# HG changeset patch
# User rnateam
# Date 1481891689 18000
# Node ID b797e13169a0b072d8e10dd7bdca449d4db43f6d

planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit 21aaee40723b5341b4236edeb0e72995c2054053

diff -r 000000000000 -r b797e13169a0 evaluation.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/evaluation.py	Fri Dec 16 07:34:49 2016 -0500
@@ -0,0 +1,51 @@
+import glob
+from os import system
+import re
+
+
+def sh(script):
+    system("bash -c '%s'" % script)
+
+
+dataNames = "FASTA/data.names"
+listOfClusters = []
+listOfClasses = []
+cluster_seqs_stats_path = "RESULTS/*.cluster.all"
+cluster_seqs_stats_files = glob.glob(cluster_seqs_stats_path)
+
+blackList = []
+numberOfClusters = 0
+for singleFile in sorted(cluster_seqs_stats_files):
+    numberOfClusters += 1
+    with open(singleFile, "r") as f:
+        for line in f.readlines():
+            uniqueId = line.split()[6]
+            clustNum = line.split()[1]
+            rnaClass, sep, tail = uniqueId.partition("_")
+            listOfClasses.append(rnaClass)
+            listOfClusters.append(clustNum)
+            with open(dataNames, "r") as names:
+                for line in names.readlines():
+                    fullUniqeId = line.split()[3]
+                    rnaClass, sep, tail = fullUniqeId.partition("_")
+                    short_unique = re.findall("_".join(["[^_]+"] * 2), fullUniqeId)[0]
+                    if short_unique == uniqueId:
+                        blackList.append(uniqueId)
+
+numberOfClusters += 1  # 1 cluster for all unassigned seqs
+with open(dataNames, "r") as names:
+    for line in names.readlines():
+        fullUniqeId = line.split()[3]
+        rnaClass, sep, tail = fullUniqeId.partition("_")
+        short_unique = re.findall("_".join(["[^_]+"] * 2), fullUniqeId)[0]
+        rnaClass, sep, tail = fullUniqeId.partition("_")
+        if short_unique not in blackList:
+            listOfClasses.append(rnaClass)
+            listOfClusters.append(str(numberOfClusters))
+            numberOfClusters += 1  # separate cluster for all unassigned seqs
+
+toWrite = ""
+for i in range(len(listOfClusters)):
+    toWrite += listOfClasses[i] + "\t" + listOfClusters[i] + '\n'
+with open("RESULTS/fullTab.tabular", "w") as full:
+    full.write(toWrite)
diff -r 000000000000 -r b797e13169a0 glob_report.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/glob_report.xml	Fri Dec 16 07:34:49 2016 -0500
@@ -0,0 +1,139 @@
+<tool id="glob_report" name="Report_Results" version="0.1">
+	<requirements>
+		<requirement type="package" version="0.1">graphclust-wrappers</requirement>
+		<requirement type="package" version='0.5'>perl-array-utils</requirement>
+	</requirements>
+	<stdio>
+		<exit_code range="1:" />
+	</stdio>
+	<command>
+		<![CDATA[
+
+        unzip $FASTA  &> /dev/null &&
+
+        #set $inputFiles = ""
+
+        #for $cms_res in $cmsearch_results:
+            #set $inputFiles += str($cms_res)+','
+        #end for
+        #set $inputFiles = $inputFiles[:-1]
+
+        #set $inputFilesTrees = ""
+
+        #for $mods in $model_tree_files:
+            #set $inputFilesTrees += str($mods)+','
+        #end for
+        #set $inputFilesTrees = $inputFilesTrees[:-1]
+
+		    'glob_res.pl' '$inputFiles' $merge_cluster_ol $merge_overlap $min_cluster_size $cm_min_bitscore $cm_max_eval $cm_bitscore_sig $partition_type '' $cut_type '$inputFilesTrees'
+        #if  $iteration_num.iteration_num_selector:
+          $iteration_num.CI
+
+          $final_partition_soft
+          $final_partition_used_cmsearch
+        #end if
+
+        &&
+        python '$__tool_directory__/evaluation.py'
+]]>
+	</command>
+	<inputs>
+		<param type="data" name="FASTA" format="zip" />
+		<param type="data" name="cmsearch_results" format="tabular" multiple="True"/>
+		<param type="data" name="model_tree_files" format="txt" multiple="True"/>
+		<param name="partition_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Hard partition"/>
+		<param name="cut_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Use CM score for cutoff" help="otherwise use E-value"/>
+		<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="final_partition_soft" format="txt" />
+				<param type="data" name="final_partition_used_cmsearch" format="txt" />
+			</when>
+			<when value="false" ></when>
+		</conditional>
+		<param name="merge_cluster_ol" type="float" value="0.66" size="5" label="merge_cluster_ol" help=""/>
+		<param name="merge_overlap" type="float" value="0.51" size="5" label="merge_overlap" help=""/>
+		<param name="min_cluster_size" type="integer" value="3" size="5" label="min_cluster_size" help=""/>
+		<param name="cm_min_bitscore" type="integer" value="20" size="5" label="cm_min_bitscore" help=""/>
+		<param name="cm_max_eval" type="float" value="0.001" size="5" label="cm_max_eval" help=""/>
+		<param name="cm_bitscore_sig" type="integer" value="1" size="5" label="cm_bitscore_sig" help=""/>
+	</inputs>
+	<outputs>
+		<data name="final_stats" format="txt" from_work_dir="RESULTS/cluster.final.stats" label="cluster.final.stats"  />
+		<data name="tableForEval" format="tabular" from_work_dir="RESULTS/fullTab.tabular" label="tableForEval"  />
+		<data name="final_soft" format="txt" from_work_dir="RESULTS/partitions/final_partition.soft" label="soft_part"   />
+		<data name="final_used_cmsearch" format="txt" from_work_dir="RESULTS/partitions/final_partition.used_cmsearch" label="final_partition_used_cmsearch"   />
+		<collection name="clusters" type="list" label="CLUSTERS">
+			<discover_datasets pattern="(?P&lt;name&gt;^.*\.all$)" directory="RESULTS"  />
+		</collection>
+		<collection name="partitions" type="list" label="Partitions">
+			<discover_datasets pattern="(?P&lt;name&gt;^.*$)" directory="RESULTS/partitions" />
+		</collection>
+	</outputs>
+	<tests>
+		<test>
+			<param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/>
+			<param name="cmsearch_results" value="1.tabular,2.tabular"/>
+			<param name="model_tree_files" value="1.1.model.tree.fa,1.2.model.tree.fa"/>
+			<param name="partition_type" value="0"/>
+			<param name="cut_type" value="0"/>
+			<conditional name="iteration_num">
+				<param name="iteration_num_selector" value="false"/>
+			</conditional>
+			<param name="merge_cluster_ol" value="0.66"/>
+			<param name="merge_overlap" value="0.51"/>
+			<param name="min_cluster_size" value="3"/>
+			<param name="cm_min_bitscore" value="20"/>
+			<param name="cm_max_eval" value="0.001"/>
+			<param name="cm_bitscore_sig" value="1"/>
+			<output name="final_stats" file="RESULTS/cluster.final.stats" />
+			<output_collection name="clusters" type="list">
+				<element name="1.cluster.all" file="RESULTS/1.cluster.all" compare="contains"/>
+				<element name="2.cluster.all" file="RESULTS/2.cluster.all" compare="contains"/>
+			</output_collection>
+			<output_collection name="partitions">
+				<element name="final_overlap.map" file="RESULTS/partitions/final_overlap.map" compare="contains">
+					<assert_contents>
+						<has_text text="1.1  1.1" />
+						<has_text text="1.2  1.2" />
+					</assert_contents>
+				</element>
+				<element name="final_overlap.matrix" file="RESULTS/partitions/final_overlap.matrix" compare="contains">
+					<assert_contents>
+						<has_text text="MODEL CLASS 0 0" />
+						<has_text text="1.2" />
+						<has_text text="1.1" />
+					</assert_contents>
+				</element>
+				<element name="final_partition.hard.best" file="RESULTS/partitions/final_partition.hard.best" />
+				<element name="final_partition.hard.merged" file="RESULTS/partitions/final_partition.hard.merged" />
+				<element name="final_partition.soft" file="RESULTS/partitions/final_partition.soft" />
+				<element name="final_partition.used_cmsearch" file="RESULTS/partitions/final_partition.used_cmsearch" compare="contains"/>
+			</output_collection>
+		</test>
+	</tests>
+	<help>
+		<![CDATA[
+
+**What it does**
+
+Post-processing. Redundant clusters are merged and instances that belong to multiple clusters
+are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of
+instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.
+Cluster members are finally ranked by their CM bitscore.
