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changeset 0:9959fa526f1a draft

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planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/compare_humann2_output commit c16428041ae3d60b61b6570035c9268726730543-dirty
author bebatut
date Wed, 20 Apr 2016 08:30:08 -0400
parents
children c1aca37cb1fc
files compare_humann2_output.py compare_humann2_output.xml test-data/humann2_fasta_pathabundance_relab_renormalized.csv test-data/humann2_m8_pathabundance_cmp_renormalized.tsv test-data/log_output.txt test-data/more_abundant_output.tabular test-data/similar_output.tabular test-data/specific_to_sample1_output.txt test-data/specific_to_sample2_output.txt
diffstat 9 files changed, 811 insertions(+), 0 deletions(-) [+]
line wrap: on
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/compare_humann2_output.py	Wed Apr 20 08:30:08 2016 -0400
@@ -0,0 +1,138 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import sys
+import os
+import argparse
+import re
+
+def extract_abundances(filepath, nb_charact_to_extract):
+    abundances = {}
+    more_abund_charact = []
+    abund_sum = 0
+    with open(filepath, 'r') as abundance_file:
+        for line in abundance_file.readlines()[1:]:
+            split_line = line[:-1].split('\t')
+            charact_id = split_line[0]
+            abund = float(split_line[1])
+            abundances[charact_id] = 100*abund
+            abund_sum += abundances[charact_id]
+
+            if len(more_abund_charact) < nb_charact_to_extract:
+                more_abund_charact.append(charact_id)
+            else:
+                best_pos = None
+                for i in range(len(more_abund_charact)-1,-1,-1):
+                    if abundances[more_abund_charact[i]] < abund:
+                        best_pos = i
+                    else:
+                        break
+                if best_pos != None:
+                    tmp_more_abund_charact = more_abund_charact
+                    more_abund_charact = tmp_more_abund_charact[:best_pos]
+                    more_abund_charact += [charact_id]
+                    more_abund_charact += tmp_more_abund_charact[best_pos:-1]
+    return abundances, more_abund_charact
+
+def format_characteristic_name(all_name):
+    if all_name.find(':') != -1:
+        charact_id = all_name.split(':')[0]
+        charact_name = all_name.split(':')[1][1:]
+    else:
+        charact_id = all_name
+        charact_name = ''
+
+    charact_name = charact_name.replace('/',' ')
+    charact_name = charact_name.replace('-',' ')
+    charact_name = charact_name.replace("'",'')
+    if charact_name.find('(') != -1 and charact_name.find(')') != -1:
+        open_bracket = charact_name.find('(')
+        close_bracket = charact_name.find(')')+1
+        charact_name = charact_name[:open_bracket] + charact_name[close_bracket:]
+    return charact_id,charact_name
+
+def write_more_abundant_charat(abundances,more_abund_charact, output_filepath):
+    with open(output_filepath,'w') as output_file:
+        output_file.write('id\tname\t')
+        output_file.write('\t'.join(abundances.keys()) + '\n')
+
+        for mac in more_abund_charact:
+            charact_id,charact_name = format_characteristic_name(mac)
+            output_file.write(charact_id + '\t' + charact_name)
+            for sample in abundances:
+                abund = abundances[sample].get(mac, 0)
+                output_file.write('\t' + str(abund))
+            output_file.write('\n')
+
+def extract_similar_characteristics(abundances, sim_output_filepath,
+    specific_output_files):
+    sim_characteristics = set(abundances[abundances.keys()[0]].keys())
+    for sample in abundances.keys()[1:]:
+        sim_characteristics.intersection_update(abundances[sample].keys())
+    print 'Similar between all samples:', len(sim_characteristics)
+
+    with open(sim_output_filepath, 'w') as sim_output_file:
+        sim_output_file.write('id\tname\t' + '\t'.join(abundances.keys()) + '\n')
+        for charact in list(sim_characteristics):
+            charact_id,charact_name = format_characteristic_name(charact)
+            sim_output_file.write(charact_id + '\t' + charact_name)
+            for sample in abundances.keys():
+                sim_output_file.write('\t' + str(abundances[sample][charact]))
+            sim_output_file.write('\n')
+
+    print 'Specific to samples:'
+    diff_characteristics = {}
+    for i in range(len(abundances.keys())):
+        sample = abundances.keys()[i]
+        print ' ', sample, ""
+        print '    All:', len(abundances[sample].keys())
+        diff_characteristics[sample] = set(abundances[sample].keys())
+        diff_characteristics[sample].difference_update(sim_characteristics)
+        print '    Number of specific characteristics:', 
+        print len(diff_characteristics[sample])
+        print '    Percentage of specific characteristics:',
+        print 100*len(diff_characteristics[sample])/(1.*len(abundances[sample].keys()))
+
+        relative_abundance = 0
+        with open(specific_output_files[i], 'w') as output_file:
+            output_file.write('id\tname\tabundances\n')
+            for charact in list(diff_characteristics[sample]):
+                charact_id,charact_name = format_characteristic_name(charact)
+                output_file.write(charact_id + '\t' + charact_name + '\t')
+                output_file.write(str(abundances[sample][charact]) + '\n')
+                relative_abundance += abundances[sample][charact]
+        print '    Relative abundance of specific characteristics(%):', relative_abundance
+
+    return sim_characteristics
+
+def compare_humann2_output(args):
+    abundances = {}
+    more_abund_charact = []
+
+    for i in range(len(args.sample_name)):
+        abundances[args.sample_name[i]], mac = extract_abundances(args.charact_input_file[i],
+            args.most_abundant_characteristics_to_extract)
+        more_abund_charact += mac
+
+    write_more_abundant_charat(abundances, list(set(more_abund_charact)), 
+        args.more_abundant_output_file)
+    sim_characteristics = extract_similar_characteristics(abundances, 
+        args.similar_output_file, args.specific_output_file)
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--sample_name', required=True, action='append')
