAAAAUUUUGGUGCAACUCCAAAUAAAAGUA
+>49 SEQ49#1#68#+ ORIGID RF00005_rep.8_AF134583.1/1599-1666_49 ORIGHEAD RF00005_rep.8
+AGAAAUUUAGGUUAAAUACAGACCAAGAGCCUUCAAAGCCCUCAGUAAGUUGCAAUACUUAAUUUCUG
+>50 SEQ50#1#73#+ ORIGID RF00005_rep.9_AP000442.6/2022-1950_50 ORIGHEAD RF00005_rep.9
+GCCCGGAUAGCUCAGUCGGUAGAGCAUCAGACUUUUAAUCUGAGGGUCCAGGGUUCAAGUCCCUGUUCGGGCG
+>51 SEQ51#1#88#+ ORIGID RF00006_rep.0_AF045145.1/1-88_51 ORIGHEAD RF00006_rep.0
+GGCUGGCUUUAGCUCAGCGGUUACUUCGCGUGUCAUCAAACCACCUCUCUGGGUUGUUCGAGACCCGCGGGCGCUCUCCAGCCCUCUU
+>52 SEQ52#1#101#+ ORIGID RF00006_rep.1_AC005219.1/49914-50014_52 ORIGHEAD RF00006_rep.1
+GGGUCGGAGUUAGCUCAAGCGGUUACCUCCUCAUGCCGGACUUUCUAUCUGUCCAUCUCUGUGCUGGGGUUCGAGACCCGCGGGUGCUUACUGACCCUUUU
+>53 SEQ53#1#98#+ ORIGID RF00006_rep.2_AF045143.1/1-98_53 ORIGHEAD RF00006_rep.2
+GGCUGGCUUUAGCUCAGCGGUUACUUCGACAGUUCUUUAAUUGAAACAAGCAACCUGUCUGGGUUGUUCGAGACCCGCGGGCGCUCUCCAGUCCUUUU
+>54 SEQ54#1#88#+ ORIGID RF00006_rep.3_AF045144.1/1-88_54 ORIGHEAD RF00006_rep.3
+GGCUGGCUUUAGCUCAGCGGUUACUUCGAGUACAUUGUAACCACCUCUCUGGGUGGUUCGAGACCCGCGGGUGCUUUCCAGCUCUUUU
+>55 SEQ55#1#113#+ ORIGID RF00019_rep.0_V00584.1/39-151_55 ORIGHEAD RF00019_rep.0
+GGCUGGUCCGAAGGUAGUGAGUUAUCUCAAUUGAUUGUUCACAGUCAGUUACAGAUCGAACUCCUUGUUCUACUCUUUCCCCCCUUCUCACUACUGCACUUGACUAGUCUUUU
+>56 SEQ56#1#95#+ ORIGID RF00019_rep.1_L32608.1/283-377_56 ORIGHEAD RF00019_rep.1
+GGCUGGUCCGAUGGUAGUGGGUUAUCAGAACUUAUUAACAUUAGUGUCACUAAAGUUGGUAUACAACCCCCCACUGCUAAAUUUGACUGGCUUUU
+>57 SEQ57#1#102#+ ORIGID RF00019_rep.2_ABBA01033605.1/1707-1808_57 ORIGHEAD RF00019_rep.2
+GGCUGGUCCGAGUGCAGUGGUGUUUACAACUAAUUGAUCACAACCAGUUACAGAUUUCUUUGUUCCUUCUCCACUCCCACUGCUUCACUUGACUAGCCUUUU
+>58 SEQ58#1#84#+ ORIGID RF00019_rep.3_AADD01087475.1/2469-2552_58 ORIGHEAD RF00019_rep.3
+AGUUGGUCCGAGUGUUGUGGGUUAUUGUUAAGUUGAUUUAACAUUGUCUCCCCCCACAACCGCGCUUGACUAGCUUGCUGUUUU
+>59 SEQ59#1#79#+ ORIGID RF00027_rep.0_AF480570.1/1-79_59 ORIGHEAD RF00027_rep.0
+GUGAGGUAGUAAGUUGUAUUGUUGUGGGGUAGGGAUAUUAGGCCCCAAUUAGAAGAUAACUAUACAACUUACUACUUUC
