| Previous changeset 2:05766022dfc4 (2020-09-14) Next changeset 4:844fcd42ec7c (2023-11-04) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output commit eea46077010e699403ce6995d7d4aac77b2e0b43" |
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modified:
compare_humann2_output.py |
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removed:
more_abundant_output_file similar_output_file specific_to_sample1.txt specific_to_sample2.txt |
| b |
| diff -r 05766022dfc4 -r eaa95ea1195c compare_humann2_output.py --- a/compare_humann2_output.py Mon Sep 14 13:50:30 2020 +0000 +++ b/compare_humann2_output.py Wed Oct 19 14:49:06 2022 +0000 |
| [ |
| @@ -8,19 +8,19 @@ abundances = {} more_abund_charact = [] abund_sum = 0 - with open(fp, 'r') as abundance_f: + with open(fp, "r") as abundance_f: for line in abundance_f.readlines()[1:]: - split_line = line[:-1].split('\t') + split_line = line[:-1].split("\t") charact_id = split_line[0] abund = float(split_line[1]) - abundances[charact_id] = 100*abund + 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): + for i in range(len(more_abund_charact) - 1, -1, -1): if abundances[more_abund_charact[i]] < abund: best_pos = i else: @@ -34,34 +34,34 @@ def format_characteristic_name(all_name): - if all_name.find(':') != -1: - charact_id = all_name.split(':')[0] - char_name = all_name.split(':')[1][1:] + if all_name.find(":") != -1: + charact_id = all_name.split(":")[0] + char_name = all_name.split(":")[1][1:] else: charact_id = all_name - char_name = '' + char_name = "" - char_name = char_name.replace('/', ' ') - char_name = char_name.replace('-', ' ') - char_name = char_name.replace("'", '') - if char_name.find('(') != -1 and char_name.find(')') != -1: - open_bracket = char_name.find('(') - close_bracket = char_name.find(')')+1 + char_name = char_name.replace("/", " ") + char_name = char_name.replace("-", " ") + char_name = char_name.replace("'", "") + if char_name.find("(") != -1 and char_name.find(")") != -1: + open_bracket = char_name.find("(") + close_bracket = char_name.find(")") + 1 char_name = char_name[:open_bracket] + char_name[close_bracket:] return charact_id, char_name def write_more_abundant_charat(abundances, more_abund_charact, output_fp): - with open(output_fp, 'w') as output_f: - output_f.write('id\tname\t%s\n' % '\t'.join(abundances.keys())) + with open(output_fp, "w") as output_f: + output_f.write("id\tname\t%s\n" % "\t".join(abundances.keys())) for mac in more_abund_charact: charact_id, charact_name = format_characteristic_name(mac) - output_f.write('%s\t%s' % (charact_id, charact_name)) + output_f.write("%s\t%s" % (charact_id, charact_name)) for sample in abundances: abund = abundances[sample].get(mac, 0) - output_f.write('\t%s' % (abund)) - output_f.write('\n') + output_f.write("\t%s" % (abund)) + output_f.write("\n") def extract_similar_characteristics(abund, sim_output_fp, output_files): @@ -69,38 +69,41 @@ sim_characteristics = set(abund[abund_keys[0]].keys()) for sample in abund_keys[1:]: sim_characteristics.intersection_update(abund[sample].keys()) - print('Similar between all samples: %s' % len(sim_characteristics)) + print("Similar between all samples: %s" % len(sim_characteristics)) - with open(sim_output_fp, 'w') as sim_output_f: - sim_output_f.write('id\tname\t%s\n' % '\t'.join(abund_keys)) + with open(sim_output_fp, "w") as sim_output_f: + sim_output_f.write("id\tname\t%s\n" % "\t".join(abund_keys)) for charact in list(sim_characteristics): charact_id, charact_name = format_characteristic_name(charact) - sim_output_f.write('%s\t%s' % (charact_id, charact_name)) + sim_output_f.write("%s\t%s" % (charact_id, charact_name)) for sample in abund_keys: - sim_output_f.write('\t%s' % abund[sample][charact]) - sim_output_f.write('\n') + sim_output_f.write("\t%s" % abund[sample][charact]) + sim_output_f.write("\n") - print('Specific to samples:') + print("Specific to samples:") diff_char = {} for i in range(len(abund_keys)): sample = abund_keys[i] - print(' %s' % sample ) - print(' All: %s' % len(abund[sample].keys())) + print(" %s" % sample) + print(" All: %s" % len(abund[sample].keys())) diff_char[sample] = set(abund[sample].keys()) diff_char[sample].difference_update(sim_characteristics) - perc = 100*len(diff_char[sample])/(1.