+
+    ]]>
+	</help>
+	<citations>
+    <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>
diff -r 000000000000 -r b797e13169a0 test-data/1.1.model.tree.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.1.model.tree.fa	Fri Dec 16 07:34:49 2016 -0500
@@ -0,0 +1,40 @@
+>7 SEQ7#1#83#+ ORIGID RF00005_rep.12_AC108081.2/59868-59786_7 ORIGHEAD RF00005_rep.12
+GUCAGGAUGGCCGAGCGGUCUAAGGCGCUGCGUUCAGGUCGCAGUCUCCCCUGGAGGCGUGGGUUCGAAUCCCACUUCUGACA
+>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
+>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
+>23 SEQ23#1#74#+ ORIGID RF00005_rep.27_AL352978.6/119697-119770_23 ORIGHEAD RF00005_rep.27
+GGCCGGUUAGCUCAGUUGGUUAGAGCGUGGUGCUAAUAACGCCAAGGUCGCGGGUUCGAUCCCCGUACGGGCCA
+>28 SEQ28#1#71#+ ORIGID RF00005_rep.31_AC092686.3/29631-29561_28 ORIGHEAD RF00005_rep.31
+GCAUUGGUGGUUCAGUGGUAGAAUUCUCGCCUGCCACGCGGGAGGCCCGGGUUCGAUUCCCGGCCAAUGCA
+>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
+>35 SEQ35#1#72#+ ORIGID RF00005_rep.38_J00309.1/356-427_35 ORIGHEAD RF00005_rep.38
+UCCCUGGUGGUCUAGUGGCUAGGAUUCGGCGCUUUCACCGCCGCGCCCCGGGUUCGAUUCCCGGCCAGGAAU
+>37 SEQ37#1#82#+ ORIGID RF00005_rep.3_Z54587.1/126-45_37 ORIGHEAD RF00005_rep.3
+GGUAGCGUGGCCGAGCGGUCUAAGGCGCUGGAUUUAGGCUCCAGUCUCUUCGGAGGCGUGGGUUCGAAUCCCACCGCUGCCA
+>46 SEQ46#1#72#+ ORIGID RF00005_rep.5_AL590385.23/26129-26058_46 ORIGHEAD RF00005_rep.5
+UCCCUGGUGGUCUAGUGGUUAGGAUUCGGCGCUCUCACCGCCGCGGCCCGGGUUCGAUUCCCGGUCAGGGAA
+>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
diff -r 000000000000 -r b797e13169a0 test-data/1.2.model.tree.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.2.model.tree.fa	Fri Dec 16 07:34:49 2016 -0500
@@ -0,0 +1,40 @@
+>1 SEQ1#1#120#+ ORIGID RF00001_rep.0_AL096764.11/46123-46004_1 ORIGHEAD RF00001_rep.0
+GUCUAUGGCCAUACCACCCUGAAUGUGCUUGAUCUCAUCUGAUCUCGUGAAGCCAAGCAGGGUGGGGCCUAGUUAGUACUUGGAUGGGAGACUUCCUGGGAAUAUAAGCUGCUGUUGGCU
+>3 SEQ3#1#104#+ ORIGID RF00001_rep.2_AJ508600.1/161-58_3 ORIGHEAD RF00001_rep.2
+GUCUACAGCCAUACCAUCCUGAACAUGCCAGAUCUUGUCUGACCUCUGAAGCUAAGCAGGGUCAAGCCUGGUUAGUACUUGGGAGAAGCUGGUGUGGCUAGACC
+>39 SEQ39#1#69#+ ORIGID RF00005_rep.41_AC093311.2/140036-139968_39 ORIGHEAD RF00005_rep.41
+GUUCUUGUAGUUGAAAUACAACGAUGGUUUUUCAUAUCAUUGGUCGUGGUUGUAGUCCGUGCGAGAAUA
+>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
+>59 SEQ59#1#79#+ ORIGID RF00027_rep.0_AF480570.1/1-79_59 ORIGHEAD RF00027_rep.0
+GUGAGGUAGUAAGUUGUAUUGUUGUGGGGUAGGGAUAUUAGGCCCCAAUUAGAAGAUAACUAUACAACUUACUACUUUC
+>72 SEQ72#1#126#+ ORIGID RF00618_rep.0_AL135914.25/92223-92098_72 ORIGHEAD RF00618_rep.0
+ACCAUCCUUUUCUUGGGGUUGCACUACUGUCCAAUGGGUACCUAGUGAGGGCAGUACUGCUAACUCCUGCACAACACACCGAAAUCAACUAGAGCUUUGCUUUGCCUUGGUGCAGUUUUUGGAGAA
+>75 SEQ75#1#126#+ ORIGID RF00618_rep.3_AL389925.10/20736-20611_75 ORIGHEAD RF00618_rep.3
+ACCAUCCUUUUCUUGGGGUUGCACUACUGUCUAAUGAGUGCAUAAUGAGGGCAGUAUUGCUAACGCCUAUACAAUGCACCUGCAUCAACUAGAACUUUGCUUUACCUUGGUACAAUUUUUGGAAAA
+>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
+>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
diff -r 000000000000 -r b797e13169a0 test-data/1.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.tabular	Fri Dec 16 07:34:49 2016 -0500
@@ -0,0 +1,46 @@
+SEQ11	-	dataset_2087	-	cm	1	72	1	82	+	no	1	0.62	0.0	88.8	1.1e-38	!	ORIGID RF00005_rep.16_AL133551.13/12355-12436_11 ORIGHEAD RF00005_rep.16
+SEQ13	-	dataset_2087	-	cm	1	72	1	82	+	no	1	0.56	0.0	87.5	3.5e-38	!	ORIGID RF00005_rep.18_AL021918.1/81116-81197_13 ORIGHEAD RF00005_rep.18
+SEQ31	-	dataset_2087	-	cm	1	72	1	73	+	no	1	0.56	0.0	84.9	3.1e-37	!	ORIGID RF00005_rep.34_AC008443.10/43006-42934_31 ORIGHEAD RF00005_rep.34
+SEQ37	-	dataset_2087	-	cm	1	72	1	82	+	no	1	0.63	0.0	84.9	3.4e-37	!	ORIGID RF00005_rep.3_Z54587.1/126-45_37 ORIGHEAD RF00005_rep.3
+SEQ12	-	dataset_2087	-	cm	1	72	1	82	+	no	1	0.57	0.0	84.8	3.7e-37	!	ORIGID RF00005_rep.17_AL021918.1/54817-54736_12 ORIGHEAD RF00005_rep.17
+SEQ9	-	dataset_2087	-	cm	1	72	1	73	+	no	1	0.56	0.0	83.8	8.7e-37	!	ORIGID RF00005_rep.14_AL021808.2/65570-65498_9 ORIGHEAD RF00005_rep.14
+SEQ32	-	dataset_2087	-	cm	1	72	1	73	+	no	1	0.58	0.0	82.5	2.6e-36	!	ORIGID RF00005_rep.35_AC005783.1/27398-27326_32 ORIGHEAD RF00005_rep.35
+SEQ28	-	dataset_2087	-	cm	1	72	1	71	+	no	1	0.62	0.0	82.4	3e-36	!	ORIGID RF00005_rep.31_AC092686.3/29631-29561_28 ORIGHEAD RF00005_rep.31
+SEQ7	-	dataset_2087	-	cm	1	72	1	83	+	no	1	0.63	0.0	81.0	9.6e-36	!	ORIGID RF00005_rep.12_AC108081.2/59868-59786_7 ORIGHEAD RF00005_rep.12
+SEQ46	-	dataset_2087	-	cm	1	72	1	72	+	no	1	0.65	0.0	80.9	1.1e-35	!	ORIGID RF00005_rep.5_AL590385.23/26129-26058_46 ORIGHEAD RF00005_rep.5
+SEQ26	-	dataset_2087	-	cm	1	72	1	72	+	no	1	0.50	0.0	80.0	2.4e-35	!	ORIGID RF00005_rep.2_AL662865.4/12206-12135_26 ORIGHEAD RF00005_rep.2
+SEQ5	-	dataset_2087	-	cm	1	72	1	72	+	no	1	0.51	0.0	79.6	3.2e-35	!	ORIGID RF00005_rep.10_X58792.1/174-245_5 ORIGHEAD RF00005_rep.10
+SEQ24	-	dataset_2087	-	cm	1	72	1	73	+	no	1	0.56	0.0	79.0	5.6e-35	!	ORIGID RF00005_rep.28_X04779.1/1-73_24 ORIGHEAD RF00005_rep.28
+SEQ17	-	dataset_2087	-	cm	1	72	1	71	+	no	1	0.59	0.0	78.9	6.2e-35	!	ORIGID RF00005_rep.21_AL355149.13/15278-15208_17 ORIGHEAD RF00005_rep.21
+SEQ36	-	dataset_2087	-	cm	1	72	1	73	+	no	1	0.51	0.0	78.5	8.3e-35	!	ORIGID RF00005_rep.39_AL031229.2/40502-40430_36 ORIGHEAD RF00005_rep.39
