# HG changeset patch
# User rnateam
# Date 1540662540 14400
# Node ID 0a48b2db75e7fdeb38360fb2f0b77464e19e46a8

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign commit 2a6fd70c1bcec36ffdf0bba2ec82489b39cfc84e

diff -r 000000000000 -r 0a48b2db75e7 evaluation.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/evaluation.py	Sat Oct 27 13:49:00 2018 -0400
@@ -0,0 +1,105 @@
+#!/usr/bin/env python
+import glob
+from os import system
+import re
+from sklearn import metrics
+from shutil import make_archive
+import sys
+import fnmatch, os
+
+def sh(script):
+    system("bash -c '%s'" % script)
+
+fasta_dir = sys.argv[1]
+results_dir = sys.argv[2]
+dataNames = os.path.join(fasta_dir,"data.names")
+
+listOfClusters = []
+listOfHeaders = []
+headersNames = set()
+idsNames = set()
+
+
+names = os.listdir(results_dir)
+cluster_seqs_stats_files = fnmatch.filter(names, '*.cluster.all')
+with open(dataNames, "r") as names:
+    for line2 in names:
+        splits2 = line2.split()
+        fullHeader = ''
+        if len(splits2) >= 6:
+            fullHeader = splits2[5]
+            headersNames.add(fullHeader)
+            fullID = splits2[3]
+            idsNames.add(fullID)
+
+blackList = []
+numberOfClusters = 0
+for singleFile in sorted(cluster_seqs_stats_files):
+    singleFile = os.path.join(results_dir,singleFile)
+    numberOfClusters += 1
+    with open(singleFile, "r") as f:
+        for line in f:
+            splits = line.split()
+            header = ''
+            idd = ''
+            if len(splits) >= 11:
+                header = splits[10]
+                idd = splits[8]
+            clustNum = splits[2]
+            listOfHeaders.append(header)
+            listOfClusters.append(clustNum)
+            if idd in idsNames: #header in headersNames:
+                blackList.append(idd)
+
+numberOfClusters += 1  # 1 cluster for all unassigned seqs
+ignoreBlackList = False
+with open(dataNames, "r") as names:
+    for line in names:
+        splits = line.split() 
+        fullUniqeId = splits[3]
+        fullHeader = ''
+        fullID = ''
+        if len(splits) >= 6:
+            fullHeader = line.split()[5]
+            fullID = line.split()[3]
+        if ignoreBlackList or ( fullID not in blackList #fullHeader not in blackList 
+            or len(fullHeader) == 0):
+            listOfHeaders.append(fullHeader)
+            listOfClusters.append(str(numberOfClusters))
+            numberOfClusters += 1  # separate cluster for all unassigned seqs
+        # else:
+        #     print ("Skip header", fullHeader)
+
+toWrite = ""
+for i in range(len(listOfClusters)):
+    toWrite += "%s\t%s\n" % (listOfHeaders[i], listOfClusters[i]) 
+ 
+with open(os.path.join(results_dir,"fullTab.tabular"), "w") as full:
+    full.write(toWrite)
+
+
+pattern = re.compile("^RF.*$")
+
+if len(listOfHeaders) > 1: # and  pattern.match(str(listOfHeaders[0])):
+
+    completeness_score = metrics.completeness_score(listOfHeaders, listOfClusters)
+    homogeneity_score = metrics.homogeneity_score(listOfHeaders, listOfClusters)
+    adjusted_rand_score = metrics.adjusted_rand_score(listOfHeaders, listOfClusters)
+    adjusted_mutual_info_score = metrics.adjusted_mutual_info_score(listOfHeaders, listOfClusters)
+    v_measure_score = metrics.v_measure_score(listOfHeaders, listOfClusters)
+
+    toWrite = "completeness_score : {}\n".format(completeness_score) 
+    toWrite += "homogeneity_score : {}\n".format(homogeneity_score) 
+    toWrite += "adjusted_rand_score : {}\n".format(adjusted_rand_score)
+    toWrite += "adjusted_mutual_info_score : {}\n".format(adjusted_mutual_info_score)
+    toWrite += "v_measure_score : {}\n".format(v_measure_score)
+
+
+else:
+    toWrite = "completeness_score : NA \nhomogeneity_score : NA \nadjusted_rand_score : NA \nadjusted_mutual_info_score : NA \nv_measure_score : NA"
+
+with open(os.path.join(results_dir,"evaluation.txt"), "w") as fOut:
+    fOut.write(toWrite)
+
+
+make_archive('RESULTS', 'zip', root_dir=results_dir)
diff -r 000000000000 -r 0a48b2db75e7 glob_report_no_align.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/glob_report_no_align.xml	Sat Oct 27 13:49:00 2018 -0400
@@ -0,0 +1,171 @@
+<tool id="graphclust_glob_report_no_align" name="Graphclust glob_report collect clusters" version="0.5" >
+  <requirements>
+    <requirement type="package" version="0.6.0">graphclust-wrappers</requirement>
+    <requirement type="package" version='0.5'>perl-array-utils</requirement>
+    <requirement type="package" version='0.18.1'>scikit-learn</requirement>
+    <requirement type="package" version='1.8.10'>locarna</requirement>
+    <requirement type="package" version='2.1'>rnaz</requirement>
+    <requirement type="package" version="1.1.2">infernal</requirement>
+    <requirement type="package" version='2.2.10'>viennarna</requirement>
+    <requirement type="package" version='1.3.30'>graphicsmagick</requirement>
+    <requirement type="package" version='0.6.1'>rscape</requirement>
+    <requirement type="package" version='6.0'>unzip</requirement>
+  </requirements>
+  <command detect_errors="exit_code">  
+    <![CDATA[
+        unzip $FASTA  &> /dev/null &&
+        mkdir ./CMSEARCH &&
+        mkdir ./MODEL &&
+        #import re
+        #for $cms_res in $cmsearch_results:
+            #set $safename_cm = re.sub('[^\w\-_\.]', '_', $cms_res.element_identifier)
+            ln -f -s  '$cms_res' ./CMSEARCH/$safename_cm &&