+    parser.add_argument('--charact_input_file', required=True, action='append')
+    parser.add_argument('--most_abundant_characteristics_to_extract', required=True,
+        type = int)
+    parser.add_argument('--more_abundant_output_file', required=True)
+    parser.add_argument('--similar_output_file', required=True)
+    parser.add_argument('--specific_output_file', required=True,action='append')
+    args = parser.parse_args()
+
+    if len(args.sample_name) != len(args.charact_input_file):
+        raise ValueError("Same number of values (in same order) are expected for --sample_name and --charact_input_file")
+    if len(args.sample_name) != len(args.specific_output_file):
+        raise ValueError("Same number of values (in same order) are expected for --sample_name and --specific_output_file")
+
+    compare_humann2_output(args)
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/compare_humann2_output.xml	Wed Apr 20 08:30:08 2016 -0400
@@ -0,0 +1,86 @@
+<tool id="compare_humann2_output" name="Compare outputs of HUMAnN2 for several samples" version="0.1.0">
+    <description>and extract information</description>
+
+    <requirements>
+    </requirements>
+
+    <stdio>
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+
+    <version_command></version_command>
+
+    <command><![CDATA[
+        mkdir specifics 
+        &&
+
+        python $__tool_directory__/compare_humann2_output.py
+            #for $sample in $samples:
+                --sample_name "${sample.sample_name}"
+                --charact_input_file "${sample.input}"
+                --specific_output_file "specifics/specific_to_${sample.sample_name}.txt"
+            #end for
+
+            --most_abundant_characteristics_to_extract $charact_nb
+            --more_abundant_output_file $more_abundant_output_file
+            --similar_output_file $similar_output_file
+            > $log
+                
+    ]]></command>
+
+    <inputs>
+        <repeat name="samples" title="Add sample and input file (HUMAnN2 output after normalization)" >
+            <param name="sample_name" type="text" label="Name of the sample" help="(--sample_name)"/>
+            <param name="input" format="txt,tabular" type="data" label="Input file corresponding to HUMAnN2 output" help="The HUMAnN2 output file contains relative abundance of gene families or pathways (after normalization, --charact_input_file)"/>
+        </repeat>
+
+        <param name="charact_nb" type="integer" value="10" label="Number of most abundant characteristics to extract for each sample" help="(--most_abundant_characteristics_to_extract)"/>
+    </inputs>
+
+    <outputs>
+        <data name="more_abundant_output_file" format="tabular"
+            label="${tool.name} on ${on_string}: More abundant characteristics for each sample" />
+        <data name="similar_output_file" format="tabular"
+            label="${tool.name} on ${on_string}: Similar characteristics and the relative abundances for all samples" />
+        <data name="log" format="txt"
+            label="${tool.name} on ${on_string}: Log" />
+        <collection name="specific_files" type="list">
+            <discover_datasets pattern="__designation_and_ext__" directory="specifics"/>
+        </collection>
+
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="samples_0|sample_name" value="sample1"/>
+            <param name="samples_0|input" value="humann2_m8_pathabundance_cmp_renormalized.tsv"/>
+            <param name="samples_1|sample_name" value="sample2"/>
+            <param name="samples_1|input" value="humann2_fasta_pathabundance_relab_renormalized.csv"/>
+            <param name="charact_nb" value="10"/>
+            <output name="more_abundant_output_file" file="more_abundant_output.tabular"/>
+            <output name="similar_output_file" file="similar_output.tabular"/>
+            <output name="log" file="log_output.txt"/>
+            <output_collection name="specific_files" type="list">
+                <element name="specific_to_sample1" file="specific_to_sample1_output.txt" />
+                <element name="specific_to_sample2" file="specific_to_sample2_output.txt" />
+            </output_collection>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+**What it does**
+
+This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples. Several files are extracted:
+
+  * Similar gene families or pathways between the samples and the relative abundances of these similar characteristics
+
+  * Most abundant gene families or pathways for each sample and the corresponding relative abundance in all samples
+  
+  * Specific gene families and pathways for each samples and the relative abundances of these specific characteristics
+
+    ]]></help>
+
+    <citations>
+    </citations>
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/humann2_fasta_pathabundance_relab_renormalized.csv	Wed Apr 20 08:30:08 2016 -0400
@@ -0,0 +1,267 @@
+# Pathway	humann2_Abundance
+PYRIDOXSYN-PWY: pyridoxal 5'-phosphate biosynthesis I	0.0245442
+PYRIDOXSYN-PWY: pyridoxal 5'-phosphate biosynthesis I|unclassified	0.0341296
+PWY-3841: folate transformations II	0.0238544
+PWY-3841: folate transformations II|unclassified	0.0227477
+1CMET2-PWY: N10-formyl-tetrahydrofolate biosynthesis	0.0212689
+1CMET2-PWY: N10-formyl-tetrahydrofolate biosynthesis|unclassified	0.00834716
+PWY-7208: superpathway of pyrimidine nucleobases salvage	0.0206908
+PWY-7208: superpathway of pyrimidine nucleobases salvage|unclassified	0.0175918
+COA-PWY-1: coenzyme A biosynthesis II (mammalian)	0.019437
+PWY-7221: guanosine ribonucleotides de novo biosynthesis	0.0188123
+CALVIN-PWY: Calvin-Benson-Bassham cycle	0.0179034
+CALVIN-PWY: Calvin-Benson-Bassham cycle|unclassified	0.0240344
+PWY66-422: D-galactose degradation V (Leloir pathway)	0.0175745
+PWY66-422: D-galactose degradation V (Leloir pathway)|g__Bacteroides.s__Bacteroides_stercoris	0.0149592
+PWY66-422: D-galactose degradation V (Leloir pathway)|unclassified	0.0104266
+PWY-1042: glycolysis IV (plant cytosol)	0.0175553
+PWY-1042: glycolysis IV (plant cytosol)|unclassified	0.0193529
+PWY-5100: pyruvate fermentation to acetate and lactate II	0.0170667
+PWY-5100: pyruvate fermentation to acetate and lactate II|unclassified	0.0126625