*len(abund[sample].keys())) - print(' Number of specific characteristics: %s' % len(diff_char[sample])) - print(' Percentage of specific characteristics: %s' % perc) + perc = 100 * len(diff_char[sample]) / (1.0 * len(abund[sample].keys())) + print(" Number of specific characteristics: %s" % len(diff_char[sample])) + print(" Percentage of specific characteristics: %s" % perc) relative_abundance = 0 - with open(output_files[i], 'w') as output_f: - output_f.write('id\tname\tabundances\n') + with open(output_files[i], "w") as output_f: + output_f.write("id\tname\tabundances\n") for charact in list(diff_char[sample]): charact_id, charact_name = format_characteristic_name(charact) - output_f.write('%s\t%s' % (charact_id, charact_name)) - output_f.write('%s\n' % abund[sample][charact]) + output_f.write("%s\t%s" % (charact_id, charact_name)) + output_f.write("%s\n" % abund[sample][charact]) relative_abundance += abund[sample][charact] - print(' Relative abundance of specific characteristics: %s' % relative_abundance) + print( + " Relative abundance of specific characteristics: %s" + % relative_abundance + ) return sim_characteristics @@ -111,34 +114,28 @@ for i in range(len(args.sample_name)): abund[args.sample_name[i]], mac = extract_abundances( - args.charact_input_fp[i], - args.most_abundant_characteristics_to_extract) + args.charact_input_fp[i], args.most_abundant_characteristics_to_extract + ) more_abund_charact += mac write_more_abundant_charat( - abund, - list(set(more_abund_charact)), - args.more_abundant_output_fp) + abund, list(set(more_abund_charact)), args.more_abundant_output_fp + ) extract_similar_characteristics( - abund, - args.similar_output_fp, - args.specific_output_fp) + abund, args.similar_output_fp, args.specific_output_fp + ) -if __name__ == '__main__': +if __name__ == "__main__": parser = argparse.ArgumentParser() - parser.add_argument('--sample_name', required=True, action='append') - parser.add_argument('--charact_input_fp', required=True, action='append') + parser.add_argument("--sample_name", required=True, action="append") + parser.add_argument("--charact_input_fp", required=True, action="append") parser.add_argument( - '--most_abundant_characteristics_to_extract', - required=True, - type=int) - parser.add_argument('--more_abundant_output_fp', required=True) - parser.add_argument('--similar_output_fp', required=True) - parser.add_argument( - '--specific_output_fp', - required=True, - action='append') + "--most_abundant_characteristics_to_extract", required=True, type=int + ) + parser.add_argument("--more_abundant_output_fp", required=True) + parser.add_argument("--similar_output_fp", required=True) + parser.add_argument("--specific_output_fp", required=True, action="append") args = parser.parse_args() if len(args.sample_name) != len(args.charact_input_fp): |
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| diff -r 05766022dfc4 -r eaa95ea1195c more_abundant_output_file --- a/more_abundant_output_file Mon Sep 14 13:50:30 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,16 +0,0 @@ -id name sample1 sample2 -PWY-3781 aerobic respiration I |g__Rhodobacter.s__Rhodobacter_sphaeroides 45855.05069573 7356.870952820001 -PWY-3781 aerobic respiration I |g__Staphylococcus.s__Staphylococcus_epidermidis 29048.52870919 8522.11671136 -PWY-3781 aerobic respiration I |g__Escherichia.s__Escherichia_coli 11428.460877009999 3504.5920137499998 -PWY66-389 phytol degradation|g__Staphylococcus.s__Staphylococcus_aureus 31048.84820709 3743.72936189 -PWY-3781 aerobic respiration I |g__Acinetobacter.s__Acinetobacter_baumannii 0 10661.254254039999 -PWY66-389 phytol degradation 97948.05701095 126799.82204952001 -PWY-3781 aerobic respiration I |g__Deinococcus.s__Deinococcus_radiodurans 243.95473535000002 51964.068130520005 -PWY-3781 aerobic respiration I |g__Neisseria.s__Neisseria_meningitidis 142.20887338999998 6845.43838944 -PWY-3781 aerobic respiration I |unclassified 3699.6275521400003 1118.9863796 -PWY-3781 aerobic respiration I |g__Pseudomonas.s__Pseudomonas_aeruginosa 7491.56572789 2317.68361723 -PWY-3781 aerobic respiration I 146949.34957509 137931.17561632 -PWY-3781 aerobic respiration I |g__Staphylococcus.s__Staphylococcus_aureus 31496.03040367 2108.46546528 -PWY-3781 aerobic respiration I |g__Helicobacter.s__Helicobacter_pylori 475.85206385000004 7486.51278743 -PWY-3781 aerobic respiration I |g__Propionibacterium.s__Propionibacterium_acnes 307.60781448 14416.040401769998 -PWY-3781 aerobic respiration I |g__Actinomyces.s__Actinomyces_odontolyticus 0 2772.58262062 |