+>60 SEQ60#1#87#+ ORIGID RF00027_rep.1_AC048341.22/3536-3622_60 ORIGHEAD RF00027_rep.1
+CCUGGCUGAGGUAGUAGUUUGUGCUGUUGGUCGGGUUGUGACAUUGCCCGCUGUGGAGAUAACUGCGCAAGCUACUGCCUUGCUAGU
+>61 SEQ61#1#76#+ ORIGID RF00027_rep.2_AC018755.3/119936-120011_61 ORIGHEAD RF00027_rep.2
+CCGGGCUGAGGUAGGAGGUUGUAUAGUUGAGGAGGACACCCAAGGAGAUCACUAUACGGCCUCCUAGCUUUCCCCA
+>62 SEQ62#1#62#+ ORIGID RF00031_rep.0_X71973.1/730-791_62 ORIGHEAD RF00031_rep.0
+CCGGCACUCAUGACGGCCUGCCUGCAAACCUGCUGGUGGGGCAGACCCGAAAAUCCAGCGUG
+>63 SEQ63#1#68#+ ORIGID RF00031_rep.1_U67171.1/375-442_63 ORIGHEAD RF00031_rep.1
+GACGCUUCAUGAUAGGAAGGACUGAAAAGUCUUGUGGACACCUGGUCUUUCCCUGAUGUUCUCGUGGC
+>64 SEQ64#1#62#+ ORIGID RF00031_rep.2_S79854.1/1605-1666_64 ORIGHEAD RF00031_rep.2
+CACUGCUGAUGACGAACUAUCUCUAACUGGUCUUGACCACGAGCUAGUUCUGAAUUGCAGGG
+>65 SEQ65#1#57#+ ORIGID RF00031_rep.3_X53463.1/847-903_65 ORIGHEAD RF00031_rep.3
+UUCACAGAAUGAUGGCACCUUCCUAAACCCUCAUGGGUGGUGUCUGAGAGGCGUGAA
+>66 SEQ66#1#71#+ ORIGID RF00031_rep.4_AF195141.1/689-759_66 ORIGHEAD RF00031_rep.4
+GACUGACAUUAUGAAGGCCUGUACUGAAGACAGCAAGCUGUUAGUACAGACCAGAUGCUUUCUUGGCAGGC
+>67 SEQ67#1#66#+ ORIGID RF00031_rep.5_AF093774.1/5851-5916_67 ORIGHEAD RF00031_rep.5
+GUGUGCGGAUGAUAACUACUGACGAAAGAGUCAUCGACCUCAGUUAGUGGUUGGAUGUAGUCACAU
+>68 SEQ68#1#64#+ ORIGID RF00031_rep.6_BC003127.1/865-928_68 ORIGHEAD RF00031_rep.6
+GUCACUGCAUGAUCCGCUCUGGUCAAACCCUUCCAGGCCAGCCAGAGUGGGGAUGGUCUGUGAC
+>69 SEQ69#1#82#+ ORIGID RF00049_rep.0_X52138.1/3930-4011_69 ORIGHEAD RF00049_rep.0
+CAGCAGUCGAUCGUCAAAAUUUCUUCGGCCUCGAAAUUCACUCGUCGAAGAGUCAAAACCGAGCUUUUUAACACUGAGUCAG
+>70 SEQ70#1#68#+ ORIGID RF00049_rep.1_X97587.1/1-68_70 ORIGHEAD RF00049_rep.1
+UUGCCAAUGAUGGUUAAGAAUUUCUUCACCGUAAUAAACCAUGUGGUCAGCAUUGCAUCUGAGGCAAA
+>71 SEQ71#1#76#+ ORIGID RF00049_rep.2_X61923.1/2094-2169_71 ORIGHEAD RF00049_rep.2
+UAGCAGUCGAUGUCAAAAUUUCUUGGCUCGAAAUUACUGUGAAGAGUAAAAUCGAGCUUUUUAAGAGUGAGUCAGC
+>72 SEQ72#1#126#+ ORIGID RF00618_rep.0_AL135914.25/92223-92098_72 ORIGHEAD RF00618_rep.0
