| Previous changeset 0:31394a0c0242 (2016-04-15) Next changeset 2:fdfb35745104 (2022-10-19) |
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Commit message:
"planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit 4a40a73a6eb981310a3c1c54dfa98b5460a843f9" |
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modified:
combine_metaphlan2_humann2.py combine_metaphlan2_humann2.xml |
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added:
output output_p |
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removed:
test-data/gene_families_output.tabular test-data/pathways_output.tabular |
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| diff -r 31394a0c0242 -r e25efca0a49c combine_metaphlan2_humann2.py --- a/combine_metaphlan2_humann2.py Fri Apr 15 09:15:21 2016 -0400 +++ b/combine_metaphlan2_humann2.py Mon Sep 14 12:19:49 2020 +0000 |
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| @@ -1,15 +1,13 @@ #!/usr/bin/env python # -*- coding: utf-8 -*- -import sys -import os import argparse -import re + -def extract_clade_abundance(metaphlan2_filepath): - clade_abundance = {} - with open(metaphlan2_filepath, 'r') as metaphlan2_file: - for line in metaphlan2_file.readlines(): +def extract_clade_abundance(metaphlan2_fp): + clade_abund = {} + with open(metaphlan2_fp, 'r') as metaphlan2_f: + for line in metaphlan2_f.readlines(): if line.find('g__') == -1: continue @@ -20,91 +18,92 @@ genus = taxo[(taxo.find('g__')+3):] if genus.find('|') != -1: genus = genus[:(genus.find('|'))] - clade_abundance.setdefault(genus, {'abundance':0, 'species':{}}) + 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_abundance[genus]['species'].setdefault(species, abundance) + clade_abund[genus]['species'].setdefault( + species, + abundance) else: - clade_abundance[genus]['abundance'] = abundance - return clade_abundance + clade_abund[genus]['abundance'] = abundance + return clade_abund -def compute_overall_abundance(humann2_file): + +def compute_overall_abundance(humann2_fp): overall_abundance = 0 - with open(args.humann2_file, 'r') as humann2_file: - for line in humann2_file.readlines(): + with open(humann2_fp, 'r') as humann2_f: + for line in humann2_f.readlines(): if line.find('|') != -1 or line.startswith('#'): continue split_line = line[:-1].split('\t') overall_abundance += float(split_line[1]) return overall_abundance + def format_characteristic_name(name): - formatted_name = name - formatted_name = formatted_name.replace('/',' ') - formatted_name = formatted_name.replace('-',' ') - formatted_name = formatted_name.replace("'",'') - if formatted_name.find('(') != -1 and formatted_name.find(')') != -1: - open_bracket = formatted_name.find('(') - close_bracket = formatted_name.find(')')+1 - formatted_name = formatted_name[:open_bracket] + formatted_name[close_bracket:] - return formatted_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[:open_bracket] + formatted_n[close_bracket:] + return formatted_n + def combine_metaphlan2_humann2(args): - clade_abundance = extract_clade_abundance(args.metaphlan2_file) - overall_abundance = compute_overall_abundance(args.humann2_file) + clade_abund = extract_clade_abundance(args.metaphlan2_fp) + overall_abund = compute_overall_abundance(args.humann2_fp) - with open(args.output_file, 'w') as output_file: - output_file.write('genus\t') - output_file.write('genus_abundance\t') - output_file.write('species\t') - output_file.write('species_abundance\t') - output_file.write(args.type + '_id\t') - output_file.write(args.type + '_name\t') - output_file.write(args.type + '_abundance\n') - with open(args.humann2_file, 'r') as humann2_file: - for line in humann2_file.readlines(): + 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: + for line in humann2_f.readlines(): if line.find('|') == -1: continue split_line = line[:-1].split('\t') - abundance = 100*float(split_line[1])/overall_abundance + abundance = 100*float(split_line[1])/overall_abund annotation = split_line[0].split('|') - characteristic = annotation[0].split(':') - characteristic_id = characteristic[0] - characteristic_name = '' - if len(characteristic) > 1: - characteristic_name = format_characteristic_name(characteristic[-1]) + charact = annotation[0].split(':') + charact_id = charact[0] + char_name = '' + if len(charact) > 1: + char_name = format_characteristic_name(charact[-1]) taxo = annotation[1].split('.') - + if taxo[0] == 'unclassified': continue genus = taxo[0][3:] species = taxo[1][3:] - if not clade_abundance.has_key(genus): - print "no", genus, "found in", args.metaphlan2_file + if genus not in clade_abund: + print("no %s found in %s" % (genus, args.metaphlan2_fp)) continue - if not clade_abundance[genus]['species'].has_key(species): - print "no", species, "found in", args.metaphlan2_file, - print "for", genus + if species not in clade_abund[genus]['species']: + print("no %s found in %s for % s" % (species, args.metaphlan2_fp, genus)) continue - output_file.write(genus + '\t') - output_file.write(clade_abundance[genus]['abundance'] + '\t') - output_file.write(species + '\t') - output_file.write(clade_abundance[genus]['species'][species] + '\t') - output_file.write(characteristic_id + '\t') - output_file.write(characteristic_name + '\t') - output_file.write(str(abundance) + '\n') + + 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__': parser = argparse.ArgumentParser() - parser.add_argument('--humann2_file', required=True) - parser.add_argument('--metaphlan2_file', required=True) - parser.add_argument('--output_file', 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) \ No newline at end of file + combine_metaphlan2_humann2(args) |
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| diff -r 31394a0c0242 -r e25efca0a49c combine_metaphlan2_humann2.xml --- a/combine_metaphlan2_humann2.xml Fri Apr 15 09:15:21 2016 -0400 +++ b/combine_metaphlan2_humann2.xml Mon Sep 14 12:19:49 2020 +0000 |
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| @@ -1,40 +1,32 @@ -<tool id="combine_metaphlan2_humann2" name="Combine MetaPhlAn2 and HUMAnN2 outputs" version="0.1.0"> +<tool id="combine_metaphlan2_humann2" name="Combine MetaPhlAn2 and HUMAnN2 outputs" version="0.2.0"> <description>to relate genus/species abundances and gene families/pathways abundances</description> - <requirements> </requirements> - <stdio> <exit_code range="1:" /> <exit_code range=":-1" /> </stdio> - <version_command></version_command> - <command><![CDATA[ python $__tool_directory__/combine_metaphlan2_humann2.py - --metaphlan2_file $metaphlan2_file - --humann2_file $humann2_file - --type $type + --metaphlan2_fp '$metaphlan2_file' + --humann2_fp '$humann2_file' + --type '$type' #if str($type) == 'gene_families' - --output_file $gene_families_output_file + --output_fp '$gene_families_output_file' #else - --output_file $pathway_output_file + --output_fp '$pathway_output_file' #end if ]]></command> - <inputs> <param name="metaphlan2_file" format="txt,tabular" type="data" label="Input file corresponding to MetaPhlAn2 output" help="The MetaPhlAn2 output file contains relative abundance of clades at different taxonomic levels (--metaphlan2_file)"/> - <param name="humann2_file" format="txt,tabular" type="data" label="Input file corresponding to HUMAnN2 output" help="The HUMAnN2 output file contains relative abundance of gene families or pathways with corresponding taxonomic stratification (--humann2_file)"/> - <param name='type' type="select" label="Type of characteristics in HUMAnN2 file" help="(--type)"> <option value="gene_families" selected="true">Gene families</option> <option value="pathways">Pathways</option> </param> </inputs> - <outputs> <data name="gene_families_output_file" format="tabular" label="${tool.name} on ${on_string}: Gene family abundances related to genus/species abundances" > @@ -45,30 +37,45 @@ <filter>type=="pathways"</filter> </data> </outputs> - <tests> <test> - <param name="metaphlan2_file" value="metaphlan2_input.txt"/> - <param name="humann2_file" value="humann2_gene_families_input.tabular"/> - <param name='type' value="gene_families"/> - <output name="gene_families_output_file" file="gene_families_output.tabular"/> + <param name="metaphlan2_file" value="metaphlan2_input.txt"/> + <param name="humann2_file" value="humann2_gene_families_input.tabular"/> + <param