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| diff -r 05766022dfc4 -r eaa95ea1195c similar_output_file --- a/similar_output_file Mon Sep 14 13:50:30 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,1921 +0,0 @@\n-id\tname\tsample1\tsample2\n-PWY-821\tsuperpathway of sulfur amino acid biosynthesis |g__Staphylococcus.s__Staphylococcus_epidermidis\t10880.14677635\t2695.08502543\n-PWY-6318\tL phenylalanine degradation IV |g__Streptococcus.s__Streptococcus_mutans\t1598.93459295\t477.28733176000003\n-P105-PWY\tTCA cycle IV |unclassified\t417.22426747\t298.08991033\n-HOMOSER-METSYN-PWY\tL methionine biosynthesis I|g__Escherichia.s__Escherichia_coli\t3776.83864118\t695.70708218\n-POLYISOPRENSYN-PWY\tpolyisoprenoid biosynthesis |g__Staphylococcus.s__Staphylococcus_epidermidis\t12410.21918677\t3402.87724422\n-PWY-3841\tfolate transformations II|g__Rhodobacter.s__Rhodobacter_sphaeroides\t4568.53278951\t242.13420068999997\n-DTDPRHAMSYN-PWY\tdTDP L rhamnose biosynthesis I|g__Rhodobacter.s__Rhodobacter_sphaeroides\t25871.992567709996\t3493.0071529899997\n-PWY-5345\tsuperpathway of L methionine biosynthesis \t45016.41648231\t40305.835161430005\n-MET-SAM-PWY\tsuperpathway of S adenosyl L methionine biosynthesis|g__Pseudomonas.s__Pseudomonas_aeruginosa\t452.55553718000004\t238.97560409\n-PWY-7228\tsuperpathway of guanosine nucleotides de novo biosynthesis I|g__Deinococcus.s__Deinococcus_radiodurans\t187.59460807\t21248.594380040002\n-REDCITCYC\tTCA cycle VIII \t48658.12042871\t30732.22044426\n-PWYG-321\tmycolate biosynthesis|g__Rhodobacter.s__Rhodobacter_sphaeroides\t20343.72192787\t3516.1051310700004\n-PWY-7196\tsuperpathway of pyrimidine ribonucleosides salvage\t40398.22784233\t41832.91851937\n-PWY-6606\tguanosine nucleotides degradation II|g__Rhodobacter.s__Rhodobacter_sphaeroides\t2736.23201469\t471.84886441\n-PWY-5897\tsuperpathway of menaquinol 11 biosynthesis|g__Escherichia.s__Escherichia_coli\t3694.00663281\t527.00700198\n-PWY-4981\tL proline biosynthesis II |g__Staphylococcus.s__Staphylococcus_epidermidis\t15181.20229661\t2233.73828052\n-PWY-5173\tsuperpathway of acetyl CoA biosynthesis|g__Staphylococcus.s__Staphylococcus_aureus\t15599.502940190001\t1720.86327384\n-METSYN-PWY\tL homoserine and L methionine biosynthesis\t42751.19552667\t32239.21002944\n-PWY-6737\tstarch degradation V|unclassified\t48.21577448\t239.03206251000003\n-PWY-7013\tL 1,2 propanediol degradation\t4148.3920522299995\t10375.048369639999\n-COA-PWY-1\tcoenzyme A biosynthesis II |g__Staphylococcus.s__Staphylococcus_epidermidis\t9071.2442565\t580.96446474\n-PWY-821\tsuperpathway of sulfur amino acid biosynthesis |g__Pseudomonas.s__Pseudomonas_aeruginosa\t605.30096054\t321.46343092\n-PWY-6891\tthiazole biosynthesis II |unclassified\t32.229173779999996\t74.15115623\n-PWY66-400\tglycolysis VI |g__Streptococcus.s__Streptococcus_mutans\t6043.58140287\t848.32486235\n-PWY-7117\tC4 photosynthetic carbon assimilation cycle, PEPCK type|unclassified\t22.263231910000002\t367.15187651\n-PWY-6386\tUDP N acetylmuramoyl pentapeptide biosynthesis II |g__Pseudomonas.s__Pseudomonas_aeruginosa\t606.94449313\t145.93585417\n-PWY-7663\tgondoate biosynthesis |unclassified\t623.9800982\t867.35110658\n-UDPNAGSYN-PWY\tUDP N acetyl D glucosamine biosynthesis I|g__Methanobrevibacter.s__Methanobrevibacter_smithii\t5123.88198898\t554.81214991\n-PENTOSE-P-PWY\tpentose phosphate pathway|g__Staphylococcus.s__Staphylococcus_epidermidis\t9462.89698214\t1831.25439958\n-PWY-6282\tpalmitoleate biosynthesis I dodec 5 enoate)|g__Escherichia.s__Escherichia_coli\t5235.734033500001\t1550.00566836\n-NONOXIPENT-PWY\tpentose phosphate pathway |g__Acinetobacter.s__Acinetobacter_baumannii\t207.44599457\t5015.152257039999\n-3-HYDROXYPHENYLACETATE-DEGRADATION-PWY\t4 hydroxyphenylacetate degradation\t5939.43167638\t13973.278780050001\n-PWY66-391\tfatty acid β oxidation VI |unclassified\t82.70659416000001\t143.2949423\n-PWY-6313\tserotonin