+        #end for
+        #for $mods in $model_tree_files:
+            #set $safename_tr = re.sub('[^\w\-_\.]', '_', $mods.element_identifier)
+            ln -f -s  '$mods' ./MODEL/$safename_tr &&
+        #end for
+
+        'glob_res.pl'
+                $merge_cluster_ol
+                $merge_overlap
+                $min_cluster_size
+                $cm_min_bitscore
+                $cm_max_eval
+                1 ## cm_bitscore_sig
+                $partition_type ''
+                $cut_type
+                0 ## zero means do not align
+        #if  $iteration_num.iteration_num_selector:
+          $iteration_num.CI
+          $final_partition_soft
+          $final_partition_used_cmsearch
+          '$combined_cm'
+
+        #end if
+
+        &&
+        python '$__tool_directory__/evaluation.py' FASTA/ RESULTS/
+       
+        #if $cdhit:
+        &&
+          python '$__tool_directory__/addCdhitseqs.py' '$cdhit'
+        #end if
+]]>
+  </command>
+  <inputs>
+    <param type="data" name="FASTA" format="zip" help="FASTA.zip from pre-processing step"/>
+    <param type="data" name="cmsearch_results" format="tabular" multiple="True" 
+      help="Tabular cmsearch results of the candidate clusters from the cmsearch step"/>
+    <param type="data" name="model_tree_files" format="txt" multiple="True" label="model-tree-stk"
+      help="model.tree.stk files from pgma_graphclust candidate clustering step"/>
+    <param name="partition_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Hard partition"
+      help="Whether to do hard partitioning (no overlap) or soft mode(cluster elements may overlap) "/>
+    <param name="cut_type" type="boolean" checked="True" truevalue="0" falsevalue="1" label="Use CM score for cutoff" help="otherwise use E-value"/>
+    <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_E-val" help=""/>
+    <param type="data" name="cdhit" format="txt" optional="true" label="CD-HIT output" 
+      help="Optional CD-HIT pre-clustering output to be combined into the final clustering output"/>
+    <param name="merge_cluster_ol" type="float" value="0.66" size="5" label="merge_cluster_ovelap" 
+      help="Overlapping ratio criteria to merge overlapping clusters or keep separate clusters (soft partitioning)"/>
+    <param name="merge_overlap" type="float" value="0.51" size="5" label="merge_fraction_overlap" 
+      help="Overlapping ratio criteria to merge overlapping sequence fractions from same input sequence"/>
+    <param name="min_cluster_size" type="integer" value="3" size="5" label="minimum cluster size" 
+      help="Minimum number of elements that can form a cluster. Higher values discard small clusters and may produce larger merged clusters"/>
+    <!-- <param name="cm_bitscore_sig" type="integer" value="1" size="5" label="cm_bitscore_sig" help=""/> -->
+
+    <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" />
+        <param type="data" name="combined_cm" format="txt" />
+      </when>
+      <when value="false" ></when>
+    </conditional>
+
+  </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"   />
+    <data name="evaluation" format="txt" from_work_dir="RESULTS/evaluation.txt" label="evaluation_of_clusters"  />
+    <data name="combined_cm_out" format="txt" from_work_dir="combined_cm_out" label="combined_cmsearch_output"  />
+    <collection name="clusters" type="list" label="CLUSTERS-cmsearch">
+      <discover_datasets format="txt" pattern="(?P&lt;name&gt;^.*\.all$)" directory="RESULTS"  />
+    </collection>
+    <collection name="allFastaSorted" type="list" label="cluster-sequences-sorted">
+      <discover_datasets format="fasta" pattern="(?P&lt;name&gt;^.*\.sorted.fa$)" directory="RESULTS"  />
+    </collection>
+
+    <collection name="partitions" type="list" label="Partitions">
+      <discover_datasets pattern="(?P&lt;name&gt;^.*$)" directory="RESULTS/partitions" />
+    </collection>
+    <data name="RESULTS_zip" format="zip" from_work_dir="RESULTS.zip" label="RESULTS.zip"  />
+  </outputs>
+  <tests>
+    <test>
+      <param name="FASTA" value="FASTA.zip" ftype="searchgui_archive"/>
+      <param name="cmsearch_results" value="1.1.tree,1.2.tree"/>
+      <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="0"/> -->
+      <output name="final_stats" file="RESULTS/cluster.final.stats" />
+      <output name="combined_cm_out" file="combined_cm_out"/>
+      <output name="evaluation" file="evaluation1.txt"/>
+      <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>
+
+      <output name="RESULTS_zip" file="RESULTS.zip" ftype="zip" compare="sim_size" delta="20000"/>
+
+    </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="doi">10.5281/zenodo.597695</citation>
+  </citations>
+</tool>
diff -r 000000000000 -r 0a48b2db75e7 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	Sat Oct 27 13:49:00 2018 -0400
@@ -0,0 +1,40 @@
+>9 SEQ7#1#83#+ ORIGID RF00005_rep.12_AC108081.2/59868-59786_7 ORIGHEAD RF00005
+GUCAGGAUGGCCGAGCGGUCUAAGGCGCUGCGUUCAGGUCGCAGUCUCCCCUGGAGGCGUGGGUUCGAAUCCCACUUCUGACA
+>11 SEQ9#1#73#+ ORIGID RF00005_rep.14_AL021808.2/65570-65498_9 ORIGHEAD RF00005
+GCUUCUGUAGUGUAGUGGUUAUCACGUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAAACCGGGCAGAAGCA
+>12 SEQ10#1#73#+ ORIGID RF00005_rep.15_AC008443.10/42590-42518_10 ORIGHEAD RF00005
+GCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCG
+>15 SEQ13#1#82#+ ORIGID RF00005_rep.18_AL021918.1/81116-81197_13 ORIGHEAD RF00005
+GUAGUCGUGGCCGAGUGGUUAAGGCGAUGGACUAGAAAUCCAUUGGGGUUUCCCCACGCAGGUUCGAAUCCUGCCGACUACG
+>18 SEQ16#1#72#+ ORIGID RF00005_rep.20_AL671879.2/100356-100285_16 ORIGHEAD RF00005
+GGGGAUGUAGCUCAGUGGUAGAGCGCAUGCUUCGCAUGUAUGAGGCCCCGGGUUCGAUCCCCGGCAUCUCCA
+>19 SEQ17#1#71#+ ORIGID RF00005_rep.21_AL355149.13/15278-15208_17 ORIGHEAD RF00005
+GCAUUGGUGGUUCAGUGGUAGAAUUCUCGCCUCCCACGCGGGAGACCCGGGUUCAAUUCCCGGCCAAUGCA
+>20 SEQ18#1#72#+ ORIGID RF00005_rep.22_AL590385.23/26487-26416_18 ORIGHEAD RF00005
+GCGUUGGUGGUAUAGUGGUGAGCAUAGCUGCCUUCCAAGCAGUUGACCCGGGUUCGAUUCCCGGCCAACGCA
+>25 SEQ23#1#74#+ ORIGID RF00005_rep.27_AL352978.6/119697-119770_23 ORIGHEAD RF00005
+GGCCGGUUAGCUCAGUUGGUUAGAGCGUGGUGCUAAUAACGCCAAGGUCGCGGGUUCGAUCCCCGUACGGGCCA
+>30 SEQ28#1#71#+ ORIGID RF00005_rep.31_AC092686.3/29631-29561_28 ORIGHEAD RF00005
+GCAUUGGUGGUUCAGUGGUAGAAUUCUCGCCUGCCACGCGGGAGGCCCGGGUUCGAUUCCCGGCCAAUGCA
+>32 SEQ30#1#72#+ ORIGID RF00005_rep.33_AC018638.5/4694-4623_30 ORIGHEAD RF00005
+GGCUCGUUGGUCUAGGGGUAUGAUUCUCGCUUAGGGUGCGAGAGGUCCCGGGUUCAAAUCCCGGACGAGCCC
+>33 SEQ31#1#73#+ ORIGID RF00005_rep.34_AC008443.10/43006-42934_31 ORIGHEAD RF00005
+GUUUCCGUAGUGUAGUGGUUAUCACGUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAAACCGGGCGGAAACA
+>34 SEQ32#1#73#+ ORIGID RF00005_rep.35_AC005783.1/27398-27326_32 ORIGHEAD RF00005
+GUUUCCGUAGUGUAGCGGUUAUCACAUUCGCCUCACACGCGAAAGGUCCCCGGUUCGAUCCCGGGCGGAAACA
+>35 SEQ33#1#72#+ ORIGID RF00005_rep.36_AC007298.17/145366-145295_33 ORIGHEAD RF00005
+UCCUCGUUAGUAUAGUGGUGAGUAUCCCCGCCUGUCACGCGGGAGACCGGGGUUCGAUUCCCCGACGGGGAG
+>37 SEQ35#1#72#+ ORIGID RF00005_rep.38_J00309.1/356-427_35 ORIGHEAD RF00005
+UCCCUGGUGGUCUAGUGGCUAGGAUUCGGCGCUUUCACCGCCGCGCCCCGGGUUCGAUUCCCGGCCAGGAAU
+>39 SEQ37#1#82#+ ORIGID RF00005_rep.3_Z54587.1/126-45_37 ORIGHEAD RF00005
+GGUAGCGUGGCCGAGCGGUCUAAGGCGCUGGAUUUAGGCUCCAGUCUCUUCGGAGGCGUGGGUUCGAAUCCCACCGCUGCCA
+>48 SEQ46#1#72#+ ORIGID RF00005_rep.5_AL590385.23/26129-26058_46 ORIGHEAD RF00005
+UCCCUGGUGGUCUAGUGGUUAGGAUUCGGCGCUCUCACCGCCGCGGCCCGGGUUCGAUUCCCGGUCAGGGAA
+>53 SEQ51#1#88#+ ORIGID RF00006_rep.0_AF045145.1/1-88_51 ORIGHEAD RF00006
+GGCUGGCUUUAGCUCAGCGGUUACUUCGCGUGUCAUCAAACCACCUCUCUGGGUUGUUCGAGACCCGCGGGCGCUCUCCAGCCCUCUU
+>54 SEQ52#2#101#+ ORIGID RF00006_rep.1_AC005219.1/49914-50014_52 ORIGHEAD RF00006
+GGUCGGAGUUAGCUCAAGCGGUUACCUCCUCAUGCCGGACUUUCUAUCUGUCCAUCUCUGUGCUGGGGUUCGAGACCCGCGGGUGCUUACUGACCCUUUU
+>55 SEQ53#1#98#+ ORIGID RF00006_rep.2_AF045143.1/1-98_53 ORIGHEAD RF00006
+GGCUGGCUUUAGCUCAGCGGUUACUUCGACAGUUCUUUAAUUGAAACAAGCAACCUGUCUGGGUUGUUCGAGACCCGCGGGCGCUCUCCAGUCCUUUU
+>56 SEQ54#1#88#+ ORIGID RF00006_rep.3_AF045144.1/1-88_54 ORIGHEAD RF00006
+GGCUGGCUUUAGCUCAGCGGUUACUUCGAGUACAUUGUAACCACCUCUCUGGGUGGUUCGAGACCCGCGGGUGCUUUCCAGCUCUUUU
diff -r 000000000000 -r 0a48b2db75e7 test-data/1.1.tree
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.1.tree	Sat Oct 27 13:49:00 2018 -0400
@@ -0,0 +1,47 @@
+SEQ31	-	dataset_60	-	cm	1	73	1	73	+	no	1	0.56	0.0	88.9	1.2e-150	!	ORIGID RF00005_rep.34_AC008443.10/43006-42934_31 ORIGHEAD RF00005
+SEQ11	-	dataset_60	-	cm	1	73	1	82	+	no	1	0.62	0.0	88.3	8e-150	!	ORIGID RF00005_rep.16_AL133551.13/12355-12436_11 ORIGHEAD RF00005
+SEQ9	-	dataset_60	-	cm	1	73	1	73	+	no	1	0.56	0.0	87.8	4.6e-149	!	ORIGID RF00005_rep.14_AL021808.2/65570-65498_9 ORIGHEAD RF00005
+SEQ32	-	dataset_60	-	cm	1	73	1	73	+	no	1	0.58	0.0	87.3	2.6e-148	!	ORIGID RF00005_rep.35_AC005783.1/27398-27326_32 ORIGHEAD RF00005
+SEQ13	-	dataset_60	-	cm	1	73	1	82	+	no	1	0.56	0.0	86.3	8.9e-147	!	ORIGID RF00005_rep.18_AL021918.1/81116-81197_13 ORIGHEAD RF00005
+SEQ36	-	dataset_60	-	cm	1	73	1	73	+	no	1	0.51	0.0	83.0	1.1e-141	!	ORIGID RF00005_rep.39_AL031229.2/40502-40430_36 ORIGHEAD RF00005
+SEQ12	-	dataset_60	-	cm	1	73	1	82	+	no	1	0.57	0.0	82.7	3.1e-141	!	ORIGID RF00005_rep.17_AL021918.1/54817-54736_12 ORIGHEAD RF00005
+SEQ26	-	dataset_60	-	cm	1	73	1	72	+	no	1	0.50	0.0	82.0	4.9e-140	!	ORIGID RF00005_rep.2_AL662865.4/12206-12135_26 ORIGHEAD RF00005
+SEQ5	-	dataset_60	-	cm	1	73	1	72	+	no	1	0.51	0.0	81.7	1.3e-139	!	ORIGID RF00005_rep.10_X58792.1/174-245_5 ORIGHEAD RF00005
+SEQ50	-	dataset_60	-	cm	1	73	1	73	+	no	1	0.56	0.0	80.8	3.1e-138	!	ORIGID RF00005_rep.9_AP000442.6/2022-1950_50 ORIGHEAD RF00005
+SEQ28	-	dataset_60	-	cm	1	73	1	71	+	no	1	0.62	0.0	80.7	4.6e-138	!	ORIGID RF00005_rep.31_AC092686.3/29631-29561_28 ORIGHEAD RF00005
+SEQ15	-	dataset_60	-	cm	1	73	1	73	+	no	1	0.53	0.0	80.6	5.9e-138	!	ORIGID RF00005_rep.1_AC005329.1/7043-6971_15 ORIGHEAD RF00005
+SEQ24	-	dataset_60	-	cm	1	73	1	73	+	no	1	0.56	0.0	80.3	1.5e-137	!	ORIGID RF00005_rep.28_X04779.1/1-73_24 ORIGHEAD RF00005
+SEQ4	-	dataset_60	-	cm	1	73	1	73	+	no	1	0.56	0.0	79.2	7.3e-136	!	ORIGID RF00005_rep.0_M15347.1/1040-968_4 ORIGHEAD RF00005
+SEQ46	-	dataset_60	-	cm	1	73	1	72	+	no	1	0.65	0.0	78.4	1.3e-134	!	ORIGID RF00005_rep.5_AL590385.23/26129-26058_46 ORIGHEAD RF00005
+SEQ17	-	dataset_60	-	cm	1	73	1	71	+	no	1	0.59	0.0	77.7	1.6e-133	!	ORIGID RF00005_rep.21_AL355149.13/15278-15208_17 ORIGHEAD RF00005
+SEQ37	-	dataset_60	-	cm	1	73	1	82	+	no	1	0.63	0.0	76.3	2.5e-131	!	ORIGID RF00005_rep.3_Z54587.1/126-45_37 ORIGHEAD RF00005
+SEQ10	-	dataset_60	-	cm	1	73	1	73	+	no	1	0.62	0.0	76.3	2.8e-131	!	ORIGID RF00005_rep.15_AC008443.10/42590-42518_10 ORIGHEAD RF00005
+SEQ23	-	dataset_60	-	cm	1	73	1	74	+	no	1	0.61	0.0	75.9	1.2e-130	!	ORIGID RF00005_rep.27_AL352978.6/119697-119770_23 ORIGHEAD RF00005
