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changeset 0:33e8ed5a4601 draft default tip

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Imported from capsule None
author devteam
date Mon, 27 Jan 2014 09:25:34 -0500
parents
children
files lca.py lca.xml test-data/lca_input.taxonomy test-data/lca_input2.taxonomy test-data/lca_input3.taxonomy test-data/lca_output.taxonomy test-data/lca_output2.taxonomy test-data/lca_output3.taxonomy tool_dependencies.xml
diffstat 9 files changed, 450 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lca.py	Mon Jan 27 09:25:34 2014 -0500
@@ -0,0 +1,193 @@
+#!/usr/bin/env python
+#Guruprasad Ananda
+"""
+Least Common Ancestor tool.
+"""
+import sys, string, re, commands, tempfile, random
+
+def stop_err(msg):
+    sys.stderr.write(msg)
+    sys.exit()
+
+def main():
+    try:
+        inputfile = sys.argv[1]
+        outfile = sys.argv[2]
+        rank_bound = int( sys.argv[3] )
+        """
+        Mapping of ranks:
+        root        :2, 
+        superkingdom:3, 
+        kingdom     :4, 
+        subkingdom  :5, 
+        superphylum :6, 
+        phylum      :7, 
+        subphylum   :8, 
+        superclass  :9, 
+        class       :10, 
+        subclass    :11, 
+        superorder  :12, 
+        order       :13, 
+        suborder    :14, 
+        superfamily :15,
+        family      :16,
+        subfamily   :17,
+        tribe       :18,
+        subtribe    :19,
+        genus       :20,
+        subgenus    :21,
+        species     :22,
+        subspecies  :23,
+        """
+    except:
+        stop_err("Syntax error: Use correct syntax: program infile outfile")
+    
+    fin = open(sys.argv[1],'r')
+    for j, line in enumerate( fin ):
+        elems = line.strip().split('\t')
+        if len(elems) < 24:
+            stop_err("The format of the input dataset is incorrect. Taxonomy datatype should contain at least 24 columns.")
+        if j > 30:
+            break
+        cols = range(1,len(elems))
+    fin.close()
+       
+    group_col = 0
+    tmpfile = tempfile.NamedTemporaryFile()
+
+    try:
+        """
+        The -k option for the Posix sort command is as follows:
+        -k, --key=POS1[,POS2]
+        start a key at POS1, end it at POS2 (origin 1)
+        In other words, column positions start at 1 rather than 0, so 
+        we need to add 1 to group_col.
+        if POS2 is not specified, the newer versions of sort will consider the entire line for sorting. To prevent this, we set POS2=POS1.
+        """
+        command_line = "sort -f -k " + str(group_col+1) +"," + str(group_col+1) + " -o " + tmpfile.name + " " + inputfile
+    except Exception, exc:
+        stop_err( 'Initialization error -> %s' %str(exc) )
+        
+    error_code, stdout = commands.getstatusoutput(command_line)
+    
+    if error_code != 0:
+        stop_err( "Sorting input dataset resulted in error: %s: %s" %( error_code, stdout ))    
+
+    prev_item = ""
+    prev_vals = []
+    remaining_vals = []
+    skipped_lines = 0
+    fout = open(outfile, "w")
+    block_valid = False
+    
+    
+    for ii, line in enumerate( file( tmpfile.name )):
+        if line and not line.startswith( '#' ) and len(line.split('\t')) >= 24: #Taxonomy datatype should have at least 24 columns
+            line = line.rstrip( '\r\n' )
+            try:
+                fields = line.split("\t")
+                item = fields[group_col]
+                if prev_item != "":
+                    # At this level, we're grouping on values (item and prev_item) in group_col
+                    if item == prev_item:
+                        # Keep iterating and storing values until a new value is encountered.
+                        if block_valid:
+                            for i, col in enumerate(cols):
+                                if col >= 3:
+                                    prev_vals[i].append(fields[col].strip())
+                                    if len(set(prev_vals[i])) > 1:
+                                        block_valid = False
+                                        break
+                            
+                    else:   
+                        """
+                        When a new value is encountered, write the previous value and the 
+                        corresponding aggregate values into the output file.  This works 
+                        due to the sort on group_col we've applied to the data above.