degradation|g__Propionibacterium.s__Propionibacterium_acnes\t257.91056362\t3253.85903121\n-PWY-6125\tsuperpathway of guanosine nucleotides de novo biosynthesis II|unclassified\t257.44739331\t1093.60424306\n-SULFATE-CYS-PWY\tsuperpathway of sulfate assimilation and cysteine biosynthesis|g__Pseudomonas.s__Pseudomonas_aeruginosa\t1206.06770903\t368.86227068\n-P221-PWY\toctane oxidation|g__Acinetobacter.s__Acinetoba'..b'us\t13369.976352750002\t1138.58445146\n-P42-PWY\tincomplete reductive TCA cycle|g__Propionibacterium.s__Propionibacterium_acnes\t125.05394405000001\t4360.80925658\n-PANTOSYN-PWY\tpantothenate and coenzyme A biosynthesis I|g__Escherichia.s__Escherichia_coli\t2299.31537269\t337.86673042\n-PWY-6562\tnorspermidine biosynthesis\t218.86041799\t4624.32885997\n-FASYN-INITIAL-PWY\tsuperpathway of fatty acid biosynthesis initiation |g__Staphylococcus.s__Staphylococcus_aureus\t9743.57817824\t879.08031243\n-PWY-6124\tinosine 5 phosphate biosynthesis II|g__Streptococcus.s__Streptococcus_agalactiae\t341.08923605\t79.05367387\n-P42-PWY\tincomplete reductive TCA cycle|g__Staphylococcus.s__Staphylococcus_aureus\t13936.750358750001\t1191.4175682\n-PWY-7400\tL arginine biosynthesis IV |g__Staphylococcus.s__Staphylococcus_aureus\t15354.11940315\t2495.26566885\n-PWY-7664\toleate biosynthesis IV |g__Staphylococcus.s__Staphylococcus_aureus\t6208.22400634\t1214.56040809\n-PWY-6628\tsuperpathway of L phenylalanine biosynthesis|g__Escherichia.s__Escherichia_coli\t3493.26437899\t774.5820243\n-PWY-3801\tsucrose degradation II |g__Staphylococcus.s__Staphylococcus_aureus\t9958.965535970001\t1227.63555655\n-PWY-6803\tphosphatidylcholine acyl editing|g__Neisseria.s__Neisseria_meningitidis\t92.76437848\t2398.33809012\n-PWY-2942\tL lysine biosynthesis III|g__Methanobrevibacter.s__Methanobrevibacter_smithii\t2684.68361975\t271.52394734\n-PWY66-367\tketogenesis\t20586.77550017\t11739.88053451\n-GLUTORN-PWY\tL ornithine biosynthesis|unclassified\t341.67654023\t569.7612764099999\n-PWY-7208\tsuperpathway of pyrimidine nucleobases salvage|g__Streptococcus.s__Streptococcus_mutans\t7465.08545776\t1650.49554073\n-PWY66-389\tphytol degradation|g__Propionibacterium.s__Propionibacterium_acnes\t427.17229621\t4830.73518595\n-PWY0-1586\tpeptidoglycan maturation |g__Staphylococcus.s__Staphylococcus_aureus\t12323.38519243\t1001.6705746199999\n-PWY-5910\tsuperpathway of geranylgeranyldiphosphate biosynthesis I \t37359.01700251\t11927.378765090001\n-METHGLYUT-PWY\tsuperpathway of methylglyoxal degradation|unclassified\t112.17208644\t110.92868734000001\n-PWY-7111\tpyruvate fermentation to isobutanol |g__Acinetobacter.s__Acinetobacter_baumannii\t580.74819003\t16585.03150303\n-PWY-6630\tsuperpathway of L tyrosine biosynthesis|g__Streptococcus.s__Streptococcus_mutans\t3646.835713\t285.14604184\n-PWY-7391\tisoprene biosynthesis II \t30738.87869861\t8400.52258056\n-GLYCOLYSIS\tglycolysis I \t42940.06802303\t57491.91524327\n-PWY-6122\t5 aminoimidazole ribonucleotide biosynthesis II|g__Rhodobacter.s__Rhodobacter_sphaeroides\t1759.45401497\t633.23408091\n-PWY-5347\tsuperpathway of L methionine biosynthesis |g__Escherichia.s__Escherichia_coli\t5535.9622291900005\t1122.03662727\n-PWY-6353\tpurine nucleotides degradation II |g__Escherichia.s__Escherichia_coli\t8709.22987767\t981.44226721\n-PWY-7431\taromatic biogenic amine degradation |unclassified\t9.98055831\t58.30332417\n-PWY0-42\t2 methylcitrate cycle I|g__Pseudomonas.s__Pseudomonas_aeruginosa\t608.37208118\t118.40719672\n-PWY66-389\tphytol degradation\t97948.05701095\t126799.82204952001\n-PWY-7400\tL arginine biosynthesis IV |g__Streptococcus.s__Streptococcus_mutans\t7613.585259209999\t1319.31787361\n-PWY-7221\tguanosine ribonucleotides de novo biosynthesis|g__Deinococcus.s__Deinococcus_radiodurans\t159.71379076\t19876.46520516\n-SER-GLYSYN-PWY\tsuperpathway of L serine and glycine biosynthesis I|unclassified\t360.41633729\t196.35650766999998\n-PWY-6277\tsuperpathway of 5 aminoimidazole ribonucleotide biosynthesis|g__Pseudomonas.s__Pseudomonas_aeruginosa\t1056.89034552\t272.35544024\n-PWY-5659\tGDP mannose biosynthesis|g__Rhodobacter.s__Rhodobacter_sphaeroides\t4117.82806788\t694.21044438\n-NAD-BIOSYNTHESIS-II\tNAD salvage pathway II|g__Escherichia.s__Escherichia_coli\t6399.36784439\t1081.15882603\n-TRIGLSYN-PWY\tdiacylglycerol and triacylglycerol biosynthesis\t459.46669737999997\t5730.57246545\n-PWY-6823\tmolybdenum cofactor biosynthesis|unclassified\t34.30203548\t84.75362593\n-PWY-5188\ttetrapyrrole biosynthesis I |g__Pseudomonas.s__Pseudomonas_aeruginosa\t658.20873845\t335.98771892\n' |