+SEQ50	-	dataset_2087	-	cm	1	72	1	73	+	no	1	0.56	0.0	78.4	9.1e-35	!	ORIGID RF00005_rep.9_AP000442.6/2022-1950_50 ORIGHEAD RF00005_rep.9
+SEQ15	-	dataset_2087	-	cm	1	72	1	73	+	no	1	0.53	0.0	76.6	4.5e-34	!	ORIGID RF00005_rep.1_AC005329.1/7043-6971_15 ORIGHEAD RF00005_rep.1
+SEQ21	-	dataset_2087	-	cm	1	72	1	74	+	no	1	0.61	0.0	76.3	5.7e-34	!	ORIGID RF00005_rep.25_AC006449.19/196857-196784_21 ORIGHEAD RF00005_rep.25
+SEQ23	-	dataset_2087	-	cm	1	72	1	74	+	no	1	0.61	0.0	76.3	5.7e-34	!	ORIGID RF00005_rep.27_AL352978.6/119697-119770_23 ORIGHEAD RF00005_rep.27
+SEQ4	-	dataset_2087	-	cm	1	72	1	73	+	no	1	0.56	0.0	75.1	1.7e-33	!	ORIGID RF00005_rep.0_M15347.1/1040-968_4 ORIGHEAD RF00005_rep.0
+SEQ16	-	dataset_2087	-	cm	1	72	1	72	+	no	1	0.61	0.0	74.7	2.3e-33	!	ORIGID RF00005_rep.20_AL671879.2/100356-100285_16 ORIGHEAD RF00005_rep.20
+SEQ18	-	dataset_2087	-	cm	1	72	1	72	+	no	1	0.58	0.0	73.6	6.2e-33	!	ORIGID RF00005_rep.22_AL590385.23/26487-26416_18 ORIGHEAD RF00005_rep.22
+SEQ10	-	dataset_2087	-	cm	1	72	1	73	+	no	1	0.62	0.0	73.3	8.3e-33	!	ORIGID RF00005_rep.15_AC008443.10/42590-42518_10 ORIGHEAD RF00005_rep.15
+SEQ20	-	dataset_2087	-	cm	1	72	1	72	+	no	1	0.56	0.0	73.3	8.3e-33	!	ORIGID RF00005_rep.24_AC004941.2/32735-32806_20 ORIGHEAD RF00005_rep.24
+SEQ30	-	dataset_2087	-	cm	1	72	1	72	+	no	1	0.61	0.0	72.3	1.9e-32	!	ORIGID RF00005_rep.33_AC018638.5/4694-4623_30 ORIGHEAD RF00005_rep.33
+SEQ35	-	dataset_2087	-	cm	1	72	1	72	+	no	1	0.65	0.0	71.7	3.2e-32	!	ORIGID RF00005_rep.38_J00309.1/356-427_35 ORIGHEAD RF00005_rep.38
+SEQ19	-	dataset_2087	-	cm	1	72	1	82	+	no	1	0.59	0.0	69.4	2.5e-31	!	ORIGID RF00005_rep.23_M16479.1/42-123_19 ORIGHEAD RF00005_rep.23
+SEQ33	-	dataset_2087	-	cm	1	72	1	72	+	no	1	0.62	0.0	69.3	2.5e-31	!	ORIGID RF00005_rep.36_AC007298.17/145366-145295_33 ORIGHEAD RF00005_rep.36
+SEQ45	-	dataset_2087	-	cm	1	72	1	72	+	no	1	0.60	0.0	69.3	2.7e-31	!	ORIGID RF00005_rep.4_Z98744.2/66305-66234_45 ORIGHEAD RF00005_rep.4
+SEQ22	-	dataset_2087	-	cm	1	72	1	72	+	no	1	0.49	0.0	47.8	3.6e-23	!	ORIGID RF00005_rep.26_AF346999.1/4402-4331_22 ORIGHEAD RF00005_rep.26
+SEQ14	-	dataset_2087	-	cm	1	72	2	72	+	no	1	0.41	0.0	45.6	2.5e-22	!	ORIGID RF00005_rep.19_AF134583.1/1816-1744_14 ORIGHEAD RF00005_rep.19
+SEQ29	-	dataset_2087	-	cm	1	72	1	66	+	no	1	0.42	0.0	34.4	4.1e-18	!	ORIGID RF00005_rep.32_AF347015.1/5892-5827_29 ORIGHEAD RF00005_rep.32
+SEQ39	-	dataset_2087	-	cm	1	72	1	69	+	no	1	0.39	0.0	21.4	3.5e-13	!	ORIGID RF00005_rep.41_AC093311.2/140036-139968_39 ORIGHEAD RF00005_rep.41
+SEQ40	-	dataset_2087	-	cm	1	72	1	66	+	no	1	0.45	0.0	17.8	8e-12	!	ORIGID RF00005_rep.42_AF347015.1/5827-5762_40 ORIGHEAD RF00005_rep.42
+SEQ34	-	dataset_2087	-	cm	1	72	1	68	+	no	1	0.34	0.0	13.6	3.4e-10	!	ORIGID RF00005_rep.37_AF347001.1/16015-15948_34 ORIGHEAD RF00005_rep.37
+SEQ42	-	dataset_2087	-	cm	1	72	1	69	+	no	1	0.38	0.0	13.1	5e-10	!	ORIGID RF00005_rep.44_AC008670.6/83597-83665_42 ORIGHEAD RF00005_rep.44
+SEQ6	-	dataset_2087	-	cm	1	72	1	66	+	no	1	0.38	0.0	10.1	6.6e-09	!	ORIGID RF00005_rep.11_AF346992.1/15890-15955_6 ORIGHEAD RF00005_rep.11
+SEQ27	-	dataset_2087	-	cm	1	72	1	69	+	no	1	0.43	0.0	8.0	4.3e-08	!	ORIGID RF00005_rep.30_AL132988.4/95773-95841_27 ORIGHEAD RF00005_rep.30
+SEQ48	-	dataset_2087	-	cm	1	72	1	71	+	no	1	0.35	0.0	6.7	1.3e-07	!	ORIGID RF00005_rep.7_AF347005.1/12268-12338_48 ORIGHEAD RF00005_rep.7
+SEQ41	-	dataset_2087	-	cm	1	72	1	68	+	no	1	0.26	0.1	6.3	1.9e-07	!	ORIGID RF00005_rep.43_L23320.1/77-10_41 ORIGHEAD RF00005_rep.43
+SEQ25	-	dataset_2087	-	cm	1	72	1	69	+	no	1	0.29	0.0	5.3	4.5e-07	!	ORIGID RF00005_rep.29_AF381996.2/4265-4333_25 ORIGHEAD RF00005_rep.29
+SEQ43	-	dataset_2087	-	cm	1	72	1	71	+	no	1	0.41	0.0	4.7	7.6e-07	!	ORIGID RF00005_rep.45_AF382005.1/581-651_43 ORIGHEAD RF00005_rep.45
+SEQ8	-	dataset_2087	-	cm	1	72	1	70	+	no	1	0.33	0.0	3.1	3.1e-06	!	ORIGID RF00005_rep.13_AC067849.6/4771-4840_8 ORIGHEAD RF00005_rep.13
+SEQ44	-	dataset_2087	-	cm	1	72	1	69	+	no	1	0.42	0.0	0.7	2.5e-05	!	ORIGID RF00005_rep.46_AF347015.1/1604-1672_44 ORIGHEAD RF00005_rep.46
+SEQ38	-	dataset_2087	-	cm	1	72	1	65	+	no	1	0.23	0.5	-0.9	0.0001	!	ORIGID RF00005_rep.40_AF382013.1/10403-10467_38 ORIGHEAD RF00005_rep.40
+SEQ47	-	dataset_2087	-	cm	1	72	1	68	+	no	1	0.24	0.5	-5.2	0.0044	!	ORIGID RF00005_rep.6_X93334.1/6942-7009_47 ORIGHEAD RF00005_rep.6
diff -r 000000000000 -r b797e13169a0 test-data/2.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/2.tabular	Fri Dec 16 07:34:49 2016 -0500
@@ -0,0 +1,14 @@
+SEQ82	-	dataset_2088	-	cm	1	80	1	81	+	no	1	0.38	0.0	86.6	1.9e-28	!	ORIGID RF00641_rep.2_AC208187.2/29806-29886_82 ORIGHEAD RF00641_rep.2
+SEQ76	-	dataset_2088	-	cm	1	80	1	79	+	no	1	0.53	0.0	81.8	7.1e-27	!	ORIGID RF00641_rep.0_AL132709.5/95865-95787_76 ORIGHEAD RF00641_rep.0
+SEQ84	-	dataset_2088	-	cm	1	80	1	79	+	no	1	0.41	0.0	79.8	3.2e-26	!	ORIGID RF00641_rep.4_ABBA01048514.1/248685-248607_84 ORIGHEAD RF00641_rep.4
+SEQ79	-	dataset_2088	-	cm	1	80	1	79	+	no	1	0.38	0.0	76.7	3.4e-25	!	ORIGID RF00641_rep.12_AL132709.5/56006-55928_79 ORIGHEAD RF00641_rep.12
+SEQ89	-	dataset_2088	-	cm	1	80	1	80	+	no	1	0.46	0.0	75.4	9e-25	!	ORIGID RF00641_rep.9_AL132709.5/98273-98194_89 ORIGHEAD RF00641_rep.9
+SEQ78	-	dataset_2088	-	cm	1	80	1	80	+	no	1	0.43	0.0	74.4	2e-24	!	ORIGID RF00641_rep.11_AC208187.2/25743-25822_78 ORIGHEAD RF00641_rep.11
+SEQ85	-	dataset_2088	-	cm	1	80	1	79	+	no	1	0.35	0.0	73.2	5.1e-24	!	ORIGID RF00641_rep.5_AL132709.5/73699-73621_85 ORIGHEAD RF00641_rep.5
