| Previous changeset 1:e25efca0a49c (2020-09-14) Next changeset 3:01ac9954c27f (2023-07-20) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit eea46077010e699403ce6995d7d4aac77b2e0b43" |
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modified:
combine_metaphlan2_humann2.py |
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removed:
output output_p |
| b |
| diff -r e25efca0a49c -r fdfb35745104 combine_metaphlan2_humann2.py --- a/combine_metaphlan2_humann2.py Mon Sep 14 12:19:49 2020 +0000 +++ b/combine_metaphlan2_humann2.py Wed Oct 19 14:44:00 2022 +0000 |
| [ |
| @@ -6,50 +6,48 @@ def extract_clade_abundance(metaphlan2_fp): clade_abund = {} - with open(metaphlan2_fp, 'r') as metaphlan2_f: + with open(metaphlan2_fp, "r") as metaphlan2_f: for line in metaphlan2_f.readlines(): - if line.find('g__') == -1: + if line.find("g__") == -1: continue - split_line = line[:-1].split('\t') + split_line = line[:-1].split("\t") taxo = split_line[0] abundance = split_line[1] - genus = taxo[(taxo.find('g__')+3):] - if genus.find('|') != -1: - genus = genus[:(genus.find('|'))] - clade_abund.setdefault(genus, {'abundance': 0, 'species': {}}) - if taxo.find('t__') != -1: + genus = taxo[(taxo.find("g__") + 3):] + if genus.find("|") != -1: + genus = genus[: (genus.find("|"))] + clade_abund.setdefault(genus, {"abundance": 0, "species": {}}) + if taxo.find("t__") != -1: continue - elif taxo.find('s__') != -1: - species = taxo[(taxo.find('s__')+3):] - clade_abund[genus]['species'].setdefault( - species, - abundance) + elif taxo.find("s__") != -1: + species = taxo[(taxo.find("s__") + 3):] + clade_abund[genus]["species"].setdefault(species, abundance) else: - clade_abund[genus]['abundance'] = abundance + clade_abund[genus]["abundance"] = abundance return clade_abund def compute_overall_abundance(humann2_fp): overall_abundance = 0 - with open(humann2_fp, 'r') as humann2_f: + with open(humann2_fp, "r") as humann2_f: for line in humann2_f.readlines(): - if line.find('|') != -1 or line.startswith('#'): + if line.find("|") != -1 or line.startswith("#"): continue - split_line = line[:-1].split('\t') + split_line = line[:-1].split("\t") overall_abundance += float(split_line[1]) return overall_abundance def format_characteristic_name(name): formatted_n = name - formatted_n = formatted_n.replace('/', ' ') - formatted_n = formatted_n.replace('-', ' ') - formatted_n = formatted_n.replace("'", '') - if formatted_n.find('(') != -1 and formatted_n.find(')') != -1: - open_bracket = formatted_n.find('(') - close_bracket = formatted_n.find(')')+1 + formatted_n = formatted_n.replace("/", " ") + formatted_n = formatted_n.replace("-", " ") + formatted_n = formatted_n.replace("'", "") + if formatted_n.find("(") != -1 and formatted_n.find(")") != -1: + open_bracket = formatted_n.find("(") + close_bracket = formatted_n.find(")") + 1 formatted_n = formatted_n[:open_bracket] + formatted_n[close_bracket:] return formatted_n @@ -58,26 +56,26 @@ clade_abund = extract_clade_abundance(args.metaphlan2_fp) overall_abund = compute_overall_abundance(args.humann2_fp) - with open(args.output_fp, 'w') as output_f: - s = 'genus\tgenus_abundance\tspecies\tspecies_abundance\t' - s = '%s\t%s_id\t%s_name\t%s_abundance\n' % (s, args.type, args.type, args.type) + with open(args.output_fp, "w") as output_f: + s = "genus\tgenus_abundance\tspecies\tspecies_abundance\t" + s = "%s\t%s_id\t%s_name\t%s_abundance\n" % (s, args.type, args.type, args.type) output_f.write(s) - with open(args.humann2_fp, 'r') as humann2_f: + with open(args.humann2_fp, "r") as humann2_f: for line in humann2_f.readlines(): - if line.find('|') == -1: + if line.find("|") == -1: continue - split_line = line[:-1].split('\t') - abundance = 100*float(split_line[1])/overall_abund - annotation = split_line[0].split('|') - charact = annotation[0].split(':') + split_line = line[:-1].split("\t") + abundance = 100 * float(split_line[1]) / overall_abund + annotation = split_line[0].split("|") + charact = annotation[0].split(":") charact_id = charact[0] - char_name = '' + char_name = "" if len(charact) > 1: char_name = format_characteristic_name(charact[-1]) - taxo = annotation[1].split('.') + taxo = annotation[1].split(".") - if taxo[0] == 'unclassified': + if taxo[0] == "unclassified": continue genus = taxo[0][3:] species = taxo[1][3:] @@ -85,25 +83,25 @@ if genus not in clade_abund: print("no %s found in %s" % (genus, args.metaphlan2_fp)) continue - if species not in clade_abund[genus]['species']: - print("no %s found in %s for % s" % (species, args.metaphlan2_fp, genus)) + if species not in clade_abund[genus]["species"]: + print( + "no %s found in %s for % s" + % (species, args.metaphlan2_fp, genus) + ) continue - s = "%s\t%s\t" % (genus, clade_abund[genus]['abundance']) - s += "%s\t%s\t" % (species, clade_abund[genus]['species'][species]) + s = "%s\t%s\t" % (genus, clade_abund[genus]["abundance"]) + s += "%s\t%s\t" % (species, clade_abund[genus]["species"][species]) s += "%s\t%s\t%s\n" % (charact_id, char_name, abundance) output_f.write(s) -if __name__ == '__main__': +if __name__ == "__main__": parser = argparse.ArgumentParser() - parser.add_argument('--humann2_fp', required=True) - parser.add_argument('--metaphlan2_fp', required=True) - parser.add_argument('--output_fp', required=True) - parser.add_argument( - '--type', - required=True, - choices=['gene_families', 'pathways']) + parser.add_argument("--humann2_fp", required=True) + parser.add_argument("--metaphlan2_fp", required=True) + parser.add_argument("--output_fp", required=True) + parser.add_argument("--type", required=True, choices=["gene_families", "pathways"]) args = parser.parse_args() combine_metaphlan2_humann2(args) |
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| diff -r e25efca0a49c -r fdfb35745104 output --- a/output Mon Sep 14 12:19:49 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,29434 +0,0 @@\n-genus\tgenus_abundance\tspecies\tspecies_abundance\t\tgene_families_id\tgene_families_name\tgene_families_abundance\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_P19529\t Replication initiation protein\t0.4072890608\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tUniRef50_P19529\t Replication initiation protein\t0.2614808258\n-Propionibacterium\t0.36055\tPropionibacterium_acnes\t0.36055\tUniRef50_P19529\t Replication initiation protein\t0.1885828940\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tUniRef50_Q5HJZ6\t Plasmid recombination enzyme type 3\t0.3386709080\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_Q5HJZ6\t Plasmid recombination enzyme type 3\t0.2984453109\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tUniRef50_Q5HJZ6\t Plasmid recombination enzyme type 3\t0.0233463103\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tUniRef50_P02983\t Tetracycline resistance protein\t0.2559604246\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_P02983\t Tetracycline resistance protein\t0.2553000075\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_Q93GF3\t Rep\t0.3223883031\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tUniRef50_Q93GF3\t Rep\t0.0431524470\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_V6QG63\t Integrase\t0.3033525248\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_W1W6K4\t\t0.2478561185\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_D4FM51\t Plasmid recombination enzyme\t0.2140638121\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_Z6ILY0\t\t0.1967871579\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_F0P516\t