| b |
| diff -r 05766022dfc4 -r eaa95ea1195c specific_to_sample1.txt --- a/specific_to_sample1.txt Mon Sep 14 13:50:30 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,393 +0,0 @@\n-id\tname\tabundances\n-PWY-7208\tsuperpathway of pyrimidine nucleobases salvage|g__Pseudomonas.s__Pseudomonas_aeruginosa2355.2977619499998\n-PWY0-1061\tsuperpathway of L alanine biosynthesis|g__Streptococcus.s__Streptococcus_agalactiae629.81986142\n-ORNARGDEG-PWY\tsuperpathway of L arginine and L ornithine degradation|unclassified67.59290738\n-PENTOSE-P-PWY\tpentose phosphate pathway|g__Pseudomonas.s__Pseudomonas_aeruginosa232.40561581\n-PWY-7222\tguanosine deoxyribonucleotides de novo biosynthesis II|g__Streptococcus.s__Streptococcus_agalactiae705.67950476\n-PWY-7210\tpyrimidine deoxyribonucleotides biosynthesis from CTP|g__Escherichia.s__Escherichia_coli623.1847142400001\n-PWY-6612\tsuperpathway of tetrahydrofolate biosynthesis|g__Pseudomonas.s__Pseudomonas_aeruginosa320.96477039\n-P4-PWY\tsuperpathway of L lysine, L threonine and L methionine biosynthesis I|g__Pseudomonas.s__Pseudomonas_aeruginosa677.11766653\n-PWY-6700\tqueuosine biosynthesis|g__Rhodobacter.s__Rhodobacter_sphaeroides447.95699647999993\n-PWY-6527\tstachyose degradation|unclassified53.551283819999995\n-PWY-4221\tpantothenate and coenzyme A biosynthesis II |g__Rhodobacter.s__Rhodobacter_sphaeroides935.46980828\n-PWY-6703\tpreQ0 biosynthesis|g__Pseudomonas.s__Pseudomonas_aeruginosa796.0549075700001\n-PWY-6147\t6 hydroxymethyl dihydropterin diphosphate biosynthesis I|g__Rhodobacter.s__Rhodobacter_sphaeroides600.7633936799999\n-PWY-5079\tL phenylalanine degradation III|unclassified6.5206192\n-1CMET2-PWY\tN10 formyl tetrahydrofolate biosynthesis|g__Pseudomonas.s__Pseudomonas_aeruginosa752.81237337\n-PWY-561\tsuperpathway of glyoxylate cycle and fatty acid degradation|g__Pseudomonas.s__Pseudomonas_aeruginosa395.39499627\n-PWY0-781\taspartate superpathway|unclassified35.58050169\n-PWY0-1277\t3 phenylpropanoate and 3 propanoate degradation|g__Escherichia.s__Escherichia_coli2473.1533402\n-PWY-7184\tpyrimidine deoxyribonucleotides de novo biosynthesis I|g__Streptococcus.s__Streptococcus_agalactiae502.26578072\n-ARGININE-SYN4-PWY\tL ornithine de novo biosynthesis|g__Streptococcus.s__Streptococcus_agalactiae186.2324897\n-PWY-6317\tgalactose degradation I |unclassified27.43425146\n-PWY-7539\t6 hydroxymethyl dihydropterin diphosphate biosynthesis III |g__Staphylococcus.s__Staphylococcus_aureus1142.2860582\n-1CMET2-PWY\tN10 formyl tetrahydrofolate biosynthesis|g__Escherichia.s__Escherichia_coli2980.83193002\n-PWY-7219\tadenosine ribonucleotides de novo biosynthesis|g__Streptococcus.s__Streptococcus_agalactiae381.06191748\n-COMPLETE-ARO-PWY\tsuperpathway of aromatic amino acid biosynthesis|g__Rhodobacter.s__Rhodobacter_sphaeroides603.00195694\n-PWY-6123\tinosine 5 phosphate biosynthesis I|g__Pseudomonas.s__Pseudomonas_aeruginosa869.41608143\n-PWY-7409\tphospholipid remodeling |g__Escherichia.s__Escherichia_coli2324.0578138\n-PWY-2201\tfolate transformations I207.35386067000002\n-PWY-5690\tTCA cycle II |g__Methanobrevibacter.s__Methanobrevibacter_smithii2245.54201886\n-PWY-5860\tsuperpathway of demethylmenaquinol 6 biosynthesis I|g__Escherichia.s__Escherichia_coli1639.5406975899998\n-PWY-7209\tsuperpathway of pyrimidine ribonucleosides degradation|unclassified14.160067660000001\n-PWY-6562\tnorspermidine biosynthesis|unclassified70.22305715\n-PWY-2201\tfolate transformations I|unclassified115.80586462\n-FOLSYN-PWY\tsuperpathway of tetrahydrofolate biosynthesis and salvage|g__Staphylococcus.s__Staphylococcus_aureus5666.17436329\n-ARGDEG-IV-PWY\tL arginine degradation VIII 413.14165668999993\n-PWY-7663\tgondoate biosynthesis |g__Streptococcus.s__Streptococcus_agalactiae495.11402348\n-PWY-5850\tsuperpathway of menaquinol 6 biosynthesis I|g__Escherichia.s__Escherichia_coli2086.15005453\n-ARGSYNBSUB-PWY\tL