+SEQ87	-	dataset_2088	-	cm	1	80	1	78	+	no	1	0.38	0.0	72.1	1.2e-23	!	ORIGID RF00641_rep.7_AL132709.5/54880-54803_87 ORIGHEAD RF00641_rep.7
+SEQ81	-	dataset_2088	-	cm	1	80	1	77	+	no	1	0.35	0.0	70.3	4.6e-23	!	ORIGID RF00641_rep.1_AL132709.5/86350-86274_81 ORIGHEAD RF00641_rep.1
+SEQ86	-	dataset_2088	-	cm	1	80	1	79	+	no	1	0.43	0.0	69.6	7.6e-23	!	ORIGID RF00641_rep.6_AADB02234051.1/94-172_86 ORIGHEAD RF00641_rep.6
+SEQ88	-	dataset_2088	-	cm	1	80	1	81	+	no	1	0.40	0.0	62.3	2e-20	!	ORIGID RF00641_rep.8_AL132709.5/61554-61474_88 ORIGHEAD RF00641_rep.8
+SEQ80	-	dataset_2088	-	cm	1	80	1	79	+	no	1	0.53	0.0	57.6	6.6e-19	!	ORIGID RF00641_rep.13_AL132709.5/55165-55087_80 ORIGHEAD RF00641_rep.13
+SEQ77	-	dataset_2088	-	cm	1	80	1	77	+	no	1	0.55	0.0	56.6	1.5e-18	!	ORIGID RF00641_rep.10_AADD01141100.1/2839-2915_77 ORIGHEAD RF00641_rep.10
+SEQ83	-	dataset_2088	-	cm	1	80	1	79	+	no	1	0.44	0.0	18.8	4.2e-06	!	ORIGID RF00641_rep.3_AADD01141098.1/2614-2692_83 ORIGHEAD RF00641_rep.3
diff -r 000000000000 -r b797e13169a0 test-data/FASTA.zip
Binary file test-data/FASTA.zip has changed
diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/1.cluster.all
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RESULTS/1.cluster.all	Fri Dec 16 07:34:49 2016 -0500
@@ -0,0 +1,33 @@
+CLUSTER  1  CM_SCORE  84.9  MODEL     1.1  RF00005_rep.34  
+CLUSTER  1  CM_SCORE  84.9  MODEL     1.1  RF00005_rep.3   
+CLUSTER  1  CM_SCORE  83.8  MODEL     1.1  RF00005_rep.14  
+CLUSTER  1  CM_SCORE  82.5  MODEL     1.1  RF00005_rep.35  
+CLUSTER  1  CM_SCORE  82.4  MODEL     1.1  RF00005_rep.31  
+CLUSTER  1  CM_SCORE  81.0  MODEL     1.1  RF00005_rep.12  
+CLUSTER  1  CM_SCORE  80.9  MODEL     1.1  RF00005_rep.5   
+CLUSTER  1  CM_SCORE  78.9  MODEL     1.1  RF00005_rep.21  
+CLUSTER  1  CM_SCORE  76.6  MODEL     1.1  RF00005_rep.1   
+CLUSTER  1  CM_SCORE  76.3  MODEL     1.1  RF00005_rep.27  
+CLUSTER  1  CM_SCORE  74.7  MODEL     1.1  RF00005_rep.20  
+CLUSTER  1  CM_SCORE  73.6  MODEL     1.1  RF00005_rep.22  
+CLUSTER  1  CM_SCORE  73.3  MODEL     1.1  RF00005_rep.15  
+CLUSTER  1  CM_SCORE  72.3  MODEL     1.1  RF00005_rep.33  
+CLUSTER  1  CM_SCORE  71.7  MODEL     1.1  RF00005_rep.38  
+CLUSTER  1  CM_SCORE  69.3  MODEL     1.1  RF00005_rep.36  
+CLUSTER  1  CM_SCORE  21.4  MODEL     1.1  RF00005_rep.41  
+CLUSTER  1  CM_SCORE  88.8  CMSEARCH  1.1  RF00005_rep.16  
+CLUSTER  1  CM_SCORE  87.5  CMSEARCH  1.1  RF00005_rep.18  
+CLUSTER  1  CM_SCORE  84.8  CMSEARCH  1.1  RF00005_rep.17  
+CLUSTER  1  CM_SCORE  80.0  CMSEARCH  1.1  RF00005_rep.2   
+CLUSTER  1  CM_SCORE  79.6  CMSEARCH  1.1  RF00005_rep.10  
+CLUSTER  1  CM_SCORE  79.0  CMSEARCH  1.1  RF00005_rep.28  
+CLUSTER  1  CM_SCORE  78.5  CMSEARCH  1.1  RF00005_rep.39  
+CLUSTER  1  CM_SCORE  78.4  CMSEARCH  1.1  RF00005_rep.9   
+CLUSTER  1  CM_SCORE  76.3  CMSEARCH  1.1  RF00005_rep.25  
+CLUSTER  1  CM_SCORE  75.1  CMSEARCH  1.1  RF00005_rep.0   
+CLUSTER  1  CM_SCORE  73.3  CMSEARCH  1.1  RF00005_rep.24  
+CLUSTER  1  CM_SCORE  69.4  CMSEARCH  1.1  RF00005_rep.23  
+CLUSTER  1  CM_SCORE  69.3  CMSEARCH  1.1  RF00005_rep.4   
+CLUSTER  1  CM_SCORE  47.8  CMSEARCH  1.1  RF00005_rep.26  
+CLUSTER  1  CM_SCORE  45.6  CMSEARCH  1.1  RF00005_rep.19  
+CLUSTER  1  CM_SCORE  34.4  CMSEARCH  1.1  RF00005_rep.32  
diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/1.cluster.all.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RESULTS/1.cluster.all.fa	Fri Dec 16 07:34:49 2016 -0500
@@ -0,0 +1,66 @@
+>SEQ22_1_72_+ RESULT 1 SCORE 47.8 EVALUE 3.6e-23 CLUSTER 1.1 LOC  ORIGID RF00005_rep.26_AF346999.1/4402-4331_22 ORIGHEAD RF00005_rep.26
+UAGGAUGGGGUGUGAUAGGUGGCACGGAGAAUUUUGGAUUCUCAGGGAUGGGUUCGAUUCUCAUAGUCCUAG
+>SEQ37_1_82_+ RESULT 1 SCORE 84.9 EVALUE 3.4e-37 CLUSTER 1.1 LOC  ORIGID RF00005_rep.3_Z54587.1/126-45_37 ORIGHEAD RF00005_rep.3
+GGUAGCGUGGCCGAGCGGUCUAAGGCGCUGGAUUUAGGCUCCAGUCUCUUCGGAGGCGUGGGUUCGAAUCCCACCGCUGCCA
+>SEQ23_1_74_+ RESULT 1 SCORE 76.3 EVALUE 5.7e-34 CLUSTER 1.1 LOC  ORIGID RF00005_rep.27_AL352978.6/119697-119770_23 ORIGHEAD RF00005_rep.27
+GGCCGGUUAGCUCAGUUGGUUAGAGCGUGGUGCUAAUAACGCCAAGGUCGCGGGUUCGAUCCCCGUACGGGCCA
+>SEQ50_1_73_+ RESULT 1 SCORE 78.4 EVALUE 9.1e-35 CLUSTER 1.1 LOC  ORIGID RF00005_rep.9_AP000442.6/2022-1950_50 ORIGHEAD RF00005_rep.9
+GCCCGGAUAGCUCAGUCGGUAGAGCAUCAGACUUUUAAUCUGAGGGUCCAGGGUUCAAGUCCCUGUUCGGGCG
+>SEQ39_1_69_+ RESULT 1 SCORE 21.4 EVALUE 3.5e-13 CLUSTER 1.1 LOC  ORIGID RF00005_rep.41_AC093311.2/140036-139968_39 ORIGHEAD RF00005_rep.41
+GUUCUUGUAGUUGAAAUACAACGAUGGUUUUUCAUAUCAUUGGUCGUGGUUGUAGUCCGUGCGAGAAUA
+>SEQ46_1_72_+ RESULT 1 SCORE 80.9 EVALUE 1.1e-35 CLUSTER 1.1 LOC  ORIGID RF00005_rep.5_AL590385.23/26129-26058_46 ORIGHEAD RF00005_rep.5
+UCCCUGGUGGUCUAGUGGUUAGGAUUCGGCGCUCUCACCGCCGCGGCCCGGGUUCGAUUCCCGGUCAGGGAA
+>SEQ17_1_71_+ RESULT 1 SCORE 78.9 EVALUE 6.2e-35 CLUSTER 1.1 LOC  ORIGID RF00005_rep.21_AL355149.13/15278-15208_17 ORIGHEAD RF00005_rep.21
+GCAUUGGUGGUUCAGUGGUAGAAUUCUCGCCUCCCACGCGGGAGACCCGGGUUCAAUUCCCGGCCAAUGCA
+>SEQ24_1_73_+ RESULT 1 SCORE 79.0 EVALUE 5.6e-35 CLUSTER 1.1 LOC  ORIGID RF00005_rep.28_X04779.1/1-73_24 ORIGHEAD RF00005_rep.28
+CCUUCGAUAGCUCAGCUGGUAGAGCGGAGGACUGUAGAUCCUUAGGUCGCUGGUUCGAUUCCGGCUCGAAGGA