Replication initiation protein, truncated\t0.1196373464\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tUniRef50_F0P516\t Replication initiation protein, truncated\t0.0759957583\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_Q8CU99\t\t0.1730709986\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_P14491\t Protein rlx\t0.1721052589\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tUniRef50_P14491\t Protein rlx\t0.0001065027\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tUniRef50_P18358\t Transposon Tn552 resolvase\t0.1321963651\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_P18358\t Transposon Tn552 resolvase\t0.0309505072\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_Q5HRN3\t ISSep1 like transposase\t0.1255765504\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tUniRef50_Q5HRN3\t ISSep1 like transposase\t0.0183157072\n-Propionibacterium\t0.36055\tPropionibacterium_acnes\t0.36055\tUniRef50_Q5HRN3\t ISSep1 like transposase\t0.0011279924\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_Q4L351\t Staphylococcus haemolyticus JCSC1435 DNA, complete genome\t0.1307825244\n-Rhodobacter\t5.64659\tRhodobacter_sphaeroides\t5.64659\tUniRef50_Q3J5T4\t 50S ribosomal protein L11\t0.1241036553\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_N6A8S2\t\t0.1132499041\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_L7WXY9\t\t0.1075711791\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tUniRef50_P18357\t Regulatory protein BlaR1\t0.0712959296\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_P18357\t Regulatory protein BlaR1\t0.0277440504\n-Propionibacterium\t0.36055\tPropionibacterium_acnes\t0.36055\tUniRef50_P18357\t Regulatory protein BlaR1\t0.0084931424\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tUniRef50_K0LDS3\t\t0.1040703656\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_I3U5U5\t Mobilization protein C\t0.0997088242\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tUniRef50_I3U5U5\t Mobilization protein C\t0.0011422851\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_Q8CUF7\t\t0.0982704960\n-Staphylococcus\t'..b'sa\t0.81333\tUniRef50_V9WW95\t\t0.0000328340\n-Propionibacterium\t0.36055\tPropionibacterium_acnes\t0.36055\tUniRef50_G7UA09\t Glycosyl hydrolase family 38 N terminal domain protein\t0.0000323501\n-Neisseria\t0.04343\tNeisseria_meningitidis\t0.04343\tUniRef50_E3D229\t Chromosome partition protein Smc\t0.0000318199\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tUniRef50_G0LRQ0\t Serine aspartate repeat containing protein D\t0.0000314433\n-Deinococcus\t0.30974\tDeinococcus_radiodurans\t0.15196\tUniRef50_Q9RUP8\t Isoleucine tRNA ligase\t0.0000312101\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tUniRef50_C1DLW9\t\t0.0000309897\n-Acinetobacter\t0.12091\tAcinetobacter_baumannii\t0.12091\tUniRef50_A3M2F1\t IcmB protein\t0.0000309517\n-Neisseria\t0.04343\tNeisseria_meningitidis\t0.04343\tUniRef50_F0MM85\t Hemagglutinin hemolysin family protein\t0.0000306557\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tUniRef50_P58402\t Sensor protein EvgS\t0.0000301027\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tUniRef50_Q02GC2\t Type 4 fimbrial biogenesis protein PilY1\t0.0000300132\n-Acinetobacter\t0.12091\tAcinetobacter_baumannii\t0.12091\tUniRef50_J4VP36\t DNA polymerase III, alpha subunit\t0.0000297217\n-Neisseria\t0.04343\tNeisseria_meningitidis\t0.04343\tUniRef50_Q9JVX8\t DNA polymerase III subunit alpha\t0.0000294357\n-Acinetobacter\t0.12091\tAcinetobacter_baumannii\t0.12091\tUniRef50_A0A009XXP0\t RecF RecN SMC N terminal domain