arginine biosynthesis II |g__Rhodobacter.s__Rhodobacter_sphaeroides2860.34862539\n-NONOXIPENT-PWY\tpentose phosphate pathway |g__Streptococcus.s__Streptococcus_agalactiae1256.57046857\n-SALVADEHYPOX-PWY\tadenosine nucleotides degradation II|g__Staphylococcus.s__Staphylococcus_aureus796.46617638\n-PWY-5695\turate biosynthesis inosine 5 phosp'..b'6904313\n-PWY-7221\tguanosine ribonucleotides de novo biosynthesis|g__Streptococcus.s__Streptococcus_agalactiae263.18388651000004\n-TRNA-CHARGING-PWY\ttRNA charging|g__Staphylococcus.s__Staphylococcus_aureus1635.82224797\n-ARO-PWY\tchorismate biosynthesis I|g__Rhodobacter.s__Rhodobacter_sphaeroides531.17556088\n-PWY-621\tsucrose degradation III |g__Streptococcus.s__Streptococcus_agalactiae112.79225549\n-PYRIDNUCSAL-PWY\tNAD salvage pathway I|g__Pseudomonas.s__Pseudomonas_aeruginosa314.33071124\n-PWY-1541\tsuperpathway of taurine degradation|unclassified58.7739116\n-GLYCOLYSIS\tglycolysis I |g__Streptococcus.s__Streptococcus_agalactiae246.23941276000002\n-PWY-5121\tsuperpathway of geranylgeranyl diphosphate biosynthesis II |g__Pseudomonas.s__Pseudomonas_aeruginosa505.74692227\n-PWY-7200\tsuperpathway of pyrimidine deoxyribonucleoside salvage|g__Escherichia.s__Escherichia_coli524.75222768\n-COA-PWY\tcoenzyme A biosynthesis I|g__Streptococcus.s__Streptococcus_agalactiae323.6348991\n-P105-PWY\tTCA cycle IV |g__Pseudomonas.s__Pseudomonas_aeruginosa346.96109280999997\n-PWY-7200\tsuperpathway of pyrimidine deoxyribonucleoside salvage|g__Staphylococcus.s__Staphylococcus_aureus9664.74077711\n-PWY-6519\t8 amino 7 oxononanoate biosynthesis I|unclassified37.58644825\n-PWY-6386\tUDP N acetylmuramoyl pentapeptide biosynthesis II |unclassified47.18774207\n-PWY-4041\tγ glutamyl cycle|g__Streptococcus.s__Streptococcus_agalactiae357.22684804\n-PWY-6117\tspermine and spermidine degradation I|unclassified9.97625171\n-CALVIN-PWY\tCalvin Benson Bassham cycle|g__Pseudomonas.s__Pseudomonas_aeruginosa263.3999058\n-PWY-7208\tsuperpathway of pyrimidine nucleobases salvage|g__Streptococcus.s__Streptococcus_agalactiae301.65285339999997\n-PWY-7282\t4 amino 2 methyl 5 phosphomethylpyrimidine biosynthesis |unclassified125.63136519\n-PWY0-166\tsuperpathway of pyrimidine deoxyribonucleotides de novo biosynthesis |g__Pseudomonas.s__Pseudomonas_aeruginosa2909.69565583\n-PWY-7184\tpyrimidine deoxyribonucleotides de novo biosynthesis I|g__Escherichia.s__Escherichia_coli708.4604707699999\n-NONMEVIPP-PWY\tmethylerythritol phosphate pathway I|g__Pseudomonas.s__Pseudomonas_aeruginosa580.3736268499999\n-PWY-6565\tsuperpathway of polyamine biosynthesis III|unclassified65.06157163\n-OANTIGEN-PWY\tO antigen building blocks biosynthesis |g__Rhodobacter.s__Rhodobacter_sphaeroides617.65804587\n-KETOGLUCONMET-PWY\tketogluconate metabolism|g__Rhodobacter.s__Rhodobacter_sphaeroides2086.77560891\n-PWY-5484\tglycolysis II |g__Streptococcus.s__Streptococcus_agalactiae230.80642089999998\n-RUMP-PWY\tformaldehyde oxidation I|g__Staphylococcus.s__Staphylococcus_aureus10207.43071166\n-HCAMHPDEG-PWY\t3 phenylpropanoate and 3 propanoate degradation to 2 oxopent 4 enoate|g__Escherichia.s__Escherichia_coli1403.43643815\n-PWY-5417\tcatechol degradation III |g__Rhodobacter.s__Rhodobacter_sphaeroides211.99234581000002\n-PWY-7198\tpyrimidine deoxyribonucleotides de novo biosynthesis IV|g__Staphylococcus.s__Staphylococcus_aureus11389.66331209\n-PWY66-422\tD galactose degradation V |g__Streptococcus.s__Streptococcus_agalactiae254.63203563\n-PWY3O-19\tubiquinol 6 biosynthesis from 4 hydroxybenzoate |g__Rhodobacter.s__Rhodobacter_sphaeroides2645.8359955700003\n-PYRIDOXSYN-PWY\tpyridoxal 5 phosphate biosynthesis I|g__Pseudomonas.s__Pseudomonas_aeruginosa869.1164710900001\n-PWY-6387\tUDP N acetylmuramoyl pentapeptide biosynthesis I |g__Streptococcus.s__Streptococcus_agalactiae324.2241648\n-PWY-7199\tpyrimidine deoxyribonucleosides salvage|g__Staphylococcus.s__Staphylococcus_aureus10064.13020033\n-CATECHOL-ORTHO-CLEAVAGE-PWY\tcatechol degradation to β ketoadipate|g__Rhodobacter.s__Rhodobacter_sphaeroides480.71275029000003\n-TEICHOICACID-PWY\tteichoic acid biosynthesis|g__Staphylococcus.s__Staphylococcus_epidermidis7484.93061203\n-PWY-7229\tsuperpathway of adenosine nucleotides de novo biosynthesis I|g__Pseudomonas.s__Pseudomonas_aeruginosa1554.97187132\n-PWY-6124\tinosine 5 phosphate biosynthesis II|g__Methanobrevibacter.s__Methanobrevibacter_smithii3405.18193479\n' |