+                        """
+                        out_list = ['']*24
+                        out_list[0] = str(prev_item)
+                        out_list[1] = str(prev_vals[0][0])
+                        out_list[2] = str(prev_vals[1][0])
+                        
+                        for k, col in enumerate(cols):
+                            if col >= 3 and col < 24:
+                                if len(set(prev_vals[k])) == 1:
+                                    out_list[col] = prev_vals[k][0]
+                                else:
+                                    break
+                        while k < 23:
+                            out_list[k+1] = 'n' 
+                            k += 1
+                        
+                        j = 0
+                        while True:
+                            try:
+                                out_list.append(str(prev_vals[23+j][0]))
+                                j += 1
+                            except:
+                                break
+                            
+                        if rank_bound == 0:     
+                            print >>fout, '\t'.join(out_list).strip()
+                        else:
+                            if ''.join(out_list[rank_bound:24]) != 'n'*( 24 - rank_bound ):
+                                print >>fout, '\t'.join(out_list).strip()
+                        
+                        block_valid = True
+                        prev_item = item   
+                        prev_vals = [] 
+                        for col in cols:
+                            val_list = []
+                            val_list.append(fields[col].strip())
+                            prev_vals.append(val_list)
+                        
+                else:
+                    # This only occurs once, right at the start of the iteration.
+                    block_valid = True
+                    prev_item = item    #groupby item
+                    for col in cols:    #everyting else
+                        val_list = []
+                        val_list.append(fields[col].strip())
+                        prev_vals.append(val_list)
+            
+            except:
+                skipped_lines += 1
+        else:
+            skipped_lines += 1
+            
+    # Handle the last grouped value
+    out_list = ['']*24
+    out_list[0] = str(prev_item)
+    out_list[1] = str(prev_vals[0][0])
+    out_list[2] = str(prev_vals[1][0])
+    
+    for k, col in enumerate(cols):
+        if col >= 3 and col < 24:
+            if len(set(prev_vals[k])) == 1:
+                out_list[col] = prev_vals[k][0]
+            else:
+                break
+    while k < 23:
+        out_list[k+1] = 'n' 
+        k += 1
+    
+    j = 0
+    while True:
+        try:
+            out_list.append(str(prev_vals[23+j][0]))
+            j += 1
+        except:
+            break
+        
+    if rank_bound == 0:     
+        print >>fout, '\t'.join(out_list).strip()
+    else:
+        if ''.join(out_list[rank_bound:24]) != 'n'*( 24 - rank_bound ):
+            print >>fout, '\t'.join(out_list).strip()
+        
+    if skipped_lines > 0:
+        print "Skipped %d invalid lines." % ( skipped_lines )
+    
+if __name__ == "__main__":
+    main()
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lca.xml	Mon Jan 27 09:25:34 2014 -0500
@@ -0,0 +1,100 @@
+<tool id="lca1" name="Find lowest diagnostic rank" version="1.0.1">
+  <description></description>
+    <requirements>
+        <requirement type="package" version="1.0.0">taxonomy</requirement>
+    </requirements>
+  <command interpreter="python">
+    lca.py $input1 $out_file1 $rank_bound
+  </command>
+  <inputs>
+    <param format="taxonomy" name="input1" type="data" label="for taxonomy dataset"/>
+    <param name="rank_bound" label="require the lowest rank to be at least" type="select">
+        <option value="0">No restriction</option>
+        <option value="3">Superkingdom</option>
+        <option value="4">Kingdom</option>
+        <option value="5">Subkingdom</option>