+>SEQ7_1_83_+ RESULT 1 SCORE 81.0 EVALUE 9.6e-36 CLUSTER 1.1 LOC  ORIGID RF00005_rep.12_AC108081.2/59868-59786_7 ORIGHEAD RF00005_rep.12
+GUCAGGAUGGCCGAGCGGUCUAAGGCGCUGCGUUCAGGUCGCAGUCUCCCCUGGAGGCGUGGGUUCGAAUCCCACUUCUGACA
+>SEQ32_1_73_+ RESULT 1 SCORE 82.5 EVALUE 2.6e-36 CLUSTER 1.1 LOC  ORIGID RF00005_rep.35_AC005783.1/27398-27326_32 ORIGHEAD RF00005_rep.35
+GUUUCCGUAGUGUAGCGGUUAUCACAUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAUCCCGGGCGGAAACA
+>SEQ20_1_72_+ RESULT 1 SCORE 73.3 EVALUE 8.3e-33 CLUSTER 1.1 LOC  ORIGID RF00005_rep.24_AC004941.2/32735-32806_20 ORIGHEAD RF00005_rep.24
+GGGGGUAUAGCUCAGGGGUAGAGCAUUUGACUGCAGAUCAAGAGGUCCCUGGUUCAAAUCCAGGUGCCCCCU
+>SEQ36_1_73_+ RESULT 1 SCORE 78.5 EVALUE 8.3e-35 CLUSTER 1.1 LOC  ORIGID RF00005_rep.39_AL031229.2/40502-40430_36 ORIGHEAD RF00005_rep.39
+GUUUCCGUAGUGUAGUGGUUAUCACGUUCGCCUAACACGCGAAAGGUCCCUGGAUCAAAACCAGGCGGAAACA
+>SEQ10_1_73_+ RESULT 1 SCORE 73.3 EVALUE 8.3e-33 CLUSTER 1.1 LOC  ORIGID RF00005_rep.15_AC008443.10/42590-42518_10 ORIGHEAD RF00005_rep.15
+GCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCG
+>SEQ28_1_71_+ RESULT 1 SCORE 82.4 EVALUE 3e-36 CLUSTER 1.1 LOC  ORIGID RF00005_rep.31_AC092686.3/29631-29561_28 ORIGHEAD RF00005_rep.31
+GCAUUGGUGGUUCAGUGGUAGAAUUCUCGCCUGCCACGCGGGAGGCCCGGGUUCGAUUCCCGGCCAAUGCA
+>SEQ35_1_72_+ RESULT 1 SCORE 71.7 EVALUE 3.2e-32 CLUSTER 1.1 LOC  ORIGID RF00005_rep.38_J00309.1/356-427_35 ORIGHEAD RF00005_rep.38
+UCCCUGGUGGUCUAGUGGCUAGGAUUCGGCGCUUUCACCGCCGCGCCCCGGGUUCGAUUCCCGGCCAGGAAU
+>SEQ21_1_74_+ RESULT 1 SCORE 76.3 EVALUE 5.7e-34 CLUSTER 1.1 LOC  ORIGID RF00005_rep.25_AC006449.19/196857-196784_21 ORIGHEAD RF00005_rep.25
+GUCUCUGUGGCGCAAUCGGUUAGCGCGUUCGGCUGUUAACCGAAAGGUUGGUGGUUCGAGCCCACCCAGGGACG
+>SEQ16_1_72_+ RESULT 1 SCORE 74.7 EVALUE 2.3e-33 CLUSTER 1.1 LOC  ORIGID RF00005_rep.20_AL671879.2/100356-100285_16 ORIGHEAD RF00005_rep.20
+GGGGAUGUAGCUCAGUGGUAGAGCGCAUGCUUCGCAUGUAUGAGGCCCCGGGUUCGAUCCCCGGCAUCUCCA
+>SEQ30_1_72_+ RESULT 1 SCORE 72.3 EVALUE 1.9e-32 CLUSTER 1.1 LOC  ORIGID RF00005_rep.33_AC018638.5/4694-4623_30 ORIGHEAD RF00005_rep.33
+GGCUCGUUGGUCUAGGGGUAUGAUUCUCGCUUAGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGACGAGCCC
+>SEQ12_1_82_+ RESULT 1 SCORE 84.8 EVALUE 3.7e-37 CLUSTER 1.1 LOC  ORIGID RF00005_rep.17_AL021918.1/54817-54736_12 ORIGHEAD RF00005_rep.17
+GUAGUCGUGGCCGAGUGGUUAAGGCGAUGGACUUGAAAUCCAUUGGGGUUUCCCCGCGCAGGUUCGAAUCCUGUCGGCUACG
+>SEQ33_1_72_+ RESULT 1 SCORE 69.3 EVALUE 2.5e-31 CLUSTER 1.1 LOC  ORIGID RF00005_rep.36_AC007298.17/145366-145295_33 ORIGHEAD RF00005_rep.36
+UCCUCGUUAGUAUAGUGGUGAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCGAUUCCCCGACGGGGAG
+>SEQ19_1_82_+ RESULT 1 SCORE 69.4 EVALUE 2.5e-31 CLUSTER 1.1 LOC  ORIGID RF00005_rep.23_M16479.1/42-123_19 ORIGHEAD RF00005_rep.23
+GGUGGGGUUCCCGAGCGGCCAAAGGGAGCAGACUCUAAAUCUGCCGUCAUCGACUUCGAAGGUUCGAAUCCUUCCCCCACCA
+>SEQ15_1_73_+ RESULT 1 SCORE 76.6 EVALUE 4.5e-34 CLUSTER 1.1 LOC  ORIGID RF00005_rep.1_AC005329.1/7043-6971_15 ORIGHEAD RF00005_rep.1
+GCCGAAAUAGCUCAGUUGGGAGAGCGUUAGACUGAAGAUCUAAAGGUCCCUGGUUCGAUCCCGGGUUUCGGCA
+>SEQ45_1_72_+ RESULT 1 SCORE 69.3 EVALUE 2.7e-31 CLUSTER 1.1 LOC  ORIGID RF00005_rep.4_Z98744.2/66305-66234_45 ORIGHEAD RF00005_rep.4
+AGCAGAGUGGCGCAGCGGAAGCGUGCUGGGCCCAUAACCCAGAGGUCGAUGGAUCGAAACCAUCCUCUGCUA
+>SEQ14_2_72_+ RESULT 1 SCORE 45.6 EVALUE 2.5e-22 CLUSTER 1.1 LOC  ORIGID RF00005_rep.19_AF134583.1/1816-1744_14 ORIGHEAD RF00005_rep.19
+AGAUUGAAGCCAGUUGAUUAGGGUGCUUAGCUGUUAACUAAGUGUUUGUGGGUUUAAGUCCCAUUGGUCUA
+>SEQ18_1_72_+ RESULT 1 SCORE 73.6 EVALUE 6.2e-33 CLUSTER 1.1 LOC  ORIGID RF00005_rep.22_AL590385.23/26487-26416_18 ORIGHEAD RF00005_rep.22
+GCGUUGGUGGUAUAGUGGUGAGCAUAGCUGCCUUCCAAGCAGUUGACCCGGGUUCGAUUCCCGGCCAACGCA
+>SEQ9_1_73_+ RESULT 1 SCORE 83.8 EVALUE 8.7e-37 CLUSTER 1.1 LOC  ORIGID RF00005_rep.14_AL021808.2/65570-65498_9 ORIGHEAD RF00005_rep.14
+GCUUCUGUAGUGUAGUGGUUAUCACGUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAAACCGGGCAGAAGCA
+>SEQ5_1_72_+ RESULT 1 SCORE 79.6 EVALUE 3.2e-35 CLUSTER 1.1 LOC  ORIGID RF00005_rep.10_X58792.1/174-245_5 ORIGHEAD RF00005_rep.10
+GGUCCCAUGGUGUAAUGGUUAGCACUCUGGACUUUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUGGGACCU
+>SEQ11_1_82_+ RESULT 1 SCORE 88.8 EVALUE 1.1e-38 CLUSTER 1.1 LOC  ORIGID RF00005_rep.16_AL133551.13/12355-12436_11 ORIGHEAD RF00005_rep.16
+GCAGCGAUGGCCGAGUGGUUAAGGCGUUGGACUUGAAAUCCAAUGGGGUCUCCCCGCGCAGGUUCGAACCCUGCUCGCUGCG
+>SEQ29_1_66_+ RESULT 1 SCORE 34.4 EVALUE 4.1e-18 CLUSTER 1.1 LOC  ORIGID RF00005_rep.32_AF347015.1/5892-5827_29 ORIGHEAD RF00005_rep.32
+GGUAAAAUGGCUGAGUGAAGCAUUGGACUGUAAAUCUAAAGACAGGGGUUAGGCCUCUUUUUACCA
+>SEQ26_1_72_+ RESULT 1 SCORE 80.0 EVALUE 2.4e-35 CLUSTER 1.1 LOC  ORIGID RF00005_rep.2_AL662865.4/12206-12135_26 ORIGHEAD RF00005_rep.2
+GGUUCCAUGGUGUAAUGGUUAGCACUCUGGACUCUGAAUCCAGCGAUCCGAGUUCAAAUCUCGGUGGAACCU
+>SEQ4_1_73_+ RESULT 1 SCORE 75.1 EVALUE 1.7e-33 CLUSTER 1.1 LOC  ORIGID RF00005_rep.0_M15347.1/1040-968_4 ORIGHEAD RF00005_rep.0
+GGCUCCAUAGCUCAGGGGUUAGAGCACUGGUCUUGUAAACCAGGGGUCGCGAGUUCAAUUCUCGCUGGGGCUU
+>SEQ13_1_82_+ RESULT 1 SCORE 87.5 EVALUE 3.5e-38 CLUSTER 1.1 LOC  ORIGID RF00005_rep.18_AL021918.1/81116-81197_13 ORIGHEAD RF00005_rep.18
+GUAGUCGUGGCCGAGUGGUUAAGGCGAUGGACUAGAAAUCCAUUGGGGUUUCCCCACGCAGGUUCGAAUCCUGCCGACUACG
+>SEQ31_1_73_+ RESULT 1 SCORE 84.9 EVALUE 3.1e-37 CLUSTER 1.1 LOC  ORIGID RF00005_rep.34_AC008443.10/43006-42934_31 ORIGHEAD RF00005_rep.34
