Mercurial > repos > devteam > lca_wrapper

changeset 0:e1dea768b4c1 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Imported from capsule None
author devteam
date Thu, 23 Jan 2014 12:30:52 -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	Thu Jan 23 12:30:52 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	Thu Jan 23 12:30:52 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	Thu Jan 23 12:30:52 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	Thu Jan 23 12:30:52 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	Thu Jan 23 12:30:52 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
+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_1-139090	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_1-139090	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_1-144996	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_1-160446	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_1-160446	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_1-160446	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_1-160446	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	Thu Jan 23 12:30:52 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	Thu Jan 23 12:30:52 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	Thu Jan 23 12:30:52 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	Thu Jan 23 12:30:52 2014 -0500
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="taxonomy" version="1.0.0">
+      <repository changeset_revision="00dc297ecd07" name="package_taxonomy_1_0_0" owner="devteam" prior_installation_required="False" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>