+SEQ20	-	dataset_60	-	cm	1	73	1	72	+	no	1	0.56	0.0	75.8	1.7e-130	!	ORIGID RF00005_rep.24_AC004941.2/32735-32806_20 ORIGHEAD RF00005
+SEQ30	-	dataset_60	-	cm	1	73	1	72	+	no	1	0.61	0.0	74.9	4e-129	!	ORIGID RF00005_rep.33_AC018638.5/4694-4623_30 ORIGHEAD RF00005
+SEQ16	-	dataset_60	-	cm	1	73	1	72	+	no	1	0.61	0.0	74.9	4e-129	!	ORIGID RF00005_rep.20_AL671879.2/100356-100285_16 ORIGHEAD RF00005
+SEQ21	-	dataset_60	-	cm	1	73	1	74	+	no	1	0.61	0.0	74.8	4.8e-129	!	ORIGID RF00005_rep.25_AC006449.19/196857-196784_21 ORIGHEAD RF00005
+SEQ18	-	dataset_60	-	cm	1	73	1	72	+	no	1	0.58	0.0	72.9	4.3e-126	!	ORIGID RF00005_rep.22_AL590385.23/26487-26416_18 ORIGHEAD RF00005
+SEQ35	-	dataset_60	-	cm	1	73	1	72	+	no	1	0.65	0.0	71.9	1.2e-124	!	ORIGID RF00005_rep.38_J00309.1/356-427_35 ORIGHEAD RF00005
+SEQ45	-	dataset_60	-	cm	1	73	1	72	+	no	1	0.60	0.0	71.6	4.5e-124	!	ORIGID RF00005_rep.4_Z98744.2/66305-66234_45 ORIGHEAD RF00005
+SEQ7	-	dataset_60	-	cm	1	73	1	83	+	no	1	0.63	0.0	71.2	2e-123	!	ORIGID RF00005_rep.12_AC108081.2/59868-59786_7 ORIGHEAD RF00005
+SEQ33	-	dataset_60	-	cm	1	73	1	72	+	no	1	0.62	0.0	69.2	2e-120	!	ORIGID RF00005_rep.36_AC007298.17/145366-145295_33 ORIGHEAD RF00005
+SEQ19	-	dataset_60	-	cm	1	73	1	82	+	no	1	0.59	0.0	69.0	4e-120	!	ORIGID RF00005_rep.23_M16479.1/42-123_19 ORIGHEAD RF00005
+SEQ22	-	dataset_60	-	cm	1	73	1	72	+	no	1	0.49	0.0	48.1	5.1e-88	!	ORIGID RF00005_rep.26_AF346999.1/4402-4331_22 ORIGHEAD RF00005
+SEQ40	-	dataset_60	-	cm	1	73	1	66	+	no	1	0.45	0.0	44.2	4.7e-82	!	ORIGID RF00005_rep.42_AF347015.1/5827-5762_40 ORIGHEAD RF00005
+SEQ29	-	dataset_60	-	cm	1	73	1	66	+	no	1	0.42	0.0	31.0	8.7e-62	!	ORIGID RF00005_rep.32_AF347015.1/5892-5827_29 ORIGHEAD RF00005
+SEQ14	-	dataset_60	-	cm	1	73	1	73	+	no	1	0.41	0.0	29.5	2.2e-59	!	ORIGID RF00005_rep.19_AF134583.1/1816-1744_14 ORIGHEAD RF00005
+SEQ39	-	dataset_60	-	cm	1	73	1	69	+	no	1	0.39	0.0	21.6	2.5e-47	!	ORIGID RF00005_rep.41_AC093311.2/140036-139968_39 ORIGHEAD RF00005
+SEQ48	-	dataset_60	-	cm	1	73	1	71	+	no	1	0.35	0.0	12.9	5.7e-34	!	ORIGID RF00005_rep.7_AF347005.1/12268-12338_48 ORIGHEAD RF00005
+SEQ34	-	dataset_60	-	cm	1	73	1	68	+	no	1	0.34	0.0	12.8	9.6e-34	!	ORIGID RF00005_rep.37_AF347001.1/16015-15948_34 ORIGHEAD RF00005
+SEQ6	-	dataset_60	-	cm	1	73	1	66	+	no	1	0.38	0.0	12.1	1.1e-32	!	ORIGID RF00005_rep.11_AF346992.1/15890-15955_6 ORIGHEAD RF00005
+SEQ42	-	dataset_60	-	cm	1	73	1	69	+	no	1	0.38	0.0	9.4	1.4e-28	!	ORIGID RF00005_rep.44_AC008670.6/83597-83665_42 ORIGHEAD RF00005
+SEQ8	-	dataset_60	-	cm	1	73	1	70	+	no	1	0.33	0.0	9.0	6.2e-28	!	ORIGID RF00005_rep.13_AC067849.6/4771-4840_8 ORIGHEAD RF00005
+SEQ27	-	dataset_60	-	cm	1	73	1	69	+	no	1	0.43	0.0	8.6	3.1e-27	!	ORIGID RF00005_rep.30_AL132988.4/95773-95841_27 ORIGHEAD RF00005
+SEQ41	-	dataset_60	-	cm	1	73	1	68	+	no	1	0.26	0.1	7.7	6e-26	!	ORIGID RF00005_rep.43_L23320.1/77-10_41 ORIGHEAD RF00005
+SEQ43	-	dataset_60	-	cm	1	73	1	71	+	no	1	0.41	0.0	4.3	1.1e-20	!	ORIGID RF00005_rep.45_AF382005.1/581-651_43 ORIGHEAD RF00005
+SEQ25	-	dataset_60	-	cm	1	73	1	69	+	no	1	0.29	0.0	4.2	1.8e-20	!	ORIGID RF00005_rep.29_AF381996.2/4265-4333_25 ORIGHEAD RF00005
+SEQ44	-	dataset_60	-	cm	1	73	1	69	+	no	1	0.42	0.0	1.2	6.2e-16	!	ORIGID RF00005_rep.46_AF347015.1/1604-1672_44 ORIGHEAD RF00005
+SEQ38	-	dataset_60	-	cm	1	73	1	65	+	no	1	0.23	0.5	-0.9	1.1e-12	!	ORIGID RF00005_rep.40_AF382013.1/10403-10467_38 ORIGHEAD RF00005
+SEQ47	-	dataset_60	-	cm	1	73	1	68	+	no	1	0.24	0.5	-1.5	9.1e-12	!	ORIGID RF00005_rep.6_X93334.1/6942-7009_47 ORIGHEAD RF00005
+SEQ49	-	dataset_60	-	cm	1	73	1	68	+	no	1	0.35	0.0	-4.4	2.9e-07	!	ORIGID RF00005_rep.8_AF134583.1/1599-1666_49 ORIGHEAD RF00005
diff -r 000000000000 -r 0a48b2db75e7 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	Sat Oct 27 13:49:00 2018 -0400
@@ -0,0 +1,40 @@
+>1 SEQ1#1#100#+ ORIGID RF00001_rep.0_AL096764.11/46123-46004_1 ORIGHEAD RF00001
+GUCUAUGGCCAUACCACCCUGAAUGUGCUUGAUCUCAUCUGAUCUCGUGAAGCCAAGCAGGGUGGGGCCUAGUUAGUACUUGGAUGGGAGACUUCCUGGG
+>2 SEQ1#21#120#+ ORIGID RF00001_rep.0_AL096764.11/46123-46004_1 ORIGHEAD RF00001
+GAAUGUGCUUGAUCUCAUCUGAUCUCGUGAAGCCAAGCAGGGUGGGGCCUAGUUAGUACUUGGAUGGGAGACUUCCUGGGAAUAUAAGCUGCUGUUGGCU
+>3 SEQ2#1#100#+ ORIGID RF00001_rep.1_U89919.1/939-1056_2 ORIGHEAD RF00001
+CUUUACGGCCACACCACCCUGAACGCACCGGAUCUCGACUGACCUUGAAAGCUAAGCAGGAUCGGGCCUGGUUAGUAUUGGGAUGGCAGACCCCCUGGAA
+>4 SEQ2#19#118#+ ORIGID RF00001_rep.1_U89919.1/939-1056_2 ORIGHEAD RF00001
+CUGAACGCACCGGAUCUCGACUGACCUUGAAAGCUAAGCAGGAUCGGGCCUGGUUAGUAUUGGGAUGGCAGACCCCCUGGAAAUACAGGGUGCUGAAGGU
+>5 SEQ3#5#104#+ ORIGID RF00001_rep.2_AJ508600.1/161-58_3 ORIGHEAD RF00001
+ACAGCCAUACCAUCCUGAACAUGCCAGAUCUUGUCUGACCUCUGAAGCUAAGCAGGGUCAAGCCUGGUUAGUACUUGGGAGAAGCUGGUGUGGCUAGACC
+>31 SEQ29#1#66#+ ORIGID RF00005_rep.32_AF347015.1/5892-5827_29 ORIGHEAD RF00005
+GGUAAAAUGGCUGAGUGAAGCAUUGGACUGUAAAUCUAAAGACAGGGGUUAGGCCUCUUUUUACCA
+>59 SEQ56#1#95#+ ORIGID RF00019_rep.1_L32608.1/283-377_56 ORIGHEAD RF00019
+GGCUGGUCCGAUGGUAGUGGGUUAUCAGAACUUAUUAACAUUAGUGUCACUAAAGUUGGUAUACAACCCCCCACUGCUAAAUUUGACUGGCUUUU
+>60 SEQ57#3#102#+ ORIGID RF00019_rep.2_ABBA01033605.1/1707-1808_57 ORIGHEAD RF00019
+CUGGUCCGAGUGCAGUGGUGUUUACAACUAAUUGAUCACAACCAGUUACAGAUUUCUUUGUUCCUUCUCCACUCCCACUGCUUCACUUGACUAGCCUUUU
+>62 SEQ59#1#79#+ ORIGID RF00027_rep.0_AF480570.1/1-79_59 ORIGHEAD RF00027
+GUGAGGUAGUAAGUUGUAUUGUUGUGGGGUAGGGAUAUUAGGCCCCAAUUAGAAGAUAACUAUACAACUUACUACUUUC
+>69 SEQ66#1#71#+ ORIGID RF00031_rep.4_AF195141.1/689-759_66 ORIGHEAD RF00031
+GACUGACAUUAUGAAGGCCUGUACUGAAGACAGCAAGCUGUUAGUACAGACCAGAUGCUUUCUUGGCAGGC