+GUUUCCGUAGUGUAGUGGUUAUCACGUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAAACCGGGCGGAAACA
diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/1.cluster.part
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RESULTS/1.cluster.part	Fri Dec 16 07:34:49 2016 -0500
@@ -0,0 +1,33 @@
+SEQ22#1#72#+  47.8  3.6e-23  1.1  1.1  1  
+SEQ37#1#82#+  84.9  3.4e-37  1.1  1.1  1  
+SEQ23#1#74#+  76.3  5.7e-34  1.1  1.1  1  
+SEQ50#1#73#+  78.4  9.1e-35  1.1  1.1  1  
+SEQ39#1#69#+  21.4  3.5e-13  1.1  1.1  1  
+SEQ46#1#72#+  80.9  1.1e-35  1.1  1.1  1  
+SEQ17#1#71#+  78.9  6.2e-35  1.1  1.1  1  
+SEQ24#1#73#+  79.0  5.6e-35  1.1  1.1  1  
+SEQ7#1#83#+   81.0  9.6e-36  1.1  1.1  1  
+SEQ32#1#73#+  82.5  2.6e-36  1.1  1.1  1  
+SEQ20#1#72#+  73.3  8.3e-33  1.1  1.1  1  
+SEQ36#1#73#+  78.5  8.3e-35  1.1  1.1  1  
+SEQ10#1#73#+  73.3  8.3e-33  1.1  1.1  1  
+SEQ28#1#71#+  82.4  3e-36    1.1  1.1  1  
+SEQ35#1#72#+  71.7  3.2e-32  1.1  1.1  1  
+SEQ21#1#74#+  76.3  5.7e-34  1.1  1.1  1  
+SEQ16#1#72#+  74.7  2.3e-33  1.1  1.1  1  
+SEQ30#1#72#+  72.3  1.9e-32  1.1  1.1  1  
+SEQ12#1#82#+  84.8  3.7e-37  1.1  1.1  1  
+SEQ33#1#72#+  69.3  2.5e-31  1.1  1.1  1  
+SEQ19#1#82#+  69.4  2.5e-31  1.1  1.1  1  
+SEQ15#1#73#+  76.6  4.5e-34  1.1  1.1  1  
+SEQ45#1#72#+  69.3  2.7e-31  1.1  1.1  1  
+SEQ14#2#72#+  45.6  2.5e-22  1.1  1.1  1  
+SEQ18#1#72#+  73.6  6.2e-33  1.1  1.1  1  
+SEQ9#1#73#+   83.8  8.7e-37  1.1  1.1  1  
+SEQ5#1#72#+   79.6  3.2e-35  1.1  1.1  1  
+SEQ11#1#82#+  88.8  1.1e-38  1.1  1.1  1  
+SEQ29#1#66#+  34.4  4.1e-18  1.1  1.1  1  
+SEQ26#1#72#+  80.0  2.4e-35  1.1  1.1  1  
+SEQ4#1#73#+   75.1  1.7e-33  1.1  1.1  1  
+SEQ13#1#82#+  87.5  3.5e-38  1.1  1.1  1  
+SEQ31#1#73#+  84.9  3.1e-37  1.1  1.1  1  
diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/1.cluster.stats
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RESULTS/1.cluster.stats	Fri Dec 16 07:34:49 2016 -0500
@@ -0,0 +1,1 @@
+CLUSTER 1 SEQS 33 IDS_UNIQUE 33 MODELS 1 
diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/2.cluster.all
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RESULTS/2.cluster.all	Fri Dec 16 07:34:49 2016 -0500
@@ -0,0 +1,13 @@
+CLUSTER  2  CM_SCORE  86.6  MODEL     1.2  RF00641_rep.2   
+CLUSTER  2  CM_SCORE  79.8  MODEL     1.2  RF00641_rep.4   
+CLUSTER  2  CM_SCORE  76.7  MODEL     1.2  RF00641_rep.12  
+CLUSTER  2  CM_SCORE  75.4  MODEL     1.2  RF00641_rep.9   
+CLUSTER  2  CM_SCORE  74.4  MODEL     1.2  RF00641_rep.11  
+CLUSTER  2  CM_SCORE  73.2  MODEL     1.2  RF00641_rep.5   
+CLUSTER  2  CM_SCORE  72.1  MODEL     1.2  RF00641_rep.7   
+CLUSTER  2  CM_SCORE  70.3  MODEL     1.2  RF00641_rep.1   
+CLUSTER  2  CM_SCORE  69.6  MODEL     1.2  RF00641_rep.6   
+CLUSTER  2  CM_SCORE  62.3  MODEL     1.2  RF00641_rep.8   
+CLUSTER  2  CM_SCORE  57.6  MODEL     1.2  RF00641_rep.13  
+CLUSTER  2  CM_SCORE  81.8  CMSEARCH  1.2  RF00641_rep.0   
+CLUSTER  2  CM_SCORE  56.6  CMSEARCH  1.2  RF00641_rep.10  
diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/2.cluster.all.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RESULTS/2.cluster.all.fa	Fri Dec 16 07:34:49 2016 -0500
@@ -0,0 +1,26 @@
+>SEQ79_1_79_+ RESULT 2 SCORE 76.7 EVALUE 3.4e-25 CLUSTER 1.2 LOC  ORIGID RF00641_rep.12_AL132709.5/56006-55928_79 ORIGHEAD RF00641_rep.12
+GGUACUUGAAGGGAGAUCGACCGUGUUAUAUUCGCUUUAUUGACUUCGAAUAAUACAUGGUUGAUCUUUUCUCAGUAUC
+>SEQ85_1_79_+ RESULT 2 SCORE 73.2 EVALUE 5.1e-24 CLUSTER 1.2 LOC  ORIGID RF00641_rep.5_AL132709.5/73699-73621_85 ORIGHEAD RF00641_rep.5
+GGUGCUUAAAGAAUGGCUGUCCGUAGUAUGGUCUCUAUAUUUAUGAUGAUUAAUAUCGGACAACCAUUGUUUUAGUAUC
+>SEQ87_1_78_+ RESULT 2 SCORE 72.1 EVALUE 1.2e-23 CLUSTER 1.2 LOC  ORIGID RF00641_rep.7_AL132709.5/54880-54803_87 ORIGHEAD RF00641_rep.7
+GGUACCUGAAAUAGGUUGCCUGUGAGGUGUUCACUUUCUAUAUGAUGAAUAUUAUACAGUCAACCUCUUUCCGAUAUC
+>SEQ82_1_81_+ RESULT 2 SCORE 86.6 EVALUE 1.9e-28 CLUSTER 1.2 LOC  ORIGID RF00641_rep.2_AC208187.2/29806-29886_82 ORIGHEAD RF00641_rep.2
+GAUACUCGAAGGAGAGGUUGUCCGUGUUGUCUUCUCUUUAUUUAUGAUGAAACAUACACGGGAAACCUCUUUUUUAGUAUC
+>SEQ77_1_77_+ RESULT 2 SCORE 56.6 EVALUE 1.5e-18 CLUSTER 1.2 LOC  ORIGID RF00641_rep.10_AADD01141100.1/2839-2915_77 ORIGHEAD RF00641_rep.10
+GGUACUCGGGGAGAGGUUACCCGAGCAACUUUGCAUCUGGACGACGAAUGUUGCUCGGUGAACCCCUUUUCGGUAUC
+>SEQ80_1_79_+ RESULT 2 SCORE 57.6 EVALUE 6.6e-19 CLUSTER 1.2 LOC  ORIGID RF00641_rep.13_AL132709.5/55165-55087_80 ORIGHEAD RF00641_rep.13
+GGUGCCUGAGGAGAGGUGGCCUGUGUUGCAUUCACAGAAAUCAUGACACACAAGACACGAGCGGCCUCUCUUCAGUAUC
+>SEQ81_1_77_+ RESULT 2 SCORE 70.3 EVALUE 4.6e-23 CLUSTER 1.2 LOC  ORIGID RF00641_rep.1_AL132709.5/86350-86274_81 ORIGHEAD RF00641_rep.1
+GGUACUGGAGGAGAGGUUAUCUGUGUUUUUUCCCUUUAUUUAUGAUGAAAAAUAUGGUGCACUUCUAUUUGAGAAUC
+>SEQ78_1_80_+ RESULT 2 SCORE 74.4 EVALUE 2e-24 CLUSTER 1.2 LOC  ORIGID RF00641_rep.11_AC208187.2/25743-25822_78 ORIGHEAD RF00641_rep.11
+GGUAUUUGAAGAUGCGGUUGACCAUGGUGUGUACGCUUUAUUUGUGACGUAGGACACAUGGUCUACUUCUUCUCAAUAUC
+>SEQ76_1_79_+ RESULT 2 SCORE 81.8 EVALUE 7.1e-27 CLUSTER 1.2 LOC  ORIGID RF00641_rep.0_AL132709.5/95865-95787_76 ORIGHEAD RF00641_rep.0
+GGUACUUGGAGAGAGGUGGUCCGUGGCGCGUUCGCUUUAUUUAUGGCGCACAUUACACGGUCGACCUCUUUGCAGUAUC
+>SEQ86_1_79_+ RESULT 2 SCORE 69.6 EVALUE 7.6e-23 CLUSTER 1.2 LOC  ORIGID RF00641_rep.6_AADB02234051.1/94-172_86 ORIGHEAD RF00641_rep.6
