Mercurial > repos > bebatut > compare_humann2_output
changeset 1:22e031055f18 draft
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 08:29:20 -0400 |
| parents | 035a848cb73e |
| children | 9c24aa6d9a1f |
| files | 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 | 8 files changed, 608 insertions(+), 4 deletions(-) [+] |
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--- a/compare_humann2_output.xml Tue Apr 12 02:56:13 2016 -0400 +++ b/compare_humann2_output.xml Wed Apr 20 08:29:20 2016 -0400 @@ -52,15 +52,32 @@ </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** +**What it does** + +This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples. Several files are extracted: - This tool compare HUMANnN2 outputs with gene families or pathways relative abundances of several samples and extract several files: + * Similar gene families or pathways between the samples and the relative abundances of these similar characteristics - - Similar gene families or pathways between the samples and the relative abundances and these similar characteristics - - Most abundant gene families or pathways for each sample and the corresponding relative abundance in all samples + * 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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/humann2_fasta_pathabundance_relab_renormalized.csv Wed Apr 20 08:29:20 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 β-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 β-oxidation I 0.000714249 +FAO-PWY: fatty acid β-oxidation I|unclassified 0.00148771 +PWY-5136: fatty acid β-oxidation II (peroxisome) 0.000698245 +PWY-5136: fatty acid β-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: γ-glutamyl cycle 0.000269421 +PWY-4041: γ-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 08:29:20 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 08:29:20 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 08:29:20 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 08:29:20 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 08:29:20 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 08:29:20 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 β 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 β 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 γ 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 γ 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 β 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 β 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 β 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