+ACCAUCCUUUUCUUGGGGUUGCACUACUGUCCAAUGGGUACCUAGUGAGGGCAGUACUGCUAACUCCUGCACAACACACCGAAAUCAACUAGAGCUUUGCUUUGCCUUGGUGCAGUUUUUGGAGAA
+>73 SEQ73#1#126#+ ORIGID RF00618_rep.1_AL161445.10/77816-77941_73 ORIGHEAD RF00618_rep.1
+ACCAUCCUUUUCUUGGGGUUGCACUACUGUCCAAAGAGCAUGUAGUGAGGGCAGUACUGCUAACGUCUACACAACACACCCACCUCAACUAGAGCUUUGCUUUAGCUUGGUGUAAUUUUUGGAAAA
+>74 SEQ74#1#127#+ ORIGID RF00618_rep.2_U62822.1/2-128_74 ORIGHEAD RF00618_rep.2
+ACCAUCCUUUUCUUGGGGUUGCGCUACUGUCCAAUGAGCGCAUAGUGAGGGCAGUACUGCUAACGCCUGAACAACACACCCGCAUCAACUAGAGCUUUUGCUUUAUUUUGGUGCAAUUUUUGGAAAA
+>75 SEQ75#1#126#+ ORIGID RF00618_rep.3_AL389925.10/20736-20611_75 ORIGHEAD RF00618_rep.3
+ACCAUCCUUUUCUUGGGGUUGCACUACUGUCUAAUGAGUGCAUAAUGAGGGCAGUAUUGCUAACGCCUAUACAAUGCACCUGCAUCAACUAGAACUUUGCUUUACCUUGGUACAAUUUUUGGAAAA
+>76 SEQ76#1#79#+ ORIGID RF00641_rep.0_AL132709.5/95865-95787_76 ORIGHEAD RF00641_rep.0
+GGUACUUGGAGAGAGGUGGUCCGUGGCGCGUUCGCUUUAUUUAUGGCGCACAUUACACGGUCGACCUCUUUGCAGUAUC
+>77 SEQ77#1#77#+ ORIGID RF00641_rep.10_AADD01141100.1/2839-2915_77 ORIGHEAD RF00641_rep.10
+GGUACUCGGGGAGAGGUUACCCGAGCAACUUUGCAUCUGGACGACGAAUGUUGCUCGGUGAACCCCUUUUCGGUAUC
+>78 SEQ78#1#80#+ ORIGID RF00641_rep.11_AC208187.2/25743-25822_78 ORIGHEAD RF00641_rep.11
+GGUAUUUGAAGAUGCGGUUGACCAUGGUGUGUACGCUUUAUUUGUGACGUAGGACACAUGGUCUACUUCUUCUCAAUAUC
+>79 SEQ79#1#79#+ ORIGID RF00641_rep.12_AL132709.5/56006-55928_79 ORIGHEAD RF00641_rep.12
+GGUACUUGAAGGGAGAUCGACCGUGUUAUAUUCGCUUUAUUGACUUCGAAUAAUACAUGGUUGAUCUUUUCUCAGUAUC
+>80 SEQ80#1#79#+ ORIGID RF00641_rep.13_AL132709.5/55165-55087_80 ORIGHEAD RF00641_rep.13
+GGUGCCUGAGGAGAGGUGGCCUGUGUUGCAUUCACAGAAAUCAUGACACACAAGACACGAGCGGCCUCUCUUCAGUAUC
+>81 SEQ81#1#77#+ ORIGID RF00641_rep.1_AL132709.5/86350-86274_81 ORIGHEAD RF00641_rep.1
+GGUACUGGAGGAGAGGUUAUCUGUGUUUUUUCCCUUUAUUUAUGAUGAAAAAUAUGGUGCACUUCUAUUUGAGAAUC
+>82 SEQ82#1#81#+ ORIGID RF00641_rep.2_AC208187.2/29806-29886_82 ORIGHEAD RF00641_rep.2