+GGUACUUAAGGGGGAGGUGGGCUUUGAAUAAUAAGUUUAUUGACGUGGAAUAUACAAGGGCAAGCUCUCUGUGAGUAUC
+>SEQ89_1_80_+ RESULT 2 SCORE 75.4 EVALUE 9e-25 CLUSTER 1.2 LOC  ORIGID RF00641_rep.9_AL132709.5/98273-98194_89 ORIGHEAD RF00641_rep.9
+GGUACUUGGAGAGAUAGUAGACCGUAUAGCGUACGCUUUAUCUGUGACGUAUGUAACACGGUCCACUAACCCUCAGUAUC
+>SEQ88_1_81_+ RESULT 2 SCORE 62.3 EVALUE 2e-20 CLUSTER 1.2 LOC  ORIGID RF00641_rep.8_AL132709.5/61554-61474_88 ORIGHEAD RF00641_rep.8
+GGUACUGGUGGAGAGGUCUUCCAUGAUGCAUUCGAUUUAUUUUUUGACCAAUCCUACAUAGUGGACUCUUUUGAAAGCAUU
+>SEQ84_1_79_+ RESULT 2 SCORE 79.8 EVALUE 3.2e-26 CLUSTER 1.2 LOC  ORIGID RF00641_rep.4_ABBA01048514.1/248685-248607_84 ORIGHEAD RF00641_rep.4
+GGUACUCGAAUGGAGGUUGUCCAUGGUGUGUUCAUUUUAUUUAUGAUGAGUAUUACAUGGCCAAUCUCCUUUCGGUACU
diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/2.cluster.part
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RESULTS/2.cluster.part	Fri Dec 16 07:34:49 2016 -0500
@@ -0,0 +1,13 @@
+SEQ79#1#79#+  76.7  3.4e-25  1.2  1.2  2  
+SEQ85#1#79#+  73.2  5.1e-24  1.2  1.2  2  
+SEQ87#1#78#+  72.1  1.2e-23  1.2  1.2  2  
+SEQ82#1#81#+  86.6  1.9e-28  1.2  1.2  2  
+SEQ77#1#77#+  56.6  1.5e-18  1.2  1.2  2  
+SEQ80#1#79#+  57.6  6.6e-19  1.2  1.2  2  
+SEQ81#1#77#+  70.3  4.6e-23  1.2  1.2  2  
+SEQ78#1#80#+  74.4  2e-24    1.2  1.2  2  
+SEQ76#1#79#+  81.8  7.1e-27  1.2  1.2  2  
+SEQ86#1#79#+  69.6  7.6e-23  1.2  1.2  2  
+SEQ89#1#80#+  75.4  9e-25    1.2  1.2  2  
+SEQ88#1#81#+  62.3  2e-20    1.2  1.2  2  
+SEQ84#1#79#+  79.8  3.2e-26  1.2  1.2  2  
diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/2.cluster.stats
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RESULTS/2.cluster.stats	Fri Dec 16 07:34:49 2016 -0500
@@ -0,0 +1,1 @@
+CLUSTER 2 SEQS 13 IDS_UNIQUE 13 MODELS 1 
diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/cluster.final.stats
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RESULTS/cluster.final.stats	Fri Dec 16 07:34:49 2016 -0500
@@ -0,0 +1,2 @@
+CLUSTER  1  SEQS  33  IDS_UNIQUE  33  MODELS  1  
+CLUSTER  2  SEQS  13  IDS_UNIQUE  13  MODELS  1  
diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/fullTab.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RESULTS/fullTab.tabular	Fri Dec 16 07:34:49 2016 -0500
@@ -0,0 +1,92 @@
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00005	1
+RF00641	2
+RF00641	2
+RF00641	2
+RF00641	2
+RF00641	2
+RF00641	2
+RF00641	2
+RF00641	2
+RF00641	2
+RF00641	2
+RF00641	2
+RF00641	2
+RF00641	2
+RF00001	3
+RF00001	4
+RF00001	5
+RF00005	6
+RF00005	7
+RF00005	8
+RF00005	9
+RF00005	10
+RF00005	11
+RF00005	12
+RF00005	13
+RF00005	14
+RF00005	15
+RF00005	16
+RF00005	17
+RF00005	18
+RF00005	19
+RF00006	20
+RF00006	21
+RF00006	22
+RF00006	23
+RF00019	24
+RF00019	25
+RF00019	26
+RF00019	27
+RF00027	28
+RF00027	29
+RF00027	30
+RF00031	31
+RF00031	32
+RF00031	33
+RF00031	34
+RF00031	35
+RF00031	36
+RF00031	37
+RF00049	38
+RF00049	39
+RF00049	40
+RF00618	41
+RF00618	42
+RF00618	43
+RF00618	44
+RF00641	45
+RF00693	46
+RF00693	47
+RF00693	48
diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/partitions/final_overlap.map
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RESULTS/partitions/final_overlap.map	Fri Dec 16 07:34:49 2016 -0500
@@ -0,0 +1,2 @@
+1.1  1.1  
+1.2  1.2  
diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/partitions/final_overlap.matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RESULTS/partitions/final_overlap.matrix	Fri Dec 16 07:34:49 2016 -0500
@@ -0,0 +1,4 @@
+# MODEL 1.1 1.2
+MODEL CLASS 0 0
+1.1 0 0 0
+1.2 0 0 0
diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/partitions/final_partition.hard.best
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RESULTS/partitions/final_partition.hard.best	Fri Dec 16 07:34:49 2016 -0500
@@ -0,0 +1,46 @@
+SEQ11#1#82#+  88.8  1.1e-38  1.1  1.1  1  
+SEQ13#1#82#+  87.5  3.5e-38  1.1  1.1  1  
+SEQ31#1#73#+  84.9  3.1e-37  1.1  1.1  1  
+SEQ37#1#82#+  84.9  3.4e-37  1.1  1.1  1  
+SEQ12#1#82#+  84.8  3.7e-37  1.1  1.1  1  
+SEQ9#1#73#+   83.8  8.7e-37  1.1  1.1  1  
+SEQ32#1#73#+  82.5  2.6e-36  1.1  1.1  1  
+SEQ28#1#71#+  82.4  3e-36    1.1  1.1  1  
+SEQ7#1#83#+   81.0  9.6e-36  1.1  1.1  1  
+SEQ46#1#72#+  80.9  1.1e-35  1.1  1.1  1  
+SEQ26#1#72#+  80.0  2.4e-35  1.1  1.1  1  
+SEQ5#1#72#+   79.6  3.2e-35  1.1  1.1  1  
+SEQ24#1#73#+  79.0  5.6e-35  1.1  1.1  1  
+SEQ17#1#71#+  78.9  6.2e-35  1.1  1.1  1  
+SEQ36#1#73#+  78.5  8.3e-35  1.1  1.1  1  
+SEQ50#1#73#+  78.4  9.1e-35  1.1  1.1  1  
+SEQ15#1#73#+  76.6  4.5e-34  1.1  1.1  1  
+SEQ21#1#74#+  76.3  5.7e-34  1.1  1.1  1  
+SEQ23#1#74#+  76.3  5.7e-34  1.1  1.1  1  
+SEQ4#1#73#+   75.1  1.7e-33  1.1  1.1  1  
+SEQ16#1#72#+  74.7  2.3e-33  1.1  1.1  1  
+SEQ18#1#72#+  73.6  6.2e-33  1.1  1.1  1  
+SEQ10#1#73#+  73.3  8.3e-33  1.1  1.1  1  
+SEQ20#1#72#+  73.3  8.3e-33  1.1  1.1  1  
+SEQ30#1#72#+  72.3  1.9e-32  1.1  1.1  1  
+SEQ35#1#72#+  71.7  3.2e-32  1.1  1.1  1  
+SEQ19#1#82#+  69.4  2.5e-31  1.1  1.1  1  
+SEQ33#1#72#+  69.3  2.5e-31  1.1  1.1  1  
+SEQ45#1#72#+  69.3  2.7e-31  1.1  1.1  1  
+SEQ22#1#72#+  47.8  3.6e-23  1.1  1.1  1  
+SEQ14#2#72#+  45.6  2.5e-22  1.1  1.1  1  
+SEQ29#1#66#+  34.4  4.1e-18  1.1  1.1  1  
+SEQ39#1#69#+  21.4  3.5e-13  1.1  1.1  1  
+SEQ82#1#81#+  86.6  1.9e-28  1.2  1.2  2  