+>75 SEQ72#1#100#+ ORIGID RF00618_rep.0_AL135914.25/92223-92098_72 ORIGHEAD RF00618
+ACCAUCCUUUUCUUGGGGUUGCACUACUGUCCAAUGGGUACCUAGUGAGGGCAGUACUGCUAACUCCUGCACAACACACCGAAAUCAACUAGAGCUUUGC
+>76 SEQ72#27#126#+ ORIGID RF00618_rep.0_AL135914.25/92223-92098_72 ORIGHEAD RF00618
+CUGUCCAAUGGGUACCUAGUGAGGGCAGUACUGCUAACUCCUGCACAACACACCGAAAUCAACUAGAGCUUUGCUUUGCCUUGGUGCAGUUUUUGGAGAA
+>77 SEQ73#1#100#+ ORIGID RF00618_rep.1_AL161445.10/77816-77941_73 ORIGHEAD RF00618
+ACCAUCCUUUUCUUGGGGUUGCACUACUGUCCAAAGAGCAUGUAGUGAGGGCAGUACUGCUAACGUCUACACAACACACCCACCUCAACUAGAGCUUUGC
+>78 SEQ73#27#126#+ ORIGID RF00618_rep.1_AL161445.10/77816-77941_73 ORIGHEAD RF00618
+CUGUCCAAAGAGCAUGUAGUGAGGGCAGUACUGCUAACGUCUACACAACACACCCACCUCAACUAGAGCUUUGCUUUAGCUUGGUGUAAUUUUUGGAAAA
+>79 SEQ74#1#100#+ ORIGID RF00618_rep.2_U62822.1/2-128_74 ORIGHEAD RF00618
+ACCAUCCUUUUCUUGGGGUUGCGCUACUGUCCAAUGAGCGCAUAGUGAGGGCAGUACUGCUAACGCCUGAACAACACACCCGCAUCAACUAGAGCUUUUG
+>80 SEQ74#28#127#+ ORIGID RF00618_rep.2_U62822.1/2-128_74 ORIGHEAD RF00618
+UGUCCAAUGAGCGCAUAGUGAGGGCAGUACUGCUAACGCCUGAACAACACACCCGCAUCAACUAGAGCUUUUGCUUUAUUUUGGUGCAAUUUUUGGAAAA
+>81 SEQ75#1#100#+ ORIGID RF00618_rep.3_AL389925.10/20736-20611_75 ORIGHEAD RF00618
+ACCAUCCUUUUCUUGGGGUUGCACUACUGUCUAAUGAGUGCAUAAUGAGGGCAGUAUUGCUAACGCCUAUACAAUGCACCUGCAUCAACUAGAACUUUGC
+>82 SEQ75#27#126#+ ORIGID RF00618_rep.3_AL389925.10/20736-20611_75 ORIGHEAD RF00618
+CUGUCUAAUGAGUGCAUAAUGAGGGCAGUAUUGCUAACGCCUAUACAAUGCACCUGCAUCAACUAGAACUUUGCUUUACCUUGGUACAAUUUUUGGAAAA
+>90 SEQ83#1#79#+ ORIGID RF00641_rep.3_AADD01141098.1/2614-2692_83 ORIGHEAD RF00641
+GCUACUUGAAGAGAGGUAAUCCUUCAUGCAUUUGCUUUACUUGCAAUGAUUAUACAAGGGCAGACUCUCUCUGGGGAGC
+>94 SEQ87#1#78#+ ORIGID RF00641_rep.7_AL132709.5/54880-54803_87 ORIGHEAD RF00641
+GGUACCUGAAAUAGGUUGCCUGUGAGGUGUUCACUUUCUAUAUGAUGAAUAUUAUACAGUCAACCUCUUUCCGAUAUC
diff -r 000000000000 -r 0a48b2db75e7 test-data/1.2.tree
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/1.2.tree	Sat Oct 27 13:49:00 2018 -0400
@@ -0,0 +1,4 @@
+SEQ74	-	dataset_61	-	cm	1	100	1	100	+	no	1	0.51	0.0	163.2	7.9e-68	!	ORIGID RF00618_rep.2_U62822.1/2-128_74 ORIGHEAD RF00618
+SEQ72	-	dataset_61	-	cm	1	100	1	100	+	no	1	0.49	0.0	163.1	8.9e-68	!	ORIGID RF00618_rep.0_AL135914.25/92223-92098_72 ORIGHEAD RF00618
+SEQ73	-	dataset_61	-	cm	1	100	1	100	+	no	1	0.49	0.0	161.5	3.4e-67	!	ORIGID RF00618_rep.1_AL161445.10/77816-77941_73 ORIGHEAD RF00618
+SEQ75	-	dataset_61	-	cm	1	100	1	100	+	no	1	0.44	0.0	160.5	8.2e-67	!	ORIGID RF00618_rep.3_AL389925.10/20736-20611_75 ORIGHEAD RF00618
diff -r 000000000000 -r 0a48b2db75e7 test-data/FASTA.zip
Binary file test-data/FASTA.zip has changed
diff -r 000000000000 -r 0a48b2db75e7 test-data/RESULTS.zip
Binary file test-data/RESULTS.zip has changed
diff -r 000000000000 -r 0a48b2db75e7 test-data/RESULTS/1.cluster.all
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RESULTS/1.cluster.all	Sat Oct 27 13:49:00 2018 -0400
@@ -0,0 +1,34 @@
+SEQ31#1#73#+  RESULT  1  CM_SCORE  88.9  MODEL     1.1  ORIGID  RF00005_rep.34_AC008443.10/43006-42934_31    ORIGHEAD  RF00005  
+SEQ9#1#73#+   RESULT  1  CM_SCORE  87.8  MODEL     1.1  ORIGID  RF00005_rep.14_AL021808.2/65570-65498_9      ORIGHEAD  RF00005  
+SEQ32#1#73#+  RESULT  1  CM_SCORE  87.3  MODEL     1.1  ORIGID  RF00005_rep.35_AC005783.1/27398-27326_32     ORIGHEAD  RF00005  
+SEQ13#1#82#+  RESULT  1  CM_SCORE  86.3  MODEL     1.1  ORIGID  RF00005_rep.18_AL021918.1/81116-81197_13     ORIGHEAD  RF00005  
+SEQ28#1#71#+  RESULT  1  CM_SCORE  80.7  MODEL     1.1  ORIGID  RF00005_rep.31_AC092686.3/29631-29561_28     ORIGHEAD  RF00005  
+SEQ46#1#72#+  RESULT  1  CM_SCORE  78.4  MODEL     1.1  ORIGID  RF00005_rep.5_AL590385.23/26129-26058_46     ORIGHEAD  RF00005  
+SEQ17#1#71#+  RESULT  1  CM_SCORE  77.7  MODEL     1.1  ORIGID  RF00005_rep.21_AL355149.13/15278-15208_17    ORIGHEAD  RF00005  
+SEQ37#1#82#+  RESULT  1  CM_SCORE  76.3  MODEL     1.1  ORIGID  RF00005_rep.3_Z54587.1/126-45_37             ORIGHEAD  RF00005  
+SEQ10#1#73#+  RESULT  1  CM_SCORE  76.3  MODEL     1.1  ORIGID  RF00005_rep.15_AC008443.10/42590-42518_10    ORIGHEAD  RF00005  
+SEQ23#1#74#+  RESULT  1  CM_SCORE  75.9  MODEL     1.1  ORIGID  RF00005_rep.27_AL352978.6/119697-119770_23   ORIGHEAD  RF00005  
+SEQ30#1#72#+  RESULT  1  CM_SCORE  74.9  MODEL     1.1  ORIGID  RF00005_rep.33_AC018638.5/4694-4623_30       ORIGHEAD  RF00005  
+SEQ16#1#72#+  RESULT  1  CM_SCORE  74.9  MODEL     1.1  ORIGID  RF00005_rep.20_AL671879.2/100356-100285_16   ORIGHEAD  RF00005  
+SEQ18#1#72#+  RESULT  1  CM_SCORE  72.9  MODEL     1.1  ORIGID  RF00005_rep.22_AL590385.23/26487-26416_18    ORIGHEAD  RF00005  
+SEQ35#1#72#+  RESULT  1  CM_SCORE  71.9  MODEL     1.1  ORIGID  RF00005_rep.38_J00309.1/356-427_35           ORIGHEAD  RF00005  
+SEQ7#1#83#+   RESULT  1  CM_SCORE  71.2  MODEL     1.1  ORIGID  RF00005_rep.12_AC108081.2/59868-59786_7      ORIGHEAD  RF00005  
+SEQ33#1#72#+  RESULT  1  CM_SCORE  69.2  MODEL     1.1  ORIGID  RF00005_rep.36_AC007298.17/145366-145295_33  ORIGHEAD  RF00005  
+SEQ29#1#66#+  RESULT  1  CM_SCORE  31.0  MODEL     1.1  ORIGID  RF00005_rep.32_AF347015.1/5892-5827_29       ORIGHEAD  RF00005  
+SEQ11#1#82#+  RESULT  1  CM_SCORE  88.3  CMSEARCH  1.1  ORIGID  RF00005_rep.16_AL133551.13/12355-12436_11    ORIGHEAD  RF00005  
+SEQ36#1#73#+  RESULT  1  CM_SCORE  83.0  CMSEARCH  1.1  ORIGID  RF00005_rep.39_AL031229.2/40502-40430_36     ORIGHEAD  RF00005  
+SEQ12#1#82#+  RESULT  1  CM_SCORE  82.7  CMSEARCH  1.1  ORIGID  RF00005_rep.17_AL021918.1/54817-54736_12     ORIGHEAD  RF00005  