+DTDPRHAMSYN-PWY: dTDP-L-rhamnose biosynthesis I	0.0169441
+DTDPRHAMSYN-PWY: dTDP-L-rhamnose biosynthesis I|unclassified	0.0250835
+PWY-7228: superpathway of guanosine nucleotides de novo biosynthesis I	0.0169262
+HOMOSER-METSYN-PWY: L-methionine biosynthesis I	0.0158217
+HOMOSER-METSYN-PWY: L-methionine biosynthesis I|unclassified	0.0109381
+PWY-7219: adenosine ribonucleotides de novo biosynthesis	0.0157923
+PWY-7219: adenosine ribonucleotides de novo biosynthesis|unclassified	0.0333171
+PWY-7229: superpathway of adenosine nucleotides de novo biosynthesis I	0.0155872
+PWY-7229: superpathway of adenosine nucleotides de novo biosynthesis I|unclassified	0.0261337
+PWY-6125: superpathway of guanosine nucleotides de novo biosynthesis II	0.0155645
+PWY-5505: L-glutamate and L-glutamine biosynthesis	0.0153682
+PWY-5505: L-glutamate and L-glutamine biosynthesis|unclassified	0.0196045
+PWY-5505: L-glutamate and L-glutamine biosynthesis|g__Bacteroides.s__Bacteroides_thetaiotaomicron	0.0144739
+PWY-6126: superpathway of adenosine nucleotides de novo biosynthesis II	0.0150984
+PWY-6126: superpathway of adenosine nucleotides de novo biosynthesis II|unclassified	0.0244065
+PWY-7220: adenosine deoxyribonucleotides de novo biosynthesis II	0.0148474
+PWY-7220: adenosine deoxyribonucleotides de novo biosynthesis II|unclassified	0.0201368
+PWY-7222: guanosine deoxyribonucleotides de novo biosynthesis II	0.0148474
+PWY-7222: guanosine deoxyribonucleotides de novo biosynthesis II|unclassified	0.0201368
+PWY-6703: preQ0 biosynthesis	0.0139768
+PWY-6703: preQ0 biosynthesis|unclassified	0.013368
+PWY-5659: GDP-mannose biosynthesis	0.013223
+PWY-5659: GDP-mannose biosynthesis|unclassified	0.00106616
+SER-GLYSYN-PWY: superpathway of L-serine and glycine biosynthesis I	0.012955
+SER-GLYSYN-PWY: superpathway of L-serine and glycine biosynthesis I|unclassified	0.00288758
+ILEUSYN-PWY: L-isoleucine biosynthesis I (from threonine)	0.0129401
+ILEUSYN-PWY: L-isoleucine biosynthesis I (from threonine)|unclassified	0.0159474
+VALSYN-PWY: L-valine biosynthesis	0.0129401
+VALSYN-PWY: L-valine biosynthesis|unclassified	0.0159474
+PWY-6936: seleno-amino acid biosynthesis	0.012799
+PWY-6936: seleno-amino acid biosynthesis|unclassified	0.0132349
+PWY-5030: L-histidine degradation III	0.0122713
+PWY-5030: L-histidine degradation III|unclassified	0.0120381
+HSERMETANA-PWY: L-methionine biosynthesis III	0.0121379
+HSERMETANA-PWY: L-methionine biosynthesis III|unclassified	0.00515875
+PWY0-162: superpathway of pyrimidine ribonucleotides de novo biosynthesis	0.0119161
+PWY0-162: superpathway of pyrimidine ribonucleotides de novo biosynthesis|unclassified	0.00295685
+PWY-4984: urea cycle	0.0118794
+GLUCONEO-PWY: gluconeogenesis I	0.0118442
+PWY-7400: L-arginine biosynthesis IV (archaebacteria)	0.0118235
+ARGSYN-PWY: L-arginine biosynthesis I (via L-ornithine)	0.0116946
+GALACTUROCAT-PWY: D-galacturonate degradation I	0.0112548
+ASPASN-PWY: superpathway of L-aspartate and L-asparagine biosynthesis	0.0109751
+ASPASN-PWY: superpathway of L-aspartate and L-asparagine biosynthesis|unclassified	0.0192205
+PWY-5097: L-lysine biosynthesis VI	0.0104893
+PWY-5097: L-lysine biosynthesis VI|unclassified	0.0116003
+ANAGLYCOLYSIS-PWY: glycolysis III (from glucose)	0.0103937
+ANAGLYCOLYSIS-PWY: glycolysis III (from glucose)|unclassified	0.0185171
+PWY-7242: D-fructuronate degradation	0.0103935
+BRANCHED-CHAIN-AA-SYN-PWY: superpathway of branched amino acid biosynthesis	0.0102856
+BRANCHED-CHAIN-AA-SYN-PWY: superpathway of branched amino acid biosynthesis|unclassified	0.00857417
+ARGSYNBSUB-PWY: L-arginine biosynthesis II (acetyl cycle)	0.0102161
+ARGSYNBSUB-PWY: L-arginine biosynthesis II (acetyl cycle)|unclassified	0.0131054
+PWY-6124: inosine-5'-phosphate biosynthesis II	0.0101549
+PWY-6124: inosine-5'-phosphate biosynthesis II|unclassified	0.0222455
+PWY-6507: 4-deoxy-L-threo-hex-4-enopyranuronate degradation	0.0100585
+PWY-5686: UMP biosynthesis	0.00980672
+PWY-5686: UMP biosynthesis|unclassified	0.017892
+PWY-6151: S-adenosyl-L-methionine cycle I	0.00977587
+CITRULBIO-PWY: L-citrulline biosynthesis	0.00974607
+CITRULBIO-PWY: L-citrulline biosynthesis|unclassified	0.0049408
+PWY-2942: L-lysine biosynthesis III	0.00959218
+PWY-2942: L-lysine biosynthesis III|unclassified	0.0110762
+TRNA-CHARGING-PWY: tRNA charging	0.00946058
+TRNA-CHARGING-PWY: tRNA charging|unclassified	0.00526713
+PWY66-400: glycolysis VI (metazoan)	0.00938218
+PWY66-400: glycolysis VI (metazoan)|unclassified	0.00933907
+PWY-5154: L-arginine biosynthesis III (via N-acetyl-L-citrulline)	0.00881081
+ANAEROFRUCAT-PWY: homolactic fermentation	0.0088
+ANAEROFRUCAT-PWY: homolactic fermentation|unclassified	0.0157977
+PWY-7111: pyruvate fermentation to isobutanol (engineered)	0.00876945
+PWY-7111: pyruvate fermentation to isobutanol (engineered)|unclassified	0.0173067
+NONOXIPENT-PWY: pentose phosphate pathway (non-oxidative branch)	0.00862082
+NONOXIPENT-PWY: pentose phosphate pathway (non-oxidative branch)|unclassified	0.018885
+PEPTIDOGLYCANSYN-PWY: peptidoglycan biosynthesis I (meso-diaminopimelate containing)	0.00850699
+PEPTIDOGLYCANSYN-PWY: peptidoglycan biosynthesis I (meso-diaminopimelate containing)|unclassified	0.0116221
+GLUCUROCAT-PWY: superpathway of &beta;-D-glucuronide and D-glucuronate degradation	0.00838546
+PWY-6123: inosine-5'-phosphate biosynthesis I	0.00831965
+PWY-6123: inosine-5'-phosphate biosynthesis I|unclassified	0.0182252
+PWY-5103: L-isoleucine biosynthesis III	0.00831677
+PWY-5103: L-isoleucine biosynthesis III|unclassified	0.00718443
+PWY-5104: L-isoleucine biosynthesis IV	0.00831272
+PWY-5104: L-isoleucine biosynthesis IV|unclassified	0.0065428
+PWY-6385: peptidoglycan biosynthesis III (mycobacteria)	0.00820786
+PWY-6385: peptidoglycan biosynthesis III (mycobacteria)|unclassified	0.00930133
+ARGININE-SYN4-PWY: L-ornithine de novo  biosynthesis	0.00809135
+ARGININE-SYN4-PWY: L-ornithine de novo  biosynthesis|unclassified	0.0166731
+GLUTORN-PWY: L-ornithine biosynthesis	0.00808734
+GLUTORN-PWY: L-ornithine biosynthesis|unclassified	0.00900908
+PWY-7184: pyrimidine deoxyribonucleotides de novo biosynthesis I	0.00770993
+GLYCOLYSIS: glycolysis I (from glucose 6-phosphate)	0.00769956
+GLYCOLYSIS: glycolysis I (from glucose 6-phosphate)|unclassified	0.0137456