| b |
| diff -r 05766022dfc4 -r eaa95ea1195c specific_to_sample2.txt --- a/specific_to_sample2.txt Mon Sep 14 13:50:30 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,1336 +0,0 @@\n-id\tname\tabundances\n-PWY0-1298\tsuperpathway of pyrimidine deoxyribonucleosides degradation|g__Deinococcus.s__Deinococcus_radiodurans11045.646771369999\n-THRESYN-PWY\tsuperpathway of L threonine biosynthesis|g__Actinomyces.s__Actinomyces_odontolyticus869.8459622199999\n-PWY-6122\t5 aminoimidazole ribonucleotide biosynthesis II|g__Listeria.s__Listeria_monocytogenes957.31899135\n-P221-PWY\toctane oxidation|g__Clostridium.s__Clostridium_beijerinckii451.02308636000004\n-PWY-3841\tfolate transformations II|g__Listeria.s__Listeria_monocytogenes825.20149758\n-GLUTORN-PWY\tL ornithine biosynthesis|g__Acinetobacter.s__Acinetobacter_baumannii6249.9626888\n-PWY-5345\tsuperpathway of L methionine biosynthesis |g__Acinetobacter.s__Acinetobacter_baumannii5138.44802921\n-RHAMCAT-PWY\tL rhamnose degradation I|g__Bacteroides.s__Bacteroides_vulgatus2720.4624286400003\n-P185-PWY\tformaldehyde assimilation III |g__Streptococcus.s__Streptococcus_mitis_oralis_pneumoniae2799.70889862\n-PYRIDNUCSAL-PWY\tNAD salvage pathway I|unclassified48.01244259\n-FASYN-ELONG-PWY\tfatty acid elongation saturated|g__Streptococcus.s__Streptococcus_mitis_oralis_pneumoniae2326.16249888\n-ANAEROFRUCAT-PWY\thomolactic fermentation|g__Listeria.s__Listeria_monocytogenes1159.5063759500001\n-PWY-4242\tpantothenate and coenzyme A biosynthesis III|g__Neisseria.s__Neisseria_meningitidis1177.5189052\n-PWY-7185\tUTP and CTP dephosphorylation I95.19614057\n-PWY4FS-8\tphosphatidylglycerol biosynthesis II |g__Enterococcus.s__Enterococcus_faecalis264.06357646\n-HISTSYN-PWY\tL histidine biosynthesis|g__Listeria.s__Listeria_monocytogenes622.7921232799999\n-PWY-841\tsuperpathway of purine nucleotides de novo biosynthesis I|g__Acinetobacter.s__Acinetobacter_baumannii3027.23954619\n-PWY0-321\tphenylacetate degradation I |unclassified95.84027976\n-PWY-6387\tUDP N acetylmuramoyl pentapeptide biosynthesis I |g__Deinococcus.s__Deinococcus_radiodurans819.0181925499999\n-PWY-5667\tCDP diacylglycerol biosynthesis I|g__Neisseria.s__Neisseria_meningitidis1978.55815874\n-PWY-724\tsuperpathway of L lysine, L threonine and L methionine biosynthesis II|g__Acinetobacter.s__Acinetobacter_baumannii4876.52400545\n-PWY0-1586\tpeptidoglycan maturation |g__Bacillus.s__Bacillus_cereus_thuringiensis2488.88961105\n-PWY-5103\tL isoleucine biosynthesis III|g__Actinomyces.s__Actinomyces_odontolyticus640.50375917\n-PWY-5686\tUMP biosynthesis|g__Actinomyces.s__Actinomyces_odontolyticus1155.0252265\n-PWY-7338\t10 trans heptadecenoyl CoA degradation |unclassified44.864782240000004\n-PWY-4242\tpantothenate and coenzyme A biosynthesis III|g__Helicobacter.s__Helicobacter_pylori1193.87628964\n-NAD-BIOSYNTHESIS-II\tNAD salvage pathway II|g__Bacteroides.s__Bacteroides_vulgatus1561.82848783\n-MET-SAM-PWY\tsuperpathway of S adenosyl L methionine biosynthesis|g__Bacteroides.s__Bacteroides_vulgatus2904.45909841\n-FASYN-INITIAL-PWY\tsuperpathway of fatty acid biosynthesis initiation |g__Propionibacterium.s__Propionibacterium_acnes3524.4272528899996\n-NONMEVIPP-PWY\tmethylerythritol phosphate pathway I|g__Acinetobacter.s__Acinetobacter_baumannii3071.89162094\n-PWY-4981\tL proline biosynthesis II |g__Bacteroides.s__Bacteroides_vulgatus2337.74199143\n-PWY66-400\tglycolysis VI |g__Propionibacterium.s__Propionibacterium_acnes2923.04364527\n-METHGLYUT-PWY\tsuperpathway of methylglyoxal degradation|g__Enterococcus.s__Enterococcus_faecalis807.63764403\n-ALLANTOINDEG-PWY\tsuperpathway of allantoin degradation in yeast|g__Enterococcus.s__Enterococcus_faecalis362.21552207999997\n-P185-PWY\tformaldehyde assimilation III |g__Bacillus.s__Bacillus_cereus_thuringiensis189.13084629000002\n-PWY0-1586\tpeptidoglycan maturation |g__Streptococcus.s__Streptococcus_mitis_oralis_pneumoniae6858.429670869999\n-PWY-5973\tcis vaccenate biosynthesis|g__Streptococcus.s__Streptococcus_mitis_oralis_pneumoniae2600.36043229\n-PWY-6527\tstachyose