+SEQ26#1#72#+  RESULT  1  CM_SCORE  82.0  CMSEARCH  1.1  ORIGID  RF00005_rep.2_AL662865.4/12206-12135_26      ORIGHEAD  RF00005  
+SEQ5#1#72#+   RESULT  1  CM_SCORE  81.7  CMSEARCH  1.1  ORIGID  RF00005_rep.10_X58792.1/174-245_5            ORIGHEAD  RF00005  
+SEQ50#1#73#+  RESULT  1  CM_SCORE  80.8  CMSEARCH  1.1  ORIGID  RF00005_rep.9_AP000442.6/2022-1950_50        ORIGHEAD  RF00005  
+SEQ15#1#73#+  RESULT  1  CM_SCORE  80.6  CMSEARCH  1.1  ORIGID  RF00005_rep.1_AC005329.1/7043-6971_15        ORIGHEAD  RF00005  
+SEQ24#1#73#+  RESULT  1  CM_SCORE  80.3  CMSEARCH  1.1  ORIGID  RF00005_rep.28_X04779.1/1-73_24              ORIGHEAD  RF00005  
+SEQ4#1#73#+   RESULT  1  CM_SCORE  79.2  CMSEARCH  1.1  ORIGID  RF00005_rep.0_M15347.1/1040-968_4            ORIGHEAD  RF00005  
+SEQ20#1#72#+  RESULT  1  CM_SCORE  75.8  CMSEARCH  1.1  ORIGID  RF00005_rep.24_AC004941.2/32735-32806_20     ORIGHEAD  RF00005  
+SEQ21#1#74#+  RESULT  1  CM_SCORE  74.8  CMSEARCH  1.1  ORIGID  RF00005_rep.25_AC006449.19/196857-196784_21  ORIGHEAD  RF00005  
+SEQ45#1#72#+  RESULT  1  CM_SCORE  71.6  CMSEARCH  1.1  ORIGID  RF00005_rep.4_Z98744.2/66305-66234_45        ORIGHEAD  RF00005  
+SEQ19#1#82#+  RESULT  1  CM_SCORE  69.0  CMSEARCH  1.1  ORIGID  RF00005_rep.23_M16479.1/42-123_19            ORIGHEAD  RF00005  
+SEQ22#1#72#+  RESULT  1  CM_SCORE  48.1  CMSEARCH  1.1  ORIGID  RF00005_rep.26_AF346999.1/4402-4331_22       ORIGHEAD  RF00005  
+SEQ40#1#66#+  RESULT  1  CM_SCORE  44.2  CMSEARCH  1.1  ORIGID  RF00005_rep.42_AF347015.1/5827-5762_40       ORIGHEAD  RF00005  
+SEQ14#1#73#+  RESULT  1  CM_SCORE  29.5  CMSEARCH  1.1  ORIGID  RF00005_rep.19_AF134583.1/1816-1744_14       ORIGHEAD  RF00005  
+SEQ39#1#69#+  RESULT  1  CM_SCORE  21.6  CMSEARCH  1.1  ORIGID  RF00005_rep.41_AC093311.2/140036-139968_39   ORIGHEAD  RF00005  
diff -r 000000000000 -r 0a48b2db75e7 test-data/RESULTS/2.cluster.all
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RESULTS/2.cluster.all	Sat Oct 27 13:49:00 2018 -0400
@@ -0,0 +1,4 @@
+SEQ74#1#100#+  RESULT  2  CM_SCORE  163.2  MODEL  1.2  ORIGID  RF00618_rep.2_U62822.1/2-128_74           ORIGHEAD  RF00618  
+SEQ72#1#100#+  RESULT  2  CM_SCORE  163.1  MODEL  1.2  ORIGID  RF00618_rep.0_AL135914.25/92223-92098_72  ORIGHEAD  RF00618  
+SEQ73#1#100#+  RESULT  2  CM_SCORE  161.5  MODEL  1.2  ORIGID  RF00618_rep.1_AL161445.10/77816-77941_73  ORIGHEAD  RF00618  
+SEQ75#1#100#+  RESULT  2  CM_SCORE  160.5  MODEL  1.2  ORIGID  RF00618_rep.3_AL389925.10/20736-20611_75  ORIGHEAD  RF00618  
diff -r 000000000000 -r 0a48b2db75e7 test-data/RESULTS/cluster.final.stats
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RESULTS/cluster.final.stats	Sat Oct 27 13:49:00 2018 -0400
@@ -0,0 +1,2 @@
+CLUSTER  1  SEQS  34  IDS_UNIQUE  34  MODELS  1  
+CLUSTER  2  SEQS  4   IDS_UNIQUE  4   MODELS  1  
diff -r 000000000000 -r 0a48b2db75e7 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	Sat Oct 27 13:49:00 2018 -0400
@@ -0,0 +1,2 @@
+1.1  1.1  
+1.2  1.2  
diff -r 000000000000 -r 0a48b2db75e7 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	Sat Oct 27 13:49:00 2018 -0400
@@ -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 0a48b2db75e7 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	Sat Oct 27 13:49:00 2018 -0400
@@ -0,0 +1,38 @@
+SEQ31#1#73#+   88.9   1.2e-150  1.1  1.1  1  
+SEQ11#1#82#+   88.3   8e-150    1.1  1.1  1  
+SEQ9#1#73#+    87.8   4.6e-149  1.1  1.1  1  
+SEQ32#1#73#+   87.3   2.6e-148  1.1  1.1  1  
+SEQ13#1#82#+   86.3   8.9e-147  1.1  1.1  1  
+SEQ36#1#73#+   83.0   1.1e-141  1.1  1.1  1  
+SEQ12#1#82#+   82.7   3.1e-141  1.1  1.1  1  
+SEQ26#1#72#+   82.0   4.9e-140  1.1  1.1  1  
+SEQ5#1#72#+    81.7   1.3e-139  1.1  1.1  1  
+SEQ50#1#73#+   80.8   3.1e-138  1.1  1.1  1  
+SEQ28#1#71#+   80.7   4.6e-138  1.1  1.1  1  
+SEQ15#1#73#+   80.6   5.9e-138  1.1  1.1  1  
+SEQ24#1#73#+   80.3   1.5e-137  1.1  1.1  1  
+SEQ4#1#73#+    79.2   7.3e-136  1.1  1.1  1  
+SEQ46#1#72#+   78.4   1.3e-134  1.1  1.1  1  
+SEQ17#1#71#+   77.7   1.6e-133  1.1  1.1  1  
+SEQ10#1#73#+   76.3   2.8e-131  1.1  1.1  1  
+SEQ37#1#82#+   76.3   2.5e-131  1.1  1.1  1  
+SEQ23#1#74#+   75.9   1.2e-130  1.1  1.1  1  
+SEQ20#1#72#+   75.8   1.7e-130  1.1  1.1  1  
+SEQ16#1#72#+   74.9   4e-129    1.1  1.1  1  
+SEQ30#1#72#+   74.9   4e-129    1.1  1.1  1  
+SEQ21#1#74#+   74.8   4.8e-129  1.1  1.1  1  
+SEQ18#1#72#+   72.9   4.3e-126  1.1  1.1  1  
+SEQ35#1#72#+   71.9   1.2e-124  1.1  1.1  1  
+SEQ45#1#72#+   71.6   4.5e-124  1.1  1.1  1  
+SEQ7#1#83#+    71.2   2e-123    1.1  1.1  1  
+SEQ33#1#72#+   69.2   2e-120    1.1  1.1  1  
+SEQ19#1#82#+   69.0   4e-120    1.1  1.1  1  
+SEQ22#1#72#+   48.1   5.1e-88   1.1  1.1  1  
+SEQ40#1#66#+   44.2   4.7e-82   1.1  1.1  1  
+SEQ29#1#66#+   31.0   8.7e-62   1.1  1.1  1  
+SEQ14#1#73#+   29.5   2.2e-59   1.1  1.1  1  
+SEQ39#1#69#+   21.6   2.5e-47   1.1  1.1  1  
+SEQ74#1#100#+  163.2  7.9e-68   1.2  1.2  2  
+SEQ72#1#100#+  163.1  8.9e-68   1.2  1.2  2  
+SEQ73#1#100#+  161.5  3.4e-67   1.2  1.2  2  
+SEQ75#1#100#+  160.5  8.2e-67   1.2  1.2  2  
diff -r 000000000000 -r 0a48b2db75e7 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	Sat Oct 27 13:49:00 2018 -0400
@@ -0,0 +1,38 @@
+SEQ31#1#73#+   88.9   1.2e-150  1.1  1.1  1  
+SEQ11#1#82#+   88.3   8e-150    1.1  1.1  1  
+SEQ9#1#73#+    87.8   4.6e-149  1.1  1.1  1  