+PWY-1269: CMP-3-deoxy-D-manno-octulosonate biosynthesis I	0.00755658
+PWY-1269: CMP-3-deoxy-D-manno-octulosonate biosynthesis I|unclassified	0.00644897
+PWY-5484: glycolysis II (from fructose 6-phosphate)	0.00749543
+PWY-5484: glycolysis II (from fructose 6-phosphate)|unclassified	0.0134471
+FASYN-INITIAL-PWY: superpathway of fatty acid biosynthesis initiation (E. coli)	0.00744755
+FASYN-INITIAL-PWY: superpathway of fatty acid biosynthesis initiation (E. coli)|unclassified	0.00788309
+PWY-6387: UDP-N-acetylmuramoyl-pentapeptide biosynthesis I (meso-diaminopimelate containing)	0.00731247
+PWY-6387: UDP-N-acetylmuramoyl-pentapeptide biosynthesis I (meso-diaminopimelate containing)|unclassified	0.00973219
+PWY66-389: phytol degradation	0.00548391
+PWY66-389: phytol degradation|unclassified	0.00638472
+PWY-7316: dTDP-N-acetylviosamine biosynthesis	0.00542069
+PWY-7316: dTDP-N-acetylviosamine biosynthesis|unclassified	0.0110149
+RHAMCAT-PWY: L-rhamnose degradation I	0.00539026
+PWY-841: superpathway of purine nucleotides de novo biosynthesis I	0.00531622
+PWY-7237: myo-, chiro- and scillo-inositol degradation	0.00520322
+PWY-7237: myo-, chiro- and scillo-inositol degradation|unclassified	0.0113983
+HISDEG-PWY: L-histidine degradation I	0.00519408
+HISDEG-PWY: L-histidine degradation I|unclassified	0.00770332
+PWY4FS-7: phosphatidylglycerol biosynthesis I (plastidic)	0.00518363
+PWY4FS-8: phosphatidylglycerol biosynthesis II (non-plastidic)	0.00518363
+PWY-6549: L-glutamine biosynthesis III	0.00508899
+PWY-6549: L-glutamine biosynthesis III|unclassified	0.00776607
+PWY-5101: L-isoleucine biosynthesis II	0.00492461
+PWY-5101: L-isoleucine biosynthesis II|unclassified	0.00617859
+PWY-6628: superpathway of L-phenylalanine biosynthesis	0.0049241
+PHOSLIPSYN-PWY: superpathway of phospholipid biosynthesis I (bacteria)	0.00460395
+COMPLETE-ARO-PWY: superpathway of aromatic amino acid biosynthesis	0.00439273
+COMPLETE-ARO-PWY: superpathway of aromatic amino acid biosynthesis|unclassified	0.00862669
+PWY-6897: thiamin salvage II	0.00415143
+PWY-6897: thiamin salvage II|unclassified	0.00909424
+PWY-7357: thiamin formation from pyrithiamine and oxythiamine (yeast)	0.0041402
+PWY-7357: thiamin formation from pyrithiamine and oxythiamine (yeast)|unclassified	0.00906963
+PWY-6163: chorismate biosynthesis from 3-dehydroquinate	0.00410329
+PWY-6163: chorismate biosynthesis from 3-dehydroquinate|unclassified	0.00781711
+PWY-7388: octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)	0.00409733
+PWY-7388: octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)|unclassified	0.00641891
+ARO-PWY: chorismate biosynthesis I	0.0039449
+ARO-PWY: chorismate biosynthesis I|unclassified	0.00783533
+GALACT-GLUCUROCAT-PWY: superpathway of hexuronide and hexuronate degradation	0.00391566
+PWY-5667: CDP-diacylglycerol biosynthesis I	0.00384585
+PWY-5667: CDP-diacylglycerol biosynthesis I|unclassified	0.00149856
+PWY0-1319: CDP-diacylglycerol biosynthesis II	0.00384585
+PWY0-1319: CDP-diacylglycerol biosynthesis II|unclassified	0.00149856
+PYRIDNUCSYN-PWY: NAD biosynthesis I (from aspartate)	0.00361602
+PYRIDNUCSYN-PWY: NAD biosynthesis I (from aspartate)|unclassified	0.0068348
+PWY-6527: stachyose degradation	0.00354951
+PWY-6527: stachyose degradation|unclassified	0.00683934
+DAPLYSINESYN-PWY: L-lysine biosynthesis I	0.0035429
+DAPLYSINESYN-PWY: L-lysine biosynthesis I|unclassified	0.00314147
+UDPNAGSYN-PWY: UDP-N-acetyl-D-glucosamine biosynthesis I	0.00338583
+UDPNAGSYN-PWY: UDP-N-acetyl-D-glucosamine biosynthesis I|unclassified	0.00656183
+PWY-6305: putrescine biosynthesis IV	0.00333385
+PWY-5690: TCA cycle II (plants and fungi)	0.00322218
+PWY-5690: TCA cycle II (plants and fungi)|unclassified	0.00358601
+OANTIGEN-PWY: O-antigen building blocks biosynthesis (E. coli)	0.00321981
+OANTIGEN-PWY: O-antigen building blocks biosynthesis (E. coli)|unclassified	0.00620846
+PWY-6630: superpathway of L-tyrosine biosynthesis	0.00319673
+P105-PWY: TCA cycle IV (2-oxoglutarate decarboxylase)	0.00262013
+P105-PWY: TCA cycle IV (2-oxoglutarate decarboxylase)|unclassified	0.00340536
+PWY-6121: 5-aminoimidazole ribonucleotide biosynthesis I	0.00258418
+PWY-6121: 5-aminoimidazole ribonucleotide biosynthesis I|unclassified	0.00566097
+PWY-7211: superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis	0.00250236
+PWY-6122: 5-aminoimidazole ribonucleotide biosynthesis II	0.00237867
+PWY-6122: 5-aminoimidazole ribonucleotide biosynthesis II|unclassified	0.00521078
+PWY-6277: superpathway of 5-aminoimidazole ribonucleotide biosynthesis	0.00237867
+PWY-6277: superpathway of 5-aminoimidazole ribonucleotide biosynthesis|unclassified	0.00521078
+METHGLYUT-PWY: superpathway of methylglyoxal degradation	0.00226728
+METHGLYUT-PWY: superpathway of methylglyoxal degradation|unclassified	0.00496676
+PWY0-1061: superpathway of L-alanine biosynthesis	0.00216957
+PWY0-1061: superpathway of L-alanine biosynthesis|unclassified	0.00374653
+PPGPPMET-PWY: ppGpp biosynthesis	0.00203621
+PWY-6737: starch degradation V	0.00201137
+PWY-6737: starch degradation V|unclassified	0.00316335
+PWY-7115: C4 photosynthetic carbon assimilation cycle, NAD-ME type	0.00187881
+P441-PWY: superpathway of N-acetylneuraminate degradation	0.00162577
+P441-PWY: superpathway of N-acetylneuraminate degradation|unclassified	0.00204428
+PWY-5855: ubiquinol-7 biosynthesis (prokaryotic)	0.0015637
+PWY-5855: ubiquinol-7 biosynthesis (prokaryotic)|unclassified	0.00342548
+PWY-5857: ubiquinol-10 biosynthesis (prokaryotic)	0.0015637
+PWY-5857: ubiquinol-10 biosynthesis (prokaryotic)|unclassified	0.00342548
+PWY4LZ-257: superpathway of fermentation (Chlamydomonas reinhardtii)	0.00147873
+PWY4LZ-257: superpathway of fermentation (Chlamydomonas reinhardtii)|unclassified	0.00318099
+DENOVOPURINE2-PWY: superpathway of purine nucleotides de novo biosynthesis II	0.0014462
+PWY-724: superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	0.00142842
+PWY-724: superpathway of L-lysine, L-threonine and L-methionine biosynthesis II|unclassified	0.0029625
+PWY-3001: superpathway of L-isoleucine biosynthesis I	0.00142024
+PWY-3001: superpathway of L-isoleucine biosynthesis I|unclassified	0.0027671
+KETOGLUCONMET-PWY: ketogluconate metabolism	0.00141222
+KETOGLUCONMET-PWY: ketogluconate metabolism|unclassified	0.00309365