degradation|g__Actinomyces.s__Actinomyces_odontolyticus711.43422479\n-PWY-7282\t4 amino 2 methyl 5 phosphomethylpyrimidine biosynthesis |g__Deinococcus.s__Deinococcus_radi'..b'PWY-7388\toctanoyl [acyl carrier protein] biosynthesis |g__Listeria.s__Listeria_monocytogenes507.22180871999996\n-PWY-6147\t6 hydroxymethyl dihydropterin diphosphate biosynthesis I|g__Neisseria.s__Neisseria_meningitidis947.77913253\n-HEMESYN2-PWY\theme biosynthesis II |g__Bacillus.s__Bacillus_cereus_thuringiensis322.00293305\n-PWY-6123\tinosine 5 phosphate biosynthesis I|g__Acinetobacter.s__Acinetobacter_baumannii3746.82815929\n-HEMESYN2-PWY\theme biosynthesis II |g__Listeria.s__Listeria_monocytogenes369.10390205\n-PWY-7118\tchitin degradation to ethanol|g__Bacillus.s__Bacillus_cereus_thuringiensis400.33401129000003\n-DTDPRHAMSYN-PWY\tdTDP L rhamnose biosynthesis I|g__Listeria.s__Listeria_monocytogenes187.61090748\n-PWY-6125\tsuperpathway of guanosine nucleotides de novo biosynthesis II|g__Propionibacterium.s__Propionibacterium_acnes3194.01708626\n-PWY-7663\tgondoate biosynthesis |g__Enterococcus.s__Enterococcus_faecalis1735.8151961\n-PWY-3781\taerobic respiration I |g__Bacillus.s__Bacillus_cereus_thuringiensis740.84156305\n-KETOGLUCONMET-PWY\tketogluconate metabolism|g__Propionibacterium.s__Propionibacterium_acnes3498.2123751000004\n-PWY-7220\tadenosine deoxyribonucleotides de novo biosynthesis II|g__Helicobacter.s__Helicobacter_pylori4205.54671787\n-PWY-7211\tsuperpathway of pyrimidine deoxyribonucleotides de novo biosynthesis|g__Streptococcus.s__Streptococcus_mitis_oralis_pneumoniae2318.0237892600003\n-PWY-7185\tUTP and CTP dephosphorylation I|unclassified86.86345616999999\n-PWY-2942\tL lysine biosynthesis III|g__Acinetobacter.s__Acinetobacter_baumannii4184.39331209\n-DTDPRHAMSYN-PWY\tdTDP L rhamnose biosynthesis I|g__Actinomyces.s__Actinomyces_odontolyticus1602.39397488\n-PWY-7388\toctanoyl [acyl carrier protein] biosynthesis |g__Streptococcus.s__Streptococcus_mitis_oralis_pneumoniae1522.60994915\n-PWY-7400\tL arginine biosynthesis IV |g__Neisseria.s__Neisseria_meningitidis2661.7116863\n-PWY0-1061\tsuperpathway of L alanine biosynthesis|g__Deinococcus.s__Deinococcus_radiodurans17207.619728309997\n-PWY-6151\tS adenosyl L methionine cycle I|g__Acinetobacter.s__Acinetobacter_baumannii3884.9562603800005\n-BRANCHED-CHAIN-AA-SYN-PWY\tsuperpathway of branched amino acid biosynthesis|g__Streptococcus.s__Streptococcus_mitis_oralis_pneumoniae3873.13594163\n-PWY-6703\tpreQ0 biosynthesis|g__Clostridium.s__Clostridium_beijerinckii456.48187263000005\n-PWY-6307\tL tryptophan degradation X |g__Bacteroides.s__Bacteroides_vulgatus1665.5719701100002\n-PWY-5103\tL isoleucine biosynthesis III|g__Neisseria.s__Neisseria_meningitidis2998.96553709\n-PWY-7220\tadenosine deoxyribonucleotides de novo biosynthesis II|g__Enterococcus.s__Enterococcus_faecalis1253.1079087\n-VALSYN-PWY\tL valine biosynthesis|g__Propionibacterium.s__Propionibacterium_acnes3111.11632972\n-PWY-5910\tsuperpathway of geranylgeranyldiphosphate biosynthesis I |g__Listeria.s__Listeria_monocytogenes465.60089664\n-PWY-6123\tinosine 5 phosphate biosynthesis I|g__Clostridium.s__Clostridium_beijerinckii293.81784981\n-GLYCOGENSYNTH-PWY\tglycogen biosynthesis I |g__Streptococcus.s__Streptococcus_mitis_oralis_pneumoniae3029.53758634\n-PWY-6608\tguanosine nucleotides degradation III|g__Bacteroides.s__Bacteroides_vulgatus1761.75460692\n-PWY-7197\tpyrimidine deoxyribonucleotide phosphorylation|g__Listeria.s__Listeria_monocytogenes430.81396281\n-PWY-7111\tpyruvate fermentation to isobutanol |g__Helicobacter.s__Helicobacter_pylori1895.1322225\n-PWY-6859\tall trans farnesol biosynthesis|g__Listeria.s__Listeria_monocytogenes514.9571508500001\n-PWY0-781\taspartate superpathway|g__Acinetobacter.s__Acinetobacter_baumannii5029.55209128\n-GLUCUROCAT-PWY\tsuperpathway of β D glucuronide and D glucuronate degradation|g__Propionibacterium.s__Propionibacterium_acnes3236.09786158\n-PWY-6385\tpeptidoglycan biosynthesis III |g__Bacillus.s__Bacillus_cereus_thuringiensis504.30027838000007\n-PWY0-1296\tpurine ribonucleosides degradation|g__Deinococcus.s__Deinococcus_radiodurans19916.5017068\n-PWY-5659\tGDP mannose biosynthesis|g__Listeria.s__Listeria_monocytogenes632.43764388\n' |