+        <option value="6">Superphylum</option>
+        <option value="7">Phylum</option>
+        <option value="8">Subphylum</option>
+        <option value="9">Superclass</option>
+        <option value="10">Class</option>
+        <option value="11">Subclass</option>
+        <option value="12">Superorder</option>
+        <option value="13">Order</option>
+        <option value="14">Suborder</option>
+        <option value="15">Superfamily</option>
+        <option value="16">Family</option>
+        <option value="17">Subfamily</option>
+        <option value="18">Tribe</option>
+        <option value="19">Subtribe</option>
+        <option value="20">Genus</option>
+        <option value="21">Subgenus</option>
+        <option value="22">Species</option>
+        <option value="23">Subspecies</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="taxonomy" name="out_file1" metadata_source="input1" />
+  </outputs>
+  <tests>
+     <test>
+          <param name="input1" value="lca_input.taxonomy" ftype="taxonomy"/>
+          <param name="rank_bound" value="0" />
+          <output name="out_file1" file="lca_output.taxonomy" ftype="taxonomy"/>
+     </test> 
+     <test>
+          <param name="input1" value="lca_input2.taxonomy" ftype="taxonomy"/>
+          <param name="rank_bound" value="7" />
+          <output name="out_file1" file="lca_output2.taxonomy" ftype="taxonomy"/>
+     </test> 
+     
+     <!--Test case with invalid lines -->
+     <test>
+          <param name="input1" value="lca_input3.taxonomy" ftype="taxonomy"/>
+          <param name="rank_bound" value="10" />
+          <output name="out_file1" file="lca_output3.taxonomy" ftype="taxonomy"/>
+     </test> 
+ </tests>
+
+ <help>
+
+**What it does**
+
+This tool identifies the lowest taxonomic rank for which a mategenomic sequencing read is diagnostic. It takes datasets produced by *Fetch Taxonomic Ranks* tool (aka Taxonomy format) as the input. 
+
+-------
+
+**Example**
+
+Suppose you have two reads, **read_1** and **read_2**, with the following taxonomic profiles (scroll sideways to see the entire dataset)::
+  
+    read_1 1 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 genus1 subgenus1 species1 subspecies1
+    read_1 2 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 genus2 subgenus2 species2 subspecies2
+    read_2 3 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum3 subphylum3 superclass3 class3 subclass3 superorder3 order3 suborder3 superfamily3 family3 subfamily3 tribe3 subtribe3 genus3 subgenus3 species3 subspecies3
+    read_2 4 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum4 subphylum4 superclass4 class4 subclass4 superorder4 order4 suborder4 superfamily4 family4 subfamily4 tribe4 subtribe4 genus4 subgenus4 species4 subspecies4
+
+For **read_1** taxonomic labels are consistent until the genus level, where the taxonomy splits into two branches, one ending with *subspecies1* and the other with *subspecies2*. This implies **that the lowest taxomomic rank read_1 can identify is SUBTRIBE**.  Similarly, read_2 is diagnostic up until the **superphylum** level.  As a results the output of this tool will be::
+
+    read_1 2 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 n n n n
+    read_2 3 root superkingdom1 kingdom1 subkingdom1 superphylum1 n       n          n           n      n         n           n      n         n            n       n          n      n         n n n n
+    
+where, **n** means *EMPTY*. 
+
+--------
+
+**What's up with the drop down?**
+
+Why do we need the *require the lowest rank to be at least* dropdown?  Let's look at the above example again. Suppose you need to find only those reads that are diagnostic on at least phylum level. To do this you need to set the *require the lowest rank to be at least* to **phylum**. As a result your output will look like this::
+
+    read_1 2 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 n n n n
+
+.. class:: infomark
+    
+Note, that **read_2** is now omitted as it matches two phyla (**phylum3** and **phylum4**) and therefore is not diagnostic (but rather cosmopolitan) on *phylum* level. 