+PWY-5941: glycogen degradation II (eukaryotic)	0.00127166
+PWY-5941: glycogen degradation II (eukaryotic)|unclassified	0.00241599
+PWY-6435: 4-hydroxybenzoate biosynthesis V	0.00125364
+PWY-6435: 4-hydroxybenzoate biosynthesis V|unclassified	0.00274625
+P161-PWY: acetylene degradation	0.00119177
+P161-PWY: acetylene degradation|unclassified	0.00261072
+RIBOSYN2-PWY: flavin biosynthesis I (bacteria and plants)	0.0011474
+RIBOSYN2-PWY: flavin biosynthesis I (bacteria and plants)|unclassified	0.00213182
+PWY-6606: guanosine nucleotides degradation II	0.00113088
+PWY-6606: guanosine nucleotides degradation II|unclassified	0.00247734
+PWY-5265: peptidoglycan biosynthesis II (staphylococci)	0.00106882
+PWY-5265: peptidoglycan biosynthesis II (staphylococci)|unclassified	0.00209837
+PWY-5754: 4-hydroxybenzoate biosynthesis I (eukaryotes)	0.00104748
+PWY-5754: 4-hydroxybenzoate biosynthesis I (eukaryotes)|unclassified	0.00229464
+P185-PWY: formaldehyde assimilation III (dihydroxyacetone cycle)	0.00103843
+P185-PWY: formaldehyde assimilation III (dihydroxyacetone cycle)|unclassified	0.00115303
+PWY-6595: superpathway of guanosine nucleotides degradation (plants)	0.00102956
+PWY-6595: superpathway of guanosine nucleotides degradation (plants)|unclassified	0.00225538
+PWY-5464: superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	0.000992505
+PWY-5464: superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle|unclassified	0.00172005
+THISYNARA-PWY: superpathway of thiamin diphosphate biosynthesis III (eukaryotes)	0.000973654
+THISYNARA-PWY: superpathway of thiamin diphosphate biosynthesis III (eukaryotes)|unclassified	0.0021303
+PWY-6386: UDP-N-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing)	0.000904748
+PWY-6386: UDP-N-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing)|unclassified	0.00183333
+THRESYN-PWY: superpathway of L-threonine biosynthesis	0.000904039
+THRESYN-PWY: superpathway of L-threonine biosynthesis|unclassified	0.00188356
+PWY0-1586: peptidoglycan maturation (meso-diaminopimelate containing)	0.000751931
+PWY0-1586: peptidoglycan maturation (meso-diaminopimelate containing)|unclassified	0.0014413
+FAO-PWY: fatty acid &beta;-oxidation I	0.000714249
+FAO-PWY: fatty acid &beta;-oxidation I|unclassified	0.00148771
+PWY-5136: fatty acid &beta;-oxidation II (peroxisome)	0.000698245
+PWY-5136: fatty acid &beta;-oxidation II (peroxisome)|unclassified	0.00144209
+PWY-6471: peptidoglycan biosynthesis IV (Enterococcus faecium)	0.000698193
+PWY-6471: peptidoglycan biosynthesis IV (Enterococcus faecium)|unclassified	0.00142191
+PWY-7007: methyl ketone biosynthesis	0.000659038
+PWY-7007: methyl ketone biosynthesis|unclassified	0.00122854
+GLCMANNANAUT-PWY: superpathway of N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminate degradation	0.000651572
+GLCMANNANAUT-PWY: superpathway of N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminate degradation|unclassified	0.00123299
+PWY-6769: rhamnogalacturonan type I degradation I (fungi)	0.000634893
+PWY-6769: rhamnogalacturonan type I degradation I (fungi)|unclassified	0.00139081
+PWY-6309: L-tryptophan degradation XI (mammalian, via kynurenine)	0.000615914
+PWY-6309: L-tryptophan degradation XI (mammalian, via kynurenine)|unclassified	0.00134924
+PWY-7094: fatty acid salvage	0.000597229
+PWY-7094: fatty acid salvage|unclassified	0.00125407
+GLUDEG-I-PWY: GABA shunt	0.000537709
+GLUDEG-I-PWY: GABA shunt|unclassified	0.001173
+PWY1F-823: leucopelargonidin and leucocyanidin biosynthesis	0.000501896
+PWY1F-823: leucopelargonidin and leucocyanidin biosynthesis|unclassified	0.00109947
+PWY-7234: inosine-5'-phosphate biosynthesis III	0.00045368
+PWY-7234: inosine-5'-phosphate biosynthesis III|unclassified	0.000993843
+PWY-5173: superpathway of acetyl-CoA biosynthesis	0.000372086
+PWY-5173: superpathway of acetyl-CoA biosynthesis|unclassified	0.000785602
+PWY-6731: starch degradation III	0.000336222
+PWY-6731: starch degradation III|unclassified	0.000708616
+P241-PWY: coenzyme B biosynthesis	0.000322755
+P241-PWY: coenzyme B biosynthesis|unclassified	0.000707035
+PWY-7398: coumarins biosynthesis (engineered)	0.000273932
+PWY-7398: coumarins biosynthesis (engineered)|unclassified	0.000600083
+PWY-4041: &gamma;-glutamyl cycle	0.000269421
+PWY-4041: &gamma;-glutamyl cycle|unclassified	0.000590201
+GLYOXYLATE-BYPASS: glyoxylate cycle	0.000182141
+GLYOXYLATE-BYPASS: glyoxylate cycle|unclassified	0.000395503
+GLYCOL-GLYOXDEG-PWY: superpathway of glycol metabolism and degradation	0.000175574
+GLYCOL-GLYOXDEG-PWY: superpathway of glycol metabolism and degradation|unclassified	0.000384618
+SO4ASSIM-PWY: sulfate reduction I (assimilatory)	6.96955e-05
+SO4ASSIM-PWY: sulfate reduction I (assimilatory)|unclassified	0.00015138
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/humann2_m8_pathabundance_cmp_renormalized.tsv	Wed Apr 20 08:30:08 2016 -0400
@@ -0,0 +1,17 @@
+# Pathway	humann2_Abundance
+ARGININE-SYN4-PWY: L-ornithine de novo  biosynthesis	353741
+ARGININE-SYN4-PWY: L-ornithine de novo  biosynthesis|unclassified	353741
+HSERMETANA-PWY: L-methionine biosynthesis III	150089
+HSERMETANA-PWY: L-methionine biosynthesis III|unclassified	150089
+DTDPRHAMSYN-PWY: dTDP-L-rhamnose biosynthesis I	142538
+DTDPRHAMSYN-PWY: dTDP-L-rhamnose biosynthesis I|unclassified	142538
+KETOGLUCONMET-PWY: ketogluconate metabolism	96153.8
+KETOGLUCONMET-PWY: ketogluconate metabolism|unclassified	96153.8
+PWY-1269: CMP-3-deoxy-D-manno-octulosonate biosynthesis I	82608.9
+PWY-1269: CMP-3-deoxy-D-manno-octulosonate biosynthesis I|unclassified	82608.9
+PWY-7357: thiamin formation from pyrithiamine and oxythiamine (yeast)	72056.1
+PWY-7357: thiamin formation from pyrithiamine and oxythiamine (yeast)|unclassified	72056.1
+PWY-6151: S-adenosyl-L-methionine cycle I	69841.3
+PWY-6151: S-adenosyl-L-methionine cycle I|unclassified	69841.3
+PWY-6897: thiamin salvage II	32971.5
+PWY-6897: thiamin salvage II|unclassified	32971.5
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/log_output.txt	Wed Apr 20 08:30:08 2016 -0400
@@ -0,0 +1,12 @@
+Similar between all samples: 15
+Specific to samples:
+  sample1 
+    All: 16
+    Number of specific characteristics: 1
+    Percentage of specific characteristics: 6.25
+    Relative abundance of specific characteristics(%): 6984130.0