+SEQ76#1#79#+  81.8  7.1e-27  1.2  1.2  2  
+SEQ84#1#79#+  79.8  3.2e-26  1.2  1.2  2  
+SEQ79#1#79#+  76.7  3.4e-25  1.2  1.2  2  
+SEQ89#1#80#+  75.4  9e-25    1.2  1.2  2  
+SEQ78#1#80#+  74.4  2e-24    1.2  1.2  2  
+SEQ85#1#79#+  73.2  5.1e-24  1.2  1.2  2  
+SEQ87#1#78#+  72.1  1.2e-23  1.2  1.2  2  
+SEQ81#1#77#+  70.3  4.6e-23  1.2  1.2  2  
+SEQ86#1#79#+  69.6  7.6e-23  1.2  1.2  2  
+SEQ88#1#81#+  62.3  2e-20    1.2  1.2  2  
+SEQ80#1#79#+  57.6  6.6e-19  1.2  1.2  2  
+SEQ77#1#77#+  56.6  1.5e-18  1.2  1.2  2  
diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/partitions/final_partition.hard.merged
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RESULTS/partitions/final_partition.hard.merged	Fri Dec 16 07:34:49 2016 -0500
@@ -0,0 +1,46 @@
+SEQ11#1#82#+  88.8  1.1e-38  1.1  1.1  1  
+SEQ13#1#82#+  87.5  3.5e-38  1.1  1.1  1  
+SEQ31#1#73#+  84.9  3.1e-37  1.1  1.1  1  
+SEQ37#1#82#+  84.9  3.4e-37  1.1  1.1  1  
+SEQ12#1#82#+  84.8  3.7e-37  1.1  1.1  1  
+SEQ9#1#73#+   83.8  8.7e-37  1.1  1.1  1  
+SEQ32#1#73#+  82.5  2.6e-36  1.1  1.1  1  
+SEQ28#1#71#+  82.4  3e-36    1.1  1.1  1  
+SEQ7#1#83#+   81.0  9.6e-36  1.1  1.1  1  
+SEQ46#1#72#+  80.9  1.1e-35  1.1  1.1  1  
+SEQ26#1#72#+  80.0  2.4e-35  1.1  1.1  1  
+SEQ5#1#72#+   79.6  3.2e-35  1.1  1.1  1  
+SEQ24#1#73#+  79.0  5.6e-35  1.1  1.1  1  
+SEQ17#1#71#+  78.9  6.2e-35  1.1  1.1  1  
+SEQ36#1#73#+  78.5  8.3e-35  1.1  1.1  1  
+SEQ50#1#73#+  78.4  9.1e-35  1.1  1.1  1  
+SEQ15#1#73#+  76.6  4.5e-34  1.1  1.1  1  
+SEQ21#1#74#+  76.3  5.7e-34  1.1  1.1  1  
+SEQ23#1#74#+  76.3  5.7e-34  1.1  1.1  1  
+SEQ4#1#73#+   75.1  1.7e-33  1.1  1.1  1  
+SEQ16#1#72#+  74.7  2.3e-33  1.1  1.1  1  
+SEQ18#1#72#+  73.6  6.2e-33  1.1  1.1  1  
+SEQ10#1#73#+  73.3  8.3e-33  1.1  1.1  1  
+SEQ20#1#72#+  73.3  8.3e-33  1.1  1.1  1  
+SEQ30#1#72#+  72.3  1.9e-32  1.1  1.1  1  
+SEQ35#1#72#+  71.7  3.2e-32  1.1  1.1  1  
+SEQ19#1#82#+  69.4  2.5e-31  1.1  1.1  1  
+SEQ33#1#72#+  69.3  2.5e-31  1.1  1.1  1  
+SEQ45#1#72#+  69.3  2.7e-31  1.1  1.1  1  
+SEQ22#1#72#+  47.8  3.6e-23  1.1  1.1  1  
+SEQ14#2#72#+  45.6  2.5e-22  1.1  1.1  1  
+SEQ29#1#66#+  34.4  4.1e-18  1.1  1.1  1  
+SEQ39#1#69#+  21.4  3.5e-13  1.1  1.1  1  
+SEQ82#1#81#+  86.6  1.9e-28  1.2  1.2  2  
+SEQ76#1#79#+  81.8  7.1e-27  1.2  1.2  2  
+SEQ84#1#79#+  79.8  3.2e-26  1.2  1.2  2  
+SEQ79#1#79#+  76.7  3.4e-25  1.2  1.2  2  
+SEQ89#1#80#+  75.4  9e-25    1.2  1.2  2  
+SEQ78#1#80#+  74.4  2e-24    1.2  1.2  2  
+SEQ85#1#79#+  73.2  5.1e-24  1.2  1.2  2  
+SEQ87#1#78#+  72.1  1.2e-23  1.2  1.2  2  
+SEQ81#1#77#+  70.3  4.6e-23  1.2  1.2  2  
+SEQ86#1#79#+  69.6  7.6e-23  1.2  1.2  2  
+SEQ88#1#81#+  62.3  2e-20    1.2  1.2  2  
+SEQ80#1#79#+  57.6  6.6e-19  1.2  1.2  2  
+SEQ77#1#77#+  56.6  1.5e-18  1.2  1.2  2  
diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/partitions/final_partition.soft
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RESULTS/partitions/final_partition.soft	Fri Dec 16 07:34:49 2016 -0500
@@ -0,0 +1,46 @@
+SEQ11#1#82#+  88.8  1.1e-38  1.1  1.1  1  
+SEQ13#1#82#+  87.5  3.5e-38  1.1  1.1  1  
+SEQ31#1#73#+  84.9  3.1e-37  1.1  1.1  1  
+SEQ37#1#82#+  84.9  3.4e-37  1.1  1.1  1  
+SEQ12#1#82#+  84.8  3.7e-37  1.1  1.1  1  
+SEQ9#1#73#+   83.8  8.7e-37  1.1  1.1  1  
+SEQ32#1#73#+  82.5  2.6e-36  1.1  1.1  1  
+SEQ28#1#71#+  82.4  3e-36    1.1  1.1  1  
+SEQ7#1#83#+   81.0  9.6e-36  1.1  1.1  1  
+SEQ46#1#72#+  80.9  1.1e-35  1.1  1.1  1  
+SEQ26#1#72#+  80.0  2.4e-35  1.1  1.1  1  
+SEQ5#1#72#+   79.6  3.2e-35  1.1  1.1  1  
+SEQ24#1#73#+  79.0  5.6e-35  1.1  1.1  1  
+SEQ17#1#71#+  78.9  6.2e-35  1.1  1.1  1  
+SEQ36#1#73#+  78.5  8.3e-35  1.1  1.1  1  
+SEQ50#1#73#+  78.4  9.1e-35  1.1  1.1  1  
+SEQ15#1#73#+  76.6  4.5e-34  1.1  1.1  1  
+SEQ21#1#74#+  76.3  5.7e-34  1.1  1.1  1  
+SEQ23#1#74#+  76.3  5.7e-34  1.1  1.1  1  
+SEQ4#1#73#+   75.1  1.7e-33  1.1  1.1  1  
+SEQ16#1#72#+  74.7  2.3e-33  1.1  1.1  1  
+SEQ18#1#72#+  73.6  6.2e-33  1.1  1.1  1  
+SEQ10#1#73#+  73.3  8.3e-33  1.1  1.1  1  
+SEQ20#1#72#+  73.3  8.3e-33  1.1  1.1  1  
+SEQ30#1#72#+  72.3  1.9e-32  1.1  1.1  1  
+SEQ35#1#72#+  71.7  3.2e-32  1.1  1.1  1  
+SEQ19#1#82#+  69.4  2.5e-31  1.1  1.1  1  
+SEQ33#1#72#+  69.3  2.5e-31  1.1  1.1  1  
+SEQ45#1#72#+  69.3  2.7e-31  1.1  1.1  1  
+SEQ22#1#72#+  47.8  3.6e-23  1.1  1.1  1  
+SEQ14#2#72#+  45.6  2.5e-22  1.1  1.1  1  
+SEQ29#1#66#+  34.4  4.1e-18  1.1  1.1  1  
+SEQ39#1#69#+  21.4  3.5e-13  1.1  1.1  1  
+SEQ82#1#81#+  86.6  1.9e-28  1.2  1.2  2  
+SEQ76#1#79#+  81.8  7.1e-27  1.2  1.2  2  
+SEQ84#1#79#+  79.8  3.2e-26  1.2  1.2  2  
+SEQ79#1#79#+  76.7  3.4e-25  1.2  1.2  2  
+SEQ89#1#80#+  75.4  9e-25    1.2  1.2  2  
+SEQ78#1#80#+  74.4  2e-24    1.2  1.2  2  
+SEQ85#1#79#+  73.2  5.1e-24  1.2  1.2  2  
+SEQ87#1#78#+  72.1  1.2e-23  1.2  1.2  2  
+SEQ81#1#77#+  70.3  4.6e-23  1.2  1.2  2  
+SEQ86#1#79#+  69.6  7.6e-23  1.2  1.2  2  
+SEQ88#1#81#+  62.3  2e-20    1.2  1.2  2  
+SEQ80#1#79#+  57.6  6.6e-19  1.2  1.2  2  
+SEQ77#1#77#+  56.6  1.5e-18  1.2  1.2  2  
diff -r 000000000000 -r b797e13169a0 test-data/RESULTS/partitions/final_partition.used_cmsearch
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RESULTS/partitions/final_partition.used_cmsearch	Fri Dec 16 07:34:49 2016 -0500
@@ -0,0 +1,2 @@
+1.1
+1.2