+
+
+
+
+
+</help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lca_input.taxonomy	Mon Jan 27 09:25:34 2014 -0500
@@ -0,0 +1,4 @@
+read_1	1	root	superkingdom1	kingdom1	subkingdom1	superphylum1	phylum1	subphylum1	superclass1	class1	subclass1	superorder1	order1	suborder1	superfamily1	family1	subfamily1	tribe1	subtribe1	genus1	subgenus1	species1	subspecies1	1
+read_1	2	root	superkingdom1	kingdom1	subkingdom1	superphylum1	phylum1	subphylum1	superclass1	class1	subclass1	superorder1	order1	suborder1	superfamily1	family1	subfamily1	tribe1	subtribe1	genus2	subgenus2	species2	subspecies2	1
+read_2	3	root	superkingdom1	kingdom1	subkingdom1	superphylum1	phylum3	subphylum3	superclass3	class3	subclass3	superorder3	order3	suborder3	superfamily3	family3	subfamily3	tribe3	subtribe3	genus3	subgenus3	species3	subspecies3	1
+read_2	4	root	superkingdom1	kingdom1	subkingdom1	superphylum1	phylum4	subphylum4	superclass4	class4	subclass4	superorder4	order4	suborder4	superfamily4	family4	subfamily4	tribe4	subtribe4	genus4	subgenus4	species4	subspecies4	1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lca_input2.taxonomy	Mon Jan 27 09:25:34 2014 -0500
@@ -0,0 +1,4 @@
+read_1	1	root	superkingdom1	kingdom1	subkingdom1	superphylum1	phylum1	subphylum1	superclass1	class1	subclass1	superorder1	order1	suborder1	superfamily1	family1	subfamily1	tribe1	subtribe1	genus1	subgenus1	species1	subspecies1	1	2	3	4
+read_1	2	root	superkingdom1	kingdom1	subkingdom1	superphylum1	phylum1	subphylum1	superclass1	class1	subclass1	superorder1	order1	suborder1	superfamily1	family1	subfamily1	tribe1	subtribe1	genus2	subgenus2	species2	subspecies2	1	2	3	4
+read_2	3	root	superkingdom1	kingdom1	subkingdom1	superphylum1	phylum3	subphylum3	superclass3	class3	subclass3	superorder3	order3	suborder3	superfamily3	family3	subfamily3	tribe3	subtribe3	genus3	subgenus3	species3	subspecies3	1	X	Y	Z
+read_2	4	root	superkingdom1	kingdom1	subkingdom1	superphylum1	phylum4	subphylum4	superclass4	class4	subclass4	superorder4	order4	suborder4	superfamily4	family4	subfamily4	tribe4	subtribe4	genus4	subgenus4	species4	subspecies4	1	X	Y	Z
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lca_input3.taxonomy	Mon Jan 27 09:25:34 2014 -0500
@@ -0,0 +1,100 @@
+IA_1-79371	591020	root	Bacteria	n	n	n	Proteobacteria	n	n	Gammaproteobacteria	n	n	Enterobacteriales	n	n	Enterobacteriaceae	n	n	n	Shigella	n	Shigella flexneri	n	281604065
+IA_1-84488	591020	root	Bacteria	n	n	n	Proteobacteria	n	n	Gammaproteobacteria	n	n	Enterobacteriales	n	n	Enterobacteriaceae	n	n	n	Shigella	n	Shigella flexneri	n	281604065
+IA_1-270826	591020	root	Bacteria	n	n	n	Proteobacteria	n	n	Gammaproteobacteria	n	n	Enterobacteriales	n	n	Enterobacteriaceae	n	n	n	Shigella	n	Shigella flexneri	n	281604070
+IA_1-285361	591020	root	Bacteria	n	n	n	Proteobacteria	n	n	Gammaproteobacteria	n	n	Enterobacteriales	n	n	Enterobacteriaceae	n	n	n	Shigella	n	Shigella flexneri	n	281604070
+IA_1-93958	591020	root	Bacteria	n	n	n	Proteobacteria	n	n	Gammaproteobacteria	n	n	Enterobacteriales	n	n	Enterobacteriaceae	n	n	n	Shigella	n	Shigella flexneri	n	281604070
+IA_1-99821	591020	root	Bacteria	n	n	n	Proteobacteria	n	n	Gammaproteobacteria	n	n	Enterobacteriales	n	n	Enterobacteriaceae	n	n	n	Shigella	n	Shigella flexneri	n	281604070
+IA_1-144417	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604077
+IA_1-278966	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604077
+IA_1-314709	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604077
+IA_1-324951	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604077
+IA_1-27817	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604153
+IA_1-95255	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604181
+IA_1-104173	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
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+IA_1-160446	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-160446	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-161439	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-205154	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-205154	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-205154	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-205154	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-205154	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-205154	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-205154	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-205154	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-205154	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-205154	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-216231	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-236286	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-236286	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-236286	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-236286	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-236286	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-236286	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-236286	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-236286	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-236286	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-236286	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-236286	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-236286	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-237681	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-250166	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-254274	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-254274	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-27817	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-29000	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-291427	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-291427	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-293054	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-293054	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-296315	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-296315	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus
+IA_1-310974	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-310974	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-311282	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-311282	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-322295	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n
+IA_1-42600	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-45102	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-45102	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-48105	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-48105	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-57254	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-61975	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-61975	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-66943	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-68288	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-82334	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-95526	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lca_output.taxonomy	Mon Jan 27 09:25:34 2014 -0500
@@ -0,0 +1,2 @@
+read_1	1	root	superkingdom1	kingdom1	subkingdom1	superphylum1	phylum1	subphylum1	superclass1	class1	subclass1	superorder1	order1	suborder1	superfamily1	family1	subfamily1	tribe1	subtribe1	n	n	n	n	1
+read_2	3	root	superkingdom1	kingdom1	subkingdom1	superphylum1	n	n	n	n	n	n	n	n	n	n	n	n	n	n	n	n	n	1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lca_output2.taxonomy	Mon Jan 27 09:25:34 2014 -0500
@@ -0,0 +1,1 @@
+read_1	1	root	superkingdom1	kingdom1	subkingdom1	superphylum1	phylum1	subphylum1	superclass1	class1	subclass1	superorder1	order1	suborder1	superfamily1	family1	subfamily1	tribe1	subtribe1	n	n	n	n	1	2	3	4
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lca_output3.taxonomy	Mon Jan 27 09:25:34 2014 -0500
@@ -0,0 +1,40 @@
+IA_1-104173	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-135979	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-139090	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-144417	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604077
+IA_1-144996	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-160446	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-161439	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-190855	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-205154	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-216231	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-236286	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-237681	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-250166	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-254274	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-270826	591020	root	Bacteria	n	n	n	Proteobacteria	n	n	Gammaproteobacteria	n	n	Enterobacteriales	n	n	Enterobacteriaceae	n	n	n	Shigella	n	Shigella flexneri	n	281604070
+IA_1-27817	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604153
+IA_1-278966	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604077
+IA_1-285361	591020	root	Bacteria	n	n	n	Proteobacteria	n	n	Gammaproteobacteria	n	n	Enterobacteriales	n	n	Enterobacteriaceae	n	n	n	Shigella	n	Shigella flexneri	n	281604070
+IA_1-29000	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-291427	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-293054	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-296315	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-310974	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-311282	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-314709	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604077
+IA_1-324951	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604077
+IA_1-42600	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-45102	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-48105	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-57254	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-61975	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-66943	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-68288	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-79371	591020	root	Bacteria	n	n	n	Proteobacteria	n	n	Gammaproteobacteria	n	n	Enterobacteriales	n	n	Enterobacteriaceae	n	n	n	Shigella	n	Shigella flexneri	n	281604065
+IA_1-82334	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-84488	591020	root	Bacteria	n	n	n	Proteobacteria	n	n	Gammaproteobacteria	n	n	Enterobacteriales	n	n	Enterobacteriaceae	n	n	n	Shigella	n	Shigella flexneri	n	281604065
+IA_1-93958	591020	root	Bacteria	n	n	n	Proteobacteria	n	n	Gammaproteobacteria	n	n	Enterobacteriales	n	n	Enterobacteriaceae	n	n	n	Shigella	n	Shigella flexneri	n	281604070
+IA_1-95255	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604181
+IA_1-95526	10116	root	Eukaryota	Metazoa	n	n	Chordata	Craniata	Gnathostomata	Mammalia	n	Euarchontoglires	Rodentia	Sciurognathi	n	Muridae	Murinae	n	n	Rattus	n	Rattus norvegicus	n	281604186
+IA_1-99821	591020	root	Bacteria	n	n	n	Proteobacteria	n	n	Gammaproteobacteria	n	n	Enterobacteriales	n	n	Enterobacteriaceae	n	n	n	Shigella	n	Shigella flexneri	n	281604070
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Jan 27 09:25:34 2014 -0500
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="taxonomy" version="1.0.0">
+      <repository changeset_revision="c011d4659306" name="package_taxonomy_1_0_0" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>