+  sample2 
+    All: 266
+    Number of specific characteristics: 251
+    Percentage of specific characteristics: 94.3609022556
+    Relative abundance of specific characteristics(%): 186.11689025
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/more_abundant_output.tabular	Wed Apr 20 08:30:08 2016 -0400
@@ -0,0 +1,21 @@
+id	name	sample1	sample2
+PWY-7208	superpathway of pyrimidine nucleobases salvage|unclassified	0	1.75918
+PWY-7208	superpathway of pyrimidine nucleobases salvage	0	2.06908
+PYRIDOXSYN-PWY	pyridoxal 5 phosphate biosynthesis I	0	2.45442
+ARGININE-SYN4-PWY	L ornithine de novo  biosynthesis	35374100.0	0.809135
+PYRIDOXSYN-PWY	pyridoxal 5 phosphate biosynthesis I|unclassified	0	3.41296
+HSERMETANA-PWY	L methionine biosynthesis III|unclassified	15008900.0	0.515875
+DTDPRHAMSYN-PWY	dTDP L rhamnose biosynthesis I	14253800.0	1.69441
+HSERMETANA-PWY	L methionine biosynthesis III	15008900.0	1.21379
+DTDPRHAMSYN-PWY	dTDP L rhamnose biosynthesis I|unclassified	14253800.0	2.50835
+PWY-3841	folate transformations II	0	2.38544
+ARGININE-SYN4-PWY	L ornithine de novo  biosynthesis|unclassified	35374100.0	1.66731
+1CMET2-PWY	N10 formyl tetrahydrofolate biosynthesis	0	2.12689
+1CMET2-PWY	N10 formyl tetrahydrofolate biosynthesis|unclassified	0	0.834716
+PWY-3841	folate transformations II|unclassified	0	2.27477
+PWY-1269	CMP 3 deoxy D manno octulosonate biosynthesis I	8260890.0	0.755658
+PWY-1269	CMP 3 deoxy D manno octulosonate biosynthesis I|unclassified	8260890.0	0.644897
+KETOGLUCONMET-PWY	ketogluconate metabolism	9615380.0	0.141222
+KETOGLUCONMET-PWY	ketogluconate metabolism|unclassified	9615380.0	0.309365
+COA-PWY-1	coenzyme A biosynthesis II 	0	1.9437
+PWY-7221	guanosine ribonucleotides de novo biosynthesis	0	1.88123
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/similar_output.tabular	Wed Apr 20 08:30:08 2016 -0400
@@ -0,0 +1,16 @@
+id	name	sample1	sample2
+PWY-6897	thiamin salvage II|unclassified	3297150.0	0.909424
+PWY-1269	CMP 3 deoxy D manno octulosonate biosynthesis I	8260890.0	0.755658
+ARGININE-SYN4-PWY	L ornithine de novo  biosynthesis	35374100.0	0.809135
+HSERMETANA-PWY	L methionine biosynthesis III|unclassified	15008900.0	0.515875
+PWY-6897	thiamin salvage II	3297150.0	0.415143
+PWY-7357	thiamin formation from pyrithiamine and oxythiamine 	7205610.0	0.41402
+HSERMETANA-PWY	L methionine biosynthesis III	15008900.0	1.21379
+DTDPRHAMSYN-PWY	dTDP L rhamnose biosynthesis I|unclassified	14253800.0	2.50835
+PWY-7357	thiamin formation from pyrithiamine and oxythiamine |unclassified	7205610.0	0.906963
+ARGININE-SYN4-PWY	L ornithine de novo  biosynthesis|unclassified	35374100.0	1.66731
+PWY-6151	S adenosyl L methionine cycle I	6984130.0	0.977587
+PWY-1269	CMP 3 deoxy D manno octulosonate biosynthesis I|unclassified	8260890.0	0.644897
+KETOGLUCONMET-PWY	ketogluconate metabolism	9615380.0	0.141222
+KETOGLUCONMET-PWY	ketogluconate metabolism|unclassified	9615380.0	0.309365
+DTDPRHAMSYN-PWY	dTDP L rhamnose biosynthesis I	14253800.0	1.69441
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/specific_to_sample1_output.txt	Wed Apr 20 08:30:08 2016 -0400
@@ -0,0 +1,2 @@
+id	name	abundances
+PWY-6151	S adenosyl L methionine cycle I|unclassified	6984130.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/specific_to_sample2_output.txt	Wed Apr 20 08:30:08 2016 -0400
@@ -0,0 +1,252 @@
+id	name	abundances
+PWY-6731	starch degradation III	0.0336222
+GLUDEG-I-PWY	GABA shunt	0.0537709
+PWY-6123	inosine 5 phosphate biosynthesis I	0.831965
+PWY-6769	rhamnogalacturonan type I degradation I |unclassified	0.139081
+PWY-6471	peptidoglycan biosynthesis IV 	0.0698193
+PWY-7222	guanosine deoxyribonucleotides de novo biosynthesis II	1.48474
+PPGPPMET-PWY	ppGpp biosynthesis	0.203621
+PWY-7234	inosine 5 phosphate biosynthesis III	0.045368
+PWY-5686	UMP biosynthesis|unclassified	1.7892
+PWY-3841	folate transformations II	2.38544
+P185-PWY	formaldehyde assimilation III 	0.103843
+ILEUSYN-PWY	L isoleucine biosynthesis I 	1.29401
+PWY-3001	superpathway of L isoleucine biosynthesis I	0.142024
+PWY-5754	4 hydroxybenzoate biosynthesis I |unclassified	0.229464
+PWY-6737	starch degradation V|unclassified	0.316335
+PWY-5104	L isoleucine biosynthesis IV	0.831272
+PWY-7242	D fructuronate degradation	1.03935
+OANTIGEN-PWY	O antigen building blocks biosynthesis 	0.321981
+PWY-5667	CDP diacylglycerol biosynthesis I|unclassified	0.149856
+PWY-6606	guanosine nucleotides degradation II|unclassified	0.247734
+PWY66-422	D galactose degradation V |unclassified	1.04266
+PWY66-400	glycolysis VI 	0.938218
+PWY66-389	phytol degradation	0.548391
+PWY-5097	L lysine biosynthesis VI	1.04893
+1CMET2-PWY	N10 formyl tetrahydrofolate biosynthesis|unclassified	0.834716
+PWY-6386	UDP N acetylmuramoyl pentapeptide biosynthesis II 	0.0904748
+PWY4LZ-257	superpathway of fermentation 	0.147873
+PWY-6549	L glutamine biosynthesis III	0.508899
+GLCMANNANAUT-PWY	superpathway of N acetylglucosamine, N acetylmannosamine and N acetylneuraminate degradation|unclassified	0.123299
+PWY-7111	pyruvate fermentation to isobutanol |unclassified	1.73067
+PEPTIDOGLYCANSYN-PWY	peptidoglycan biosynthesis I 	0.850699
+PWY-7115	C4 photosynthetic carbon assimilation cycle, NAD ME type	0.187881
+P241-PWY	coenzyme B biosynthesis|unclassified	0.0707035
+PWY-6124	inosine 5 phosphate biosynthesis II|unclassified	2.22455
+PWY-5173	superpathway of acetyl CoA biosynthesis|unclassified	0.0785602
+PWY-7316	dTDP N acetylviosamine biosynthesis	0.542069
+PWY-5101	L isoleucine biosynthesis II|unclassified	0.617859
+PEPTIDOGLYCANSYN-PWY	peptidoglycan biosynthesis I |unclassified	1.16221
+PWY-6769	rhamnogalacturonan type I degradation I 	0.0634893
+GLUCUROCAT-PWY	superpathway of &beta; D glucuronide and D glucuronate degradation	0.838546
+PWY-7219	adenosine ribonucleotides de novo biosynthesis|unclassified	3.33171
+PWY4LZ-257	superpathway of fermentation |unclassified	0.318099
+ARGSYN-PWY	L arginine biosynthesis I 	1.16946
+PWY-5100	pyruvate fermentation to acetate and lactate II|unclassified	1.26625
+ARO-PWY	chorismate biosynthesis I	0.39449
+ARGSYNBSUB-PWY	L arginine biosynthesis II 	1.02161
+PWY-6936	seleno amino acid biosynthesis	1.2799
+PWY-6595	superpathway of guanosine nucleotides degradation |unclassified	0.225538
+ANAGLYCOLYSIS-PWY	glycolysis III 	1.03937