protein\t0.0000292906\n-Propionibacterium\t0.36055\tPropionibacterium_acnes\t0.36055\tUniRef50_F9YY53\t\t0.0000292566\n-Acinetobacter\t0.12091\tAcinetobacter_baumannii\t0.12091\tUniRef50_B0V8Z8\t ATP dependent dsDNA exonuclease \t0.0000288553\n-Helicobacter\t0.07678\tHelicobacter_pylori\t0.07678\tUniRef50_I9V7J9\t Outer membrane protein HopL\t0.0000285776\n-Propionibacterium\t0.36055\tPropionibacterium_acnes\t0.36055\tUniRef50_Q6ABR7\t Cobalamin biosynthesis protein CobN\t0.0000285533\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tUniRef50_A6V8C8\t\t0.0000282972\n-Propionibacterium\t0.36055\tPropionibacterium_acnes\t0.36055\tUniRef50_G8VL08\t ATP dependent helicase HrpA\t0.0000282418\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tUniRef50_W1C828\t Molybdate metabolism regulator\t0.0000279758\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tUniRef50_I3GYQ4\t\t0.0000273839\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tUniRef50_Q8FJC7\t DNA translocase FtsK\t0.0000265487\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tUniRef50_G9W1N9\t Enterobactin synthetase component F\t0.0000262382\n-Neisseria\t0.04343\tNeisseria_meningitidis\t0.04343\tUniRef50_F0N1G5\t Transcription repair coupling factor\t0.0000258950\n-Neisseria\t0.04343\tNeisseria_meningitidis\t0.04343\tUniRef50_C9WZ56\t Transcription repair coupling factor\t0.0000248988\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tUniRef50_E2QDF8\t Phage lambda related protein, Side tail fiber protein homolog\t0.0000247705\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tUniRef50_L4JUW1\t Adhesin invasin\t0.0000244171\n-Neisseria\t0.04343\tNeisseria_meningitidis\t0.04343\tUniRef50_R0UE42\t Filamentous hemagglutinin family N terminal domain protein\t0.0000243935\n-Deinococcus\t0.30974\tDeinococcus_radiodurans\t0.15196\tUniRef50_Q9RWI1\t\t0.0000227142\n-Propionibacterium\t0.36055\tPropionibacterium_acnes\t0.36055\tUniRef50_F9NYB1\t RHS repeat associated core domain protein\t0.0000215782\n-Methanobrevibacter\t6.51285\tMethanobrevibacter_smithii\t6.51285\tUniRef50_A5UKU3\t Adhesin like protein\t0.0000183906\n-Acinetobacter\t0.12091\tAcinetobacter_baumannii\t0.12091\tUniRef50_V5VA04\t Hemolysin type calcium binding domain containing protein\t0.0000183472\n-Neisseria\t0.04343\tNeisseria_meningitidis\t0.04343\tUniRef50_R0YL20\t Filamentous hemagglutinin family N terminal domain protein\t0.0000182247\n-Acinetobacter\t0.12091\tAcinetobacter_baumannii\t0.12091\tUniRef50_A3M865\t\t0.0000169092\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tUniRef50_A0A024L957\t\t0.0000160746\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tUniRef50_U6ANV5\t\t0.0000152170\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tUniRef50_M4JLP2\t\t0.0000150648\n' |
| b |
| diff -r e25efca0a49c -r fdfb35745104 output_p --- a/output_p Mon Sep 14 12:19:49 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1533 +0,0 @@\n-genus\tgenus_abundance\tspecies\tspecies_abundance\t\tpathways_id\tpathways_name\tpathways_abundance\n-Rhodobacter\t5.64659\tRhodobacter_sphaeroides\t5.64659\tPWY-3781\t aerobic respiration I \t0.36855689513114914\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tPWY-3781\t aerobic respiration I \t0.25314723238576264\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tPWY-3781\t aerobic respiration I \t0.23347560163495915\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tPWY-3781\t aerobic respiration I \t0.09185548795720419\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tPWY-3781\t aerobic respiration I \t0.0602129571868334\n-Helicobacter\t0.07678\tHelicobacter_pylori\t0.07678\tPWY-3781\t aerobic respiration I \t0.003824629054671103\n-Propionibacterium\t0.36055\tPropionibacterium_acnes\t0.36055\tPWY-3781\t aerobic respiration I \t0.002472377182070903\n-Deinococcus\t0.30974\tDeinococcus_radiodurans\t0.15196\tPWY-3781\t aerobic respiration I \t0.0019607698268559472\n-Neisseria\t0.04343\tNeisseria_meningitidis\t0.04343\tPWY-3781\t aerobic respiration I \t0.0011429942839774828\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tPWY66-389\t phytol degradation\t0.24955303546680035\n-Rhodobacter\t5.64659\tRhodobacter_sphaeroides\t5.64659\tPWY66-389\t phytol degradation\t0.23712503843179414\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tPWY66-389\t phytol degradation\t0.10605973235092032\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tPWY66-389\t phytol degradation\t0.02906228375573722\n-Acinetobacter\t0.12091\tAcinetobacter_baumannii\t0.12091\tPWY66-389\t phytol degradation\t0.013846754875652437\n-Clostridium\t0.93894\tClostridium_beijerinckii\t0.93894\tPWY66-389\t phytol degradation\t0.005408612839101089\n-Propionibacterium\t0.36055\tPropionibacterium_acnes\t0.36055\tPWY66-389\t phytol degradation\t0.0034333686865133405\n-Deinococcus\t0.30974\tDeinococcus_radiodurans\t0.15196\tPWY66-389\t phytol degradation\t0.002569607624727644\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tPWY-5173\t superpathway of acetyl CoA biosynthesis\t0.29675230625262666\n-Rhodobacter\t5.64659\tRhodobacter_sphaeroides\t5.64659\tPWY-5173\t superpathway of acetyl CoA biosynthesis\t0.14853709341118693\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tPWY-5173\t superpathway of acetyl CoA biosynthesis\t0.12537995884848147\n-Streptococcus\t17.12842\tStreptococcus_mutans\t16.30896\tPWY-5173\t superpathway of acetyl CoA biosynthesis\t0.10665029539828356\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tPWY-5173\t superpathway of acetyl CoA biosynthesis\t0.04859061617109473\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tPWY-5173\t superpathway of acetyl CoA biosynthesis\t0.008595044899193908\n-Streptococcus\t17.12842\tStreptococcus_agalactiae\t0.81946\tPWY-5173\t superpathway of acetyl CoA biosynthesis\t0.0038966486986628094\n-Acinetobacter\t0.12091\tAcinetobacter_baumannii\t0.12091\tPWY-5173\t superpathway of acetyl CoA biosynthesis\t0.0011288960433164142\n-Propionibacterium\t0.36055\tPropionibacterium_acnes\t0.36055\tPWY-5173\t superpathway of acetyl CoA biosynthesis\t0.0009635889446077365\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tPWY-7111\t pyruvate fermentation to isobutanol \t0.20421529643394035\n-Rhodobacter\t5.64659\tRhodobacter_sphaeroides\t5.64659\tPWY-7111\t pyruvate fermentation to isobutanol \t0.17639758359863825\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tPWY-7111\t pyruvate fermentation to isobutanol \t0.14789632152996243\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tPWY-7111\t pyruvate fermentation to isobutanol \t0.10816832297628652\n-Streptococcus\t17.12842\tStreptococcus_mutans\t16.30896\tPWY-7111\t pyruvate fermentation to isobutanol \t0.0846845592441376\n-Methanobrevibacter\t6.51285\tMethanobrevibacter_smithii\t6.51285\tPWY-7111\t pyruvate fermentation to isobutanol \t0.029482211825282528\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tPWY-7111\t pyruvate fermentation to isobutanol \t0.013558472995391261\n-Clostridium\t0.93894\tClostridium_beijerinckii\t0.93894\tPWY-7111\t pyruvate fermentation to isobutanol \t'..b'inosa\t0.81333\tPWY-7165\t L ascorbate biosynthesis VI \t0.003308001055561411\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tLPSSYN-PWY\t superpathway of lipopolysaccharide biosynthesis\t0.018571618590985155\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tFUCCAT-PWY\t fucose degradation\t0.025899687385740715\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tPWY-7446\t sulfoglycolysis\t0.027575833175784437\n-Methanobrevibacter\t6.51285\tMethanobrevibacter_smithii\t6.51285\tP241-PWY\t