+SEQ32#1#73#+   87.3   2.6e-148  1.1  1.1  1  
+SEQ13#1#82#+   86.3   8.9e-147  1.1  1.1  1  
+SEQ36#1#73#+   83.0   1.1e-141  1.1  1.1  1  
+SEQ12#1#82#+   82.7   3.1e-141  1.1  1.1  1  
+SEQ26#1#72#+   82.0   4.9e-140  1.1  1.1  1  
+SEQ5#1#72#+    81.7   1.3e-139  1.1  1.1  1  
+SEQ50#1#73#+   80.8   3.1e-138  1.1  1.1  1  
+SEQ28#1#71#+   80.7   4.6e-138  1.1  1.1  1  
+SEQ15#1#73#+   80.6   5.9e-138  1.1  1.1  1  
+SEQ24#1#73#+   80.3   1.5e-137  1.1  1.1  1  
+SEQ4#1#73#+    79.2   7.3e-136  1.1  1.1  1  
+SEQ46#1#72#+   78.4   1.3e-134  1.1  1.1  1  
+SEQ17#1#71#+   77.7   1.6e-133  1.1  1.1  1  
+SEQ10#1#73#+   76.3   2.8e-131  1.1  1.1  1  
+SEQ37#1#82#+   76.3   2.5e-131  1.1  1.1  1  
+SEQ23#1#74#+   75.9   1.2e-130  1.1  1.1  1  
+SEQ20#1#72#+   75.8   1.7e-130  1.1  1.1  1  
+SEQ16#1#72#+   74.9   4e-129    1.1  1.1  1  
+SEQ30#1#72#+   74.9   4e-129    1.1  1.1  1  
+SEQ21#1#74#+   74.8   4.8e-129  1.1  1.1  1  
+SEQ18#1#72#+   72.9   4.3e-126  1.1  1.1  1  
+SEQ35#1#72#+   71.9   1.2e-124  1.1  1.1  1  
+SEQ45#1#72#+   71.6   4.5e-124  1.1  1.1  1  
+SEQ7#1#83#+    71.2   2e-123    1.1  1.1  1  
+SEQ33#1#72#+   69.2   2e-120    1.1  1.1  1  
+SEQ19#1#82#+   69.0   4e-120    1.1  1.1  1  
+SEQ22#1#72#+   48.1   5.1e-88   1.1  1.1  1  
+SEQ40#1#66#+   44.2   4.7e-82   1.1  1.1  1  
+SEQ29#1#66#+   31.0   8.7e-62   1.1  1.1  1  
+SEQ14#1#73#+   29.5   2.2e-59   1.1  1.1  1  
+SEQ39#1#69#+   21.6   2.5e-47   1.1  1.1  1  
+SEQ74#1#100#+  163.2  7.9e-68   1.2  1.2  2  
+SEQ72#1#100#+  163.1  8.9e-68   1.2  1.2  2  
+SEQ73#1#100#+  161.5  3.4e-67   1.2  1.2  2  
+SEQ75#1#100#+  160.5  8.2e-67   1.2  1.2  2  
diff -r 000000000000 -r 0a48b2db75e7 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	Sat Oct 27 13:49:00 2018 -0400
@@ -0,0 +1,38 @@
+SEQ31#1#73#+   88.9   1.2e-150  1.1  1.1  1  
+SEQ11#1#82#+   88.3   8e-150    1.1  1.1  1  
+SEQ9#1#73#+    87.8   4.6e-149  1.1  1.1  1  
+SEQ32#1#73#+   87.3   2.6e-148  1.1  1.1  1  
+SEQ13#1#82#+   86.3   8.9e-147  1.1  1.1  1  
+SEQ36#1#73#+   83.0   1.1e-141  1.1  1.1  1  
+SEQ12#1#82#+   82.7   3.1e-141  1.1  1.1  1  
+SEQ26#1#72#+   82.0   4.9e-140  1.1  1.1  1  
+SEQ5#1#72#+    81.7   1.3e-139  1.1  1.1  1  
+SEQ50#1#73#+   80.8   3.1e-138  1.1  1.1  1  
+SEQ28#1#71#+   80.7   4.6e-138  1.1  1.1  1  
+SEQ15#1#73#+   80.6   5.9e-138  1.1  1.1  1  
+SEQ24#1#73#+   80.3   1.5e-137  1.1  1.1  1  
+SEQ4#1#73#+    79.2   7.3e-136  1.1  1.1  1  
+SEQ46#1#72#+   78.4   1.3e-134  1.1  1.1  1  
+SEQ17#1#71#+   77.7   1.6e-133  1.1  1.1  1  
+SEQ10#1#73#+   76.3   2.8e-131  1.1  1.1  1  
+SEQ37#1#82#+   76.3   2.5e-131  1.1  1.1  1  
+SEQ23#1#74#+   75.9   1.2e-130  1.1  1.1  1  
+SEQ20#1#72#+   75.8   1.7e-130  1.1  1.1  1  
+SEQ16#1#72#+   74.9   4e-129    1.1  1.1  1  
+SEQ30#1#72#+   74.9   4e-129    1.1  1.1  1  
+SEQ21#1#74#+   74.8   4.8e-129  1.1  1.1  1  
+SEQ18#1#72#+   72.9   4.3e-126  1.1  1.1  1  
+SEQ35#1#72#+   71.9   1.2e-124  1.1  1.1  1  
+SEQ45#1#72#+   71.6   4.5e-124  1.1  1.1  1  
+SEQ7#1#83#+    71.2   2e-123    1.1  1.1  1  
+SEQ33#1#72#+   69.2   2e-120    1.1  1.1  1  
+SEQ19#1#82#+   69.0   4e-120    1.1  1.1  1  
+SEQ22#1#72#+   48.1   5.1e-88   1.1  1.1  1  
+SEQ40#1#66#+   44.2   4.7e-82   1.1  1.1  1  
+SEQ29#1#66#+   31.0   8.7e-62   1.1  1.1  1  
+SEQ14#1#73#+   29.5   2.2e-59   1.1  1.1  1  
+SEQ39#1#69#+   21.6   2.5e-47   1.1  1.1  1  
+SEQ74#1#100#+  163.2  7.9e-68   1.2  1.2  2  
+SEQ72#1#100#+  163.1  8.9e-68   1.2  1.2  2  
+SEQ73#1#100#+  161.5  3.4e-67   1.2  1.2  2  
+SEQ75#1#100#+  160.5  8.2e-67   1.2  1.2  2  
diff -r 000000000000 -r 0a48b2db75e7 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	Sat Oct 27 13:49:00 2018 -0400
@@ -0,0 +1,2 @@
+1.1
+1.2
diff -r 000000000000 -r 0a48b2db75e7 test-data/combined_cm_out
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/combined_cm_out	Sat Oct 27 13:49:00 2018 -0400
@@ -0,0 +1,53 @@
+##.1.1
+SEQ31	-	dataset_60	-	cm	1	73	1	73	+	no	1	0.56	0.0	88.9	1.2e-150	!	ORIGID RF00005_rep.34_AC008443.10/43006-42934_31 ORIGHEAD RF00005
+SEQ11	-	dataset_60	-	cm	1	73	1	82	+	no	1	0.62	0.0	88.3	8e-150	!	ORIGID RF00005_rep.16_AL133551.13/12355-12436_11 ORIGHEAD RF00005
+SEQ9	-	dataset_60	-	cm	1	73	1	73	+	no	1	0.56	0.0	87.8	4.6e-149	!	ORIGID RF00005_rep.14_AL021808.2/65570-65498_9 ORIGHEAD RF00005
+SEQ32	-	dataset_60	-	cm	1	73	1	73	+	no	1	0.58	0.0	87.3	2.6e-148	!	ORIGID RF00005_rep.35_AC005783.1/27398-27326_32 ORIGHEAD RF00005
+SEQ13	-	dataset_60	-	cm	1	73	1	82	+	no	1	0.56	0.0	86.3	8.9e-147	!	ORIGID RF00005_rep.18_AL021918.1/81116-81197_13 ORIGHEAD RF00005
+SEQ36	-	dataset_60	-	cm	1	73	1	73	+	no	1	0.51	0.0	83.0	1.1e-141	!	ORIGID RF00005_rep.39_AL031229.2/40502-40430_36 ORIGHEAD RF00005
+SEQ12	-	dataset_60	-	cm	1	73	1	82	+	no	1	0.57	0.0	82.7	3.1e-141	!	ORIGID RF00005_rep.17_AL021918.1/54817-54736_12 ORIGHEAD RF00005
+SEQ26	-	dataset_60	-	cm	1	73	1	72	+	no	1	0.50	0.0	82.0	4.9e-140	!	ORIGID RF00005_rep.2_AL662865.4/12206-12135_26 ORIGHEAD RF00005
+SEQ5	-	dataset_60	-	cm	1	73	1	72	+	no	1	0.51	0.0	81.7	1.3e-139	!	ORIGID RF00005_rep.10_X58792.1/174-245_5 ORIGHEAD RF00005
+SEQ50	-	dataset_60	-	cm	1	73	1	73	+	no	1	0.56	0.0	80.8	3.1e-138	!	ORIGID RF00005_rep.9_AP000442.6/2022-1950_50 ORIGHEAD RF00005
+SEQ28	-	dataset_60	-	cm	1	73	1	71	+	no	1	0.62	0.0	80.7	4.6e-138	!	ORIGID RF00005_rep.31_AC092686.3/29631-29561_28 ORIGHEAD RF00005
+SEQ15	-	dataset_60	-	cm	1	73	1	73	+	no	1	0.53	0.0	80.6	5.9e-138	!	ORIGID RF00005_rep.1_AC005329.1/7043-6971_15 ORIGHEAD RF00005