+PWY0-162	superpathway of pyrimidine ribonucleotides de novo biosynthesis|unclassified	0.295685
+PWY-841	superpathway of purine nucleotides de novo biosynthesis I	0.531622
+PWY-5505	L glutamate and L glutamine biosynthesis|g__Bacteroides.s__Bacteroides_thetaiotaomicron	1.44739
+THRESYN-PWY	superpathway of L threonine biosynthesis|unclassified	0.188356
+PWY-5941	glycogen degradation II 	0.127166
+PWY-7094	fatty acid salvage	0.0597229
+CITRULBIO-PWY	L citrulline biosynthesis|unclassified	0.49408
+PWY-7221	guanosine ribonucleotides de novo biosynthesis	1.88123
+ARGSYNBSUB-PWY	L arginine biosynthesis II |unclassified	1.31054
+PWY-6630	superpathway of L tyrosine biosynthesis	0.319673
+RIBOSYN2-PWY	flavin biosynthesis I |unclassified	0.213182
+PWY-2942	L lysine biosynthesis III|unclassified	1.10762
+PWY-7094	fatty acid salvage|unclassified	0.125407
+PWY-1042	glycolysis IV |unclassified	1.93529
+VALSYN-PWY	L valine biosynthesis	1.29401
+PWY-6277	superpathway of 5 aminoimidazole ribonucleotide biosynthesis|unclassified	0.521078
+PWY-7219	adenosine ribonucleotides de novo biosynthesis	1.57923
+PWY-6309	L tryptophan degradation XI 	0.0615914
+PWY-6703	preQ0 biosynthesis|unclassified	1.3368
+PWY-7007	methyl ketone biosynthesis	0.0659038
+PWY0-1319	CDP diacylglycerol biosynthesis II	0.384585
+PWY-5030	L histidine degradation III|unclassified	1.20381
+PWY0-162	superpathway of pyrimidine ribonucleotides de novo biosynthesis	1.19161
+1CMET2-PWY	N10 formyl tetrahydrofolate biosynthesis	2.12689
+VALSYN-PWY	L valine biosynthesis|unclassified	1.59474
+PWY-5857	ubiquinol 10 biosynthesis |unclassified	0.342548
+PWY-5505	L glutamate and L glutamine biosynthesis	1.53682
+PWY-6387	UDP N acetylmuramoyl pentapeptide biosynthesis I |unclassified	0.973219
+GLYCOLYSIS	glycolysis I 	0.769956
+PWY-6387	UDP N acetylmuramoyl pentapeptide biosynthesis I 	0.731247
+PWY-7208	superpathway of pyrimidine nucleobases salvage|unclassified	1.75918
+PWY-5136	fatty acid &beta; oxidation II |unclassified	0.144209
+PWY-6122	5 aminoimidazole ribonucleotide biosynthesis II|unclassified	0.521078
+PWY-2942	L lysine biosynthesis III	0.959218
+PWY-7222	guanosine deoxyribonucleotides de novo biosynthesis II|unclassified	2.01368
+PWY-6277	superpathway of 5 aminoimidazole ribonucleotide biosynthesis	0.237867
+PWY-6126	superpathway of adenosine nucleotides de novo biosynthesis II|unclassified	2.44065
+ANAEROFRUCAT-PWY	homolactic fermentation|unclassified	1.57977
+PWY0-1061	superpathway of L alanine biosynthesis|unclassified	0.374653
+PYRIDNUCSYN-PWY	NAD biosynthesis I |unclassified	0.68348
+GLYOXYLATE-BYPASS	glyoxylate cycle|unclassified	0.0395503
+GLYCOL-GLYOXDEG-PWY	superpathway of glycol metabolism and degradation	0.0175574
+PWY-4984	urea cycle	1.18794
+PWY-6549	L glutamine biosynthesis III|unclassified	0.776607
+PWY-6385	peptidoglycan biosynthesis III |unclassified	0.930133
+PWY0-1319	CDP diacylglycerol biosynthesis II|unclassified	0.149856
+PHOSLIPSYN-PWY	superpathway of phospholipid biosynthesis I 	0.460395
+FASYN-INITIAL-PWY	superpathway of fatty acid biosynthesis initiation 	0.744755
+PWY-7398	coumarins biosynthesis |unclassified	0.0600083
+PYRIDNUCSYN-PWY	NAD biosynthesis I 	0.361602
+PYRIDOXSYN-PWY	pyridoxal 5 phosphate biosynthesis I|unclassified	3.41296
+NONOXIPENT-PWY	pentose phosphate pathway 	0.862082
+PWY-5941	glycogen degradation II |unclassified	0.241599
+P161-PWY	acetylene degradation|unclassified	0.261072
+PWY-6126	superpathway of adenosine nucleotides de novo biosynthesis II	1.50984
+HOMOSER-METSYN-PWY	L methionine biosynthesis I|unclassified	1.09381
+PWY-6731	starch degradation III|unclassified	0.0708616
+PWY-6125	superpathway of guanosine nucleotides de novo biosynthesis II	1.55645
+PWY-6435	4 hydroxybenzoate biosynthesis V	0.125364
+PWY66-389	phytol degradation|unclassified	0.638472
+TRNA-CHARGING-PWY	tRNA charging	0.946058
+PWY-7237	myo , chiro  and scillo inositol degradation	0.520322
+PWY-6527	stachyose degradation|unclassified	0.683934
+PWY-7007	methyl ketone biosynthesis|unclassified	0.122854
+PWY-6124	inosine 5 phosphate biosynthesis II	1.01549
+PWY-5690	TCA cycle II |unclassified	0.358601
+PWY0-1586	peptidoglycan maturation 	0.0751931
+PWY-5100	pyruvate fermentation to acetate and lactate II	1.70667
+GLUCONEO-PWY	gluconeogenesis I	1.18442
+PWY66-400	glycolysis VI |unclassified	0.933907
+PWY-5104	L isoleucine biosynthesis IV|unclassified	0.65428
+PWY-5754	4 hydroxybenzoate biosynthesis I 	0.104748
+PWY-1042	glycolysis IV 	1.75553
+PWY-4041	&gamma; glutamyl cycle|unclassified	0.0590201
+SO4ASSIM-PWY	sulfate reduction I 	0.00696955
+THRESYN-PWY	superpathway of L threonine biosynthesis	0.0904039
+PWY-6703	preQ0 biosynthesis	1.39768
+PWY-6163	chorismate biosynthesis from 3 dehydroquinate|unclassified	0.781711
+PWY-7229	superpathway of adenosine nucleotides de novo biosynthesis I	1.55872
+PWY-7229	superpathway of adenosine nucleotides de novo biosynthesis I|unclassified	2.61337
+PWY-3001	superpathway of L isoleucine biosynthesis I|unclassified	0.27671
+SER-GLYSYN-PWY	superpathway of L serine and glycine biosynthesis I|unclassified	0.288758
+PWY-7111	pyruvate fermentation to isobutanol 	0.876945
+CALVIN-PWY	Calvin Benson Bassham cycle	1.79034
+PWY-5855	ubiquinol 7 biosynthesis 	0.15637
+PWY-5097	L lysine biosynthesis VI|unclassified	1.16003
+HOMOSER-METSYN-PWY	L methionine biosynthesis I	1.58217
+PWY66-422	D galactose degradation V |g__Bacteroides.s__Bacteroides_stercoris	1.49592
+PWY-7237	myo , chiro  and scillo inositol degradation|unclassified	1.13983
+PYRIDOXSYN-PWY	pyridoxal 5 phosphate biosynthesis I	2.45442
+PWY-5855	ubiquinol 7 biosynthesis |unclassified	0.342548
+PWY-5659	GDP mannose biosynthesis	1.3223
+FASYN-INITIAL-PWY	superpathway of fatty acid biosynthesis initiation |unclassified	0.788309
+PWY-6507	4 deoxy L threo hex 4 enopyranuronate degradation	1.00585
+PWY-7388	octanoyl [acyl carrier protein] biosynthesis 	0.409733
+PWY-6435	4 hydroxybenzoate biosynthesis V|unclassified	0.274625
+PWY-6122	5 aminoimidazole ribonucleotide biosynthesis II	0.237867
+PWY1F-823	leucopelargonidin and leucocyanidin biosynthesis|unclassified	0.109947
+PWY4FS-7	phosphatidylglycerol biosynthesis I 	0.518363
+PWY-6121	5 aminoimidazole ribonucleotide biosynthesis I|unclassified	0.566097
+PWY-5103	L isoleucine biosynthesis III|unclassified	0.718443