+GAUACUCGAAGGAGAGGUUGUCCGUGUUGUCUUCUCUUUAUUUAUGAUGAAACAUACACGGGAAACCUCUUUUUUAGUAUC
+>83 SEQ83#1#79#+ ORIGID RF00641_rep.3_AADD01141098.1/2614-2692_83 ORIGHEAD RF00641_rep.3
+GCUACUUGAAGAGAGGUAAUCCUUCAUGCAUUUGCUUUACUUGCAAUGAUUAUACAAGGGCAGACUCUCUCUGGGGAGC
+>84 SEQ84#1#79#+ ORIGID RF00641_rep.4_ABBA01048514.1/248685-248607_84 ORIGHEAD RF00641_rep.4
+GGUACUCGAAUGGAGGUUGUCCAUGGUGUGUUCAUUUUAUUUAUGAUGAGUAUUACAUGGCCAAUCUCCUUUCGGUACU
+>85 SEQ85#1#79#+ ORIGID RF00641_rep.5_AL132709.5/73699-73621_85 ORIGHEAD RF00641_rep.5
+GGUGCUUAAAGAAUGGCUGUCCGUAGUAUGGUCUCUAUAUUUAUGAUGAUUAAUAUCGGACAACCAUUGUUUUAGUAUC
+>86 SEQ86#1#79#+ ORIGID RF00641_rep.6_AADB02234051.1/94-172_86 ORIGHEAD RF00641_rep.6
+GGUACUUAAGGGGGAGGUGGGCUUUGAAUAAUAAGUUUAUUGACGUGGAAUAUACAAGGGCAAGCUCUCUGUGAGUAUC
+>87 SEQ87#1#78#+ ORIGID RF00641_rep.7_AL132709.5/54880-54803_87 ORIGHEAD RF00641_rep.7
+GGUACCUGAAAUAGGUUGCCUGUGAGGUGUUCACUUUCUAUAUGAUGAAUAUUAUACAGUCAACCUCUUUCCGAUAUC
+>88 SEQ88#1#81#+ ORIGID RF00641_rep.8_AL132709.5/61554-61474_88 ORIGHEAD RF00641_rep.8
+GGUACUGGUGGAGAGGUCUUCCAUGAUGCAUUCGAUUUAUUUUUUGACCAAUCCUACAUAGUGGACUCUUUUGAAAGCAUU
+>89 SEQ89#1#80#+ ORIGID RF00641_rep.9_AL132709.5/98273-98194_89 ORIGHEAD RF00641_rep.9
+GGUACUUGGAGAGAUAGUAGACCGUAUAGCGUACGCUUUAUCUGUGACGUAUGUAACACGGUCCACUAACCCUCAGUAUC
+>90 SEQ90#1#66#+ ORIGID RF00693_rep.0_AADD01093451.1/1636-1571_90 ORIGHEAD RF00693_rep.0
+AAUCUUAUGGAAACAUUUCUGCACACAAUAAAGAAACUAGUGUACAGAAAUGUUUACUUGUCUAUG
+>91 SEQ91#1#69#+ ORIGID RF00693_rep.1_AL031669.28/23303-23371_91 ORIGHEAD RF00693_rep.1
+GGUCUAGUGGAAACAUUUCUGCACAACCAGAAUACUCAAACUAGCAUGAGGAAAGGCUUCUGUAACAGU
+>92 SEQ92#1#69#+ ORIGID RF00693_rep.2_ABBA01075050.1/41249-41181_92 ORIGHEAD RF00693_rep.2
+UAUUUCGUGGAUGAUUUCUACACAGACUAGGCCAUAGAAACCAGUGCGUAGAAAUGCUUCUGUUACAUG
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/data.names	Thu Dec 15 18:18:52 2016 -0500
@@ -0,0 +1,92 @@
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Binary file test-data/data.svector.1 has changed