+SEQ24	-	dataset_60	-	cm	1	73	1	73	+	no	1	0.56	0.0	80.3	1.5e-137	!	ORIGID RF00005_rep.28_X04779.1/1-73_24 ORIGHEAD RF00005
+SEQ4	-	dataset_60	-	cm	1	73	1	73	+	no	1	0.56	0.0	79.2	7.3e-136	!	ORIGID RF00005_rep.0_M15347.1/1040-968_4 ORIGHEAD RF00005
+SEQ46	-	dataset_60	-	cm	1	73	1	72	+	no	1	0.65	0.0	78.4	1.3e-134	!	ORIGID RF00005_rep.5_AL590385.23/26129-26058_46 ORIGHEAD RF00005
+SEQ17	-	dataset_60	-	cm	1	73	1	71	+	no	1	0.59	0.0	77.7	1.6e-133	!	ORIGID RF00005_rep.21_AL355149.13/15278-15208_17 ORIGHEAD RF00005
+SEQ37	-	dataset_60	-	cm	1	73	1	82	+	no	1	0.63	0.0	76.3	2.5e-131	!	ORIGID RF00005_rep.3_Z54587.1/126-45_37 ORIGHEAD RF00005
+SEQ10	-	dataset_60	-	cm	1	73	1	73	+	no	1	0.62	0.0	76.3	2.8e-131	!	ORIGID RF00005_rep.15_AC008443.10/42590-42518_10 ORIGHEAD RF00005
+SEQ23	-	dataset_60	-	cm	1	73	1	74	+	no	1	0.61	0.0	75.9	1.2e-130	!	ORIGID RF00005_rep.27_AL352978.6/119697-119770_23 ORIGHEAD RF00005
+SEQ20	-	dataset_60	-	cm	1	73	1	72	+	no	1	0.56	0.0	75.8	1.7e-130	!	ORIGID RF00005_rep.24_AC004941.2/32735-32806_20 ORIGHEAD RF00005
+SEQ30	-	dataset_60	-	cm	1	73	1	72	+	no	1	0.61	0.0	74.9	4e-129	!	ORIGID RF00005_rep.33_AC018638.5/4694-4623_30 ORIGHEAD RF00005
+SEQ16	-	dataset_60	-	cm	1	73	1	72	+	no	1	0.61	0.0	74.9	4e-129	!	ORIGID RF00005_rep.20_AL671879.2/100356-100285_16 ORIGHEAD RF00005
+SEQ21	-	dataset_60	-	cm	1	73	1	74	+	no	1	0.61	0.0	74.8	4.8e-129	!	ORIGID RF00005_rep.25_AC006449.19/196857-196784_21 ORIGHEAD RF00005
+SEQ18	-	dataset_60	-	cm	1	73	1	72	+	no	1	0.58	0.0	72.9	4.3e-126	!	ORIGID RF00005_rep.22_AL590385.23/26487-26416_18 ORIGHEAD RF00005
+SEQ35	-	dataset_60	-	cm	1	73	1	72	+	no	1	0.65	0.0	71.9	1.2e-124	!	ORIGID RF00005_rep.38_J00309.1/356-427_35 ORIGHEAD RF00005
+SEQ45	-	dataset_60	-	cm	1	73	1	72	+	no	1	0.60	0.0	71.6	4.5e-124	!	ORIGID RF00005_rep.4_Z98744.2/66305-66234_45 ORIGHEAD RF00005
+SEQ7	-	dataset_60	-	cm	1	73	1	83	+	no	1	0.63	0.0	71.2	2e-123	!	ORIGID RF00005_rep.12_AC108081.2/59868-59786_7 ORIGHEAD RF00005
+SEQ33	-	dataset_60	-	cm	1	73	1	72	+	no	1	0.62	0.0	69.2	2e-120	!	ORIGID RF00005_rep.36_AC007298.17/145366-145295_33 ORIGHEAD RF00005
+SEQ19	-	dataset_60	-	cm	1	73	1	82	+	no	1	0.59	0.0	69.0	4e-120	!	ORIGID RF00005_rep.23_M16479.1/42-123_19 ORIGHEAD RF00005
+SEQ22	-	dataset_60	-	cm	1	73	1	72	+	no	1	0.49	0.0	48.1	5.1e-88	!	ORIGID RF00005_rep.26_AF346999.1/4402-4331_22 ORIGHEAD RF00005
+SEQ40	-	dataset_60	-	cm	1	73	1	66	+	no	1	0.45	0.0	44.2	4.7e-82	!	ORIGID RF00005_rep.42_AF347015.1/5827-5762_40 ORIGHEAD RF00005
+SEQ29	-	dataset_60	-	cm	1	73	1	66	+	no	1	0.42	0.0	31.0	8.7e-62	!	ORIGID RF00005_rep.32_AF347015.1/5892-5827_29 ORIGHEAD RF00005
+SEQ14	-	dataset_60	-	cm	1	73	1	73	+	no	1	0.41	0.0	29.5	2.2e-59	!	ORIGID RF00005_rep.19_AF134583.1/1816-1744_14 ORIGHEAD RF00005
+SEQ39	-	dataset_60	-	cm	1	73	1	69	+	no	1	0.39	0.0	21.6	2.5e-47	!	ORIGID RF00005_rep.41_AC093311.2/140036-139968_39 ORIGHEAD RF00005
+SEQ48	-	dataset_60	-	cm	1	73	1	71	+	no	1	0.35	0.0	12.9	5.7e-34	!	ORIGID RF00005_rep.7_AF347005.1/12268-12338_48 ORIGHEAD RF00005
+SEQ34	-	dataset_60	-	cm	1	73	1	68	+	no	1	0.34	0.0	12.8	9.6e-34	!	ORIGID RF00005_rep.37_AF347001.1/16015-15948_34 ORIGHEAD RF00005
+SEQ6	-	dataset_60	-	cm	1	73	1	66	+	no	1	0.38	0.0	12.1	1.1e-32	!	ORIGID RF00005_rep.11_AF346992.1/15890-15955_6 ORIGHEAD RF00005
+SEQ42	-	dataset_60	-	cm	1	73	1	69	+	no	1	0.38	0.0	9.4	1.4e-28	!	ORIGID RF00005_rep.44_AC008670.6/83597-83665_42 ORIGHEAD RF00005
+SEQ8	-	dataset_60	-	cm	1	73	1	70	+	no	1	0.33	0.0	9.0	6.2e-28	!	ORIGID RF00005_rep.13_AC067849.6/4771-4840_8 ORIGHEAD RF00005
+SEQ27	-	dataset_60	-	cm	1	73	1	69	+	no	1	0.43	0.0	8.6	3.1e-27	!	ORIGID RF00005_rep.30_AL132988.4/95773-95841_27 ORIGHEAD RF00005
+SEQ41	-	dataset_60	-	cm	1	73	1	68	+	no	1	0.26	0.1	7.7	6e-26	!	ORIGID RF00005_rep.43_L23320.1/77-10_41 ORIGHEAD RF00005
+SEQ43	-	dataset_60	-	cm	1	73	1	71	+	no	1	0.41	0.0	4.3	1.1e-20	!	ORIGID RF00005_rep.45_AF382005.1/581-651_43 ORIGHEAD RF00005
+SEQ25	-	dataset_60	-	cm	1	73	1	69	+	no	1	0.29	0.0	4.2	1.8e-20	!	ORIGID RF00005_rep.29_AF381996.2/4265-4333_25 ORIGHEAD RF00005
+SEQ44	-	dataset_60	-	cm	1	73	1	69	+	no	1	0.42	0.0	1.2	6.2e-16	!	ORIGID RF00005_rep.46_AF347015.1/1604-1672_44 ORIGHEAD RF00005
+SEQ38	-	dataset_60	-	cm	1	73	1	65	+	no	1	0.23	0.5	-0.9	1.1e-12	!	ORIGID RF00005_rep.40_AF382013.1/10403-10467_38 ORIGHEAD RF00005
+SEQ47	-	dataset_60	-	cm	1	73	1	68	+	no	1	0.24	0.5	-1.5	9.1e-12	!	ORIGID RF00005_rep.6_X93334.1/6942-7009_47 ORIGHEAD RF00005
+SEQ49	-	dataset_60	-	cm	1	73	1	68	+	no	1	0.35	0.0	-4.4	2.9e-07	!	ORIGID RF00005_rep.8_AF134583.1/1599-1666_49 ORIGHEAD RF00005
+##.1.2
+SEQ74	-	dataset_61	-	cm	1	100	1	100	+	no	1	0.51	0.0	163.2	7.9e-68	!	ORIGID RF00618_rep.2_U62822.1/2-128_74 ORIGHEAD RF00618
+SEQ72	-	dataset_61	-	cm	1	100	1	100	+	no	1	0.49	0.0	163.1	8.9e-68	!	ORIGID RF00618_rep.0_AL135914.25/92223-92098_72 ORIGHEAD RF00618
+SEQ73	-	dataset_61	-	cm	1	100	1	100	+	no	1	0.49	0.0	161.5	3.4e-67	!	ORIGID RF00618_rep.1_AL161445.10/77816-77941_73 ORIGHEAD RF00618
+SEQ75	-	dataset_61	-	cm	1	100	1	100	+	no	1	0.44	0.0	160.5	8.2e-67	!	ORIGID RF00618_rep.3_AL389925.10/20736-20611_75 ORIGHEAD RF00618
diff -r 000000000000 -r 0a48b2db75e7 test-data/evaluation1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/evaluation1.txt	Sat Oct 27 13:49:00 2018 -0400
@@ -0,0 +1,5 @@
+completeness_score : 0.533962565156
+homogeneity_score : 1.0
+adjusted_rand_score : 0.551625093777
+adjusted_mutual_info_score : 0.291033044987
+v_measure_score : 0.696187217713