+PWY-7316	dTDP N acetylviosamine biosynthesis|unclassified	1.10149
+ILEUSYN-PWY	L isoleucine biosynthesis I |unclassified	1.59474
+GALACTUROCAT-PWY	D galacturonate degradation I	1.12548
+P161-PWY	acetylene degradation	0.119177
+PWY-5030	L histidine degradation III	1.22713
+PWY-5484	glycolysis II |unclassified	1.34471
+GLYCOL-GLYOXDEG-PWY	superpathway of glycol metabolism and degradation|unclassified	0.0384618
+PWY-7211	superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis	0.250236
+GLYOXYLATE-BYPASS	glyoxylate cycle	0.0182141
+PWY-7228	superpathway of guanosine nucleotides de novo biosynthesis I	1.69262
+PWY-6527	stachyose degradation	0.354951
+GLUTORN-PWY	L ornithine biosynthesis	0.808734
+PWY-7400	L arginine biosynthesis IV 	1.18235
+PWY-7220	adenosine deoxyribonucleotides de novo biosynthesis II|unclassified	2.01368
+ARO-PWY	chorismate biosynthesis I|unclassified	0.783533
+PWY-4041	&gamma; glutamyl cycle	0.0269421
+BRANCHED-CHAIN-AA-SYN-PWY	superpathway of branched amino acid biosynthesis|unclassified	0.857417
+CALVIN-PWY	Calvin Benson Bassham cycle|unclassified	2.40344
+PWY-5690	TCA cycle II 	0.322218
+P105-PWY	TCA cycle IV 	0.262013
+PWY-5136	fatty acid &beta; oxidation II 	0.0698245
+PWY-6471	peptidoglycan biosynthesis IV |unclassified	0.142191
+PWY-6386	UDP N acetylmuramoyl pentapeptide biosynthesis II |unclassified	0.183333
+PWY-5464	superpathway of cytosolic glycolysis , pyruvate dehydrogenase and TCA cycle	0.0992505
+PWY-7208	superpathway of pyrimidine nucleobases salvage	2.06908
+ANAGLYCOLYSIS-PWY	glycolysis III |unclassified	1.85171
+PWY-6309	L tryptophan degradation XI |unclassified	0.134924
+PWY4FS-8	phosphatidylglycerol biosynthesis II 	0.518363
+PWY0-1061	superpathway of L alanine biosynthesis	0.216957
+PWY0-1586	peptidoglycan maturation |unclassified	0.14413
+PWY-7220	adenosine deoxyribonucleotides de novo biosynthesis II	1.48474
+P441-PWY	superpathway of N acetylneuraminate degradation	0.162577
+SER-GLYSYN-PWY	superpathway of L serine and glycine biosynthesis I	1.2955
+PWY-7398	coumarins biosynthesis 	0.0273932
+UDPNAGSYN-PWY	UDP N acetyl D glucosamine biosynthesis I|unclassified	0.656183
+PWY-5154	L arginine biosynthesis III 	0.881081
+PWY-5484	glycolysis II 	0.749543
+UDPNAGSYN-PWY	UDP N acetyl D glucosamine biosynthesis I	0.338583
+ANAEROFRUCAT-PWY	homolactic fermentation	0.88
+THISYNARA-PWY	superpathway of thiamin diphosphate biosynthesis III |unclassified	0.21303
+PWY-6123	inosine 5 phosphate biosynthesis I|unclassified	1.82252
+PWY-6121	5 aminoimidazole ribonucleotide biosynthesis I	0.258418
+COA-PWY-1	coenzyme A biosynthesis II 	1.9437
+PWY-6936	seleno amino acid biosynthesis|unclassified	1.32349
+PWY-6163	chorismate biosynthesis from 3 dehydroquinate	0.410329
+PWY-5667	CDP diacylglycerol biosynthesis I	0.384585
+PWY-7184	pyrimidine deoxyribonucleotides de novo biosynthesis I	0.770993
+PWY-3841	folate transformations II|unclassified	2.27477
+CITRULBIO-PWY	L citrulline biosynthesis	0.974607
+RHAMCAT-PWY	L rhamnose degradation I	0.539026
+PWY-724	superpathway of L lysine, L threonine and L methionine biosynthesis II|unclassified	0.29625
+GLUTORN-PWY	L ornithine biosynthesis|unclassified	0.900908
+PWY-5265	peptidoglycan biosynthesis II |unclassified	0.209837
+PWY-5464	superpathway of cytosolic glycolysis , pyruvate dehydrogenase and TCA cycle|unclassified	0.172005
+PWY-6606	guanosine nucleotides degradation II	0.113088
+OANTIGEN-PWY	O antigen building blocks biosynthesis |unclassified	0.620846
+PWY-7388	octanoyl [acyl carrier protein] biosynthesis |unclassified	0.641891
+P185-PWY	formaldehyde assimilation III |unclassified	0.115303
+METHGLYUT-PWY	superpathway of methylglyoxal degradation	0.226728
+PWY-6737	starch degradation V	0.201137
+PWY-724	superpathway of L lysine, L threonine and L methionine biosynthesis II	0.142842
+NONOXIPENT-PWY	pentose phosphate pathway |unclassified	1.8885
+DAPLYSINESYN-PWY	L lysine biosynthesis I	0.35429
+PWY-6628	superpathway of L phenylalanine biosynthesis	0.49241
+THISYNARA-PWY	superpathway of thiamin diphosphate biosynthesis III 	0.0973654
+PWY-6385	peptidoglycan biosynthesis III 	0.820786
+PWY1F-823	leucopelargonidin and leucocyanidin biosynthesis	0.0501896
+ASPASN-PWY	superpathway of L aspartate and L asparagine biosynthesis	1.09751
+P105-PWY	TCA cycle IV |unclassified	0.340536
+TRNA-CHARGING-PWY	tRNA charging|unclassified	0.526713
+GALACT-GLUCUROCAT-PWY	superpathway of hexuronide and hexuronate degradation	0.391566
+PWY-5173	superpathway of acetyl CoA biosynthesis	0.0372086
+FAO-PWY	fatty acid &beta; oxidation I	0.0714249
+P241-PWY	coenzyme B biosynthesis	0.0322755
+COMPLETE-ARO-PWY	superpathway of aromatic amino acid biosynthesis|unclassified	0.862669
+HISDEG-PWY	L histidine degradation I	0.519408
+COMPLETE-ARO-PWY	superpathway of aromatic amino acid biosynthesis	0.439273
+DAPLYSINESYN-PWY	L lysine biosynthesis I|unclassified	0.314147
+PWY-5103	L isoleucine biosynthesis III	0.831677
+GLUDEG-I-PWY	GABA shunt|unclassified	0.1173
+GLCMANNANAUT-PWY	superpathway of N acetylglucosamine, N acetylmannosamine and N acetylneuraminate degradation	0.0651572
+P441-PWY	superpathway of N acetylneuraminate degradation|unclassified	0.204428
+PWY-5686	UMP biosynthesis	0.980672
+PWY-6595	superpathway of guanosine nucleotides degradation 	0.102956
+PWY66-422	D galactose degradation V 	1.75745
+PWY-5505	L glutamate and L glutamine biosynthesis|unclassified	1.96045
+PWY-6305	putrescine biosynthesis IV	0.333385
+HISDEG-PWY	L histidine degradation I|unclassified	0.770332
+PWY-5659	GDP mannose biosynthesis|unclassified	0.106616
+FAO-PWY	fatty acid &beta; oxidation I|unclassified	0.148771
+METHGLYUT-PWY	superpathway of methylglyoxal degradation|unclassified	0.496676
+DENOVOPURINE2-PWY	superpathway of purine nucleotides de novo biosynthesis II	0.14462
+PWY-5857	ubiquinol 10 biosynthesis 	0.15637
+PWY-5101	L isoleucine biosynthesis II	0.492461
+RIBOSYN2-PWY	flavin biosynthesis I 	0.11474
+SO4ASSIM-PWY	sulfate reduction I |unclassified	0.015138
+BRANCHED-CHAIN-AA-SYN-PWY	superpathway of branched amino acid biosynthesis	1.02856
+PWY-5265	peptidoglycan biosynthesis II 	0.106882
+ASPASN-PWY	superpathway of L aspartate and L asparagine biosynthesis|unclassified	1.92205
+PWY-7234	inosine 5 phosphate biosynthesis III|unclassified	0.0993843
+GLYCOLYSIS	glycolysis I |unclassified	1.37456