coenzyme B biosynthesis\t0.025426429513444974\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tPWY-6948\t sitosterol degradation to androstenedione\t0.0032931580219167046\n-Clostridium\t0.93894\tClostridium_beijerinckii\t0.93894\tCENTFERM-PWY\t pyruvate fermentation to butanoate\t0.0077654210394024715\n-Clostridium\t0.93894\tClostridium_beijerinckii\t0.93894\tPWY-5367\t petroselinate biosynthesis\t0.0047033518099390366\n-Streptococcus\t17.12842\tStreptococcus_agalactiae\t0.81946\tPWY-5367\t petroselinate biosynthesis\t0.0038566349341619126\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tPWY0-41\t allantoin degradation IV \t0.022293016117348016\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tPWY-6731\t starch degradation III\t0.016278474060982963\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tFUC-RHAMCAT-PWY\t superpathway of fucose and rhamnose degradation\t0.02147791902882433\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tPWY-7409\t phospholipid remodeling \t0.01867945883743567\n-Rhodobacter\t5.64659\tRhodobacter_sphaeroides\t5.64659\tPWY-3941\t β alanine biosynthesis II\t0.00804419432078\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tPWY0-1241\t ADP L glycero β D manno heptose biosynthesis\t0.020208507236915692\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tRHAMCAT-PWY\t L rhamnose degradation I\t0.01888277458006528\n-Clostridium\t0.93894\tClostridium_beijerinckii\t0.93894\tRHAMCAT-PWY\t L rhamnose degradation I\t0.002238347316481606\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tKDO-NAGLIPASYN-PWY\t superpathway of 2 lipid A biosynthesis\t0.012366617492956613\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tPWY0-1338\t polymyxin resistance\t0.020342576997641814\n-Methanobrevibacter\t6.51285\tMethanobrevibacter_smithii\t6.51285\tP261-PWY\t coenzyme M biosynthesis I\t0.018437476072281418\n-Methanobrevibacter\t6.51285\tMethanobrevibacter_smithii\t6.51285\tPWY-5198\t factor 420 biosynthesis\t0.01653297146070866\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tHCAMHPDEG-PWY\t 3 phenylpropanoate and 3 propanoate degradation to 2 oxopent 4 enoate\t0.01128002626342421\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tPWY-6690\t cinnamate and 3 hydroxycinnamate degradation to 2 oxopent 4 enoate\t0.01128002626342421\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tPWY-7090\t UDP 2,3 diacetamido 2,3 dideoxy α D mannuronate biosynthesis\t0.008121869500846222\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tPWY-6467\t Kdo transfer to lipid IVA III \t0.0073941512405605045\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tPWY-6309\t L tryptophan degradation XI \t0.0064424009235795774\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tPWY-6309\t L tryptophan degradation XI \t0.003365067343943067\n-Clostridium\t0.93894\tClostridium_beijerinckii\t0.93894\tP562-PWY\t myo inositol degradation I\t0.004119464568459301\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tPWY-6660\t 2 heptyl 3 hydroxy 4 quinolone biosynthesis\t0.007369931417270731\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tPWY66-388\t fatty acid α oxidation III\t0.007311344314520961\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tPWY-6662\t superpathway of quinolone and alkylquinolone biosynthesis\t0.007062618485762087\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tPWY-6672\t cis genanyl CoA degradation\t0.0019831868435679937\n-Acinetobacter\t0.12091\tAcinetobacter_baumannii\t0.12091\tPWY-6672\t cis genanyl CoA degradation\t0.0015908594476743442\n-Propionibacterium\t0.36055\tPropionibacterium_acnes\t0.36055\tUDPNACETYLGALSYN-PWY\t UDP N acetyl D glucosamine biosynthesis II\t0.0008441806853518248\n' |