name='type' value="gene_families"/> + <output name="gene_families_output_file"> + <assert_contents> + <has_n_columns n="8"/> + <has_n_lines n="29434"/> + <has_text text="Staphylococcus_epidermidis"/> + <has_text text="Putative transposon Tn552 DNA invertase bin3"/> + <has_size value="3467947"/> + </assert_contents> + </output> </test> <test> <param name="metaphlan2_file" value="metaphlan2_input.txt"/> <param name="humann2_file" value="humann2_pathways_input.tabular"/> <param name='type' value="pathways"/> - <output name="pathway_output_file" file="pathways_output.tabular"/> + <output name="pathway_output_file"> + <assert_contents> + <has_n_columns n="8"/> + <has_n_lines n="1533"/> + <has_text text="Rhodobacter_sphaeroides"/> + <has_text text="superpathway of acetyl CoA biosynthesis"/> + <has_size value="186363"/> + </assert_contents> + </output> </test> </tests> - <help><![CDATA[ **What it does** This tool combine MetaPhlAn2 outputs and HUMANnN2 outputs. -For each gene families/pathways and the corresponding taxonomic stratification, you get relative abundance of this gene family/pathway and the relative abundance of corresponding species and genus. +For each gene families/pathways and the corresponding taxonomic stratification, +you get relative abundance of this gene family/pathway and the relative abundance +of corresponding species and genus. ]]></help> - <citations> </citations> </tool> \ No newline at end of file |
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| diff -r 31394a0c0242 -r e25efca0a49c output --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/output Mon Sep 14 12:19:49 2020 +0000 |
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| b'@@ -0,0 +1,29434 @@\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' |
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| diff -r 31394a0c0242 -r e25efca0a49c output_p --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/output_p Mon Sep 14 12:19:49 2020 +0000 |
| b |
| b'@@ -0,0 +1,1533 @@\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' |
| b |
| diff -r 31394a0c0242 -r e25efca0a49c test-data/gene_families_output.tabular --- a/test-data/gene_families_output.tabular Fri Apr 15 09:15:21 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,29434 +0,0 @@\n-genus\tgenus_abundance\tspecies\tspecies_abundance\tgene_families_id\tgene_families_name\tgene_families_abundance\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_P19529\t Replication initiation protein\t0.40728906083\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tUniRef50_P19529\t Replication initiation protein\t0.261480825839\n-Propionibacterium\t0.36055\tPropionibacterium_acnes\t0.36055\tUniRef50_P19529\t Replication initiation protein\t0.188582893984\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tUniRef50_Q5HJZ6\t Plasmid recombination enzyme type 3\t0.338670908045\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_Q5HJZ6\t Plasmid recombination enzyme type 3\t0.298445310895\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tUniRef50_Q5HJZ6\t Plasmid recombination enzyme type 3\t0.0233463103488\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tUniRef50_P02983\t Tetracycline resistance protein\t0.25596042462\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_P02983\t Tetracycline resistance protein\t0.255300007484\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_Q93GF3\t Rep\t0.322388303126\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tUniRef50_Q93GF3\t Rep\t0.0431524470097\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_V6QG63\t Integrase\t0.303352524824\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_W1W6K4\t\t0.247856118482\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_D4FM51\t Plasmid recombination enzyme\t0.214063812113\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_Z6ILY0\t\t0.196787157891\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_F0P516\t Replication initiation protein, truncated\t0.11963734642\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tUniRef50_F0P516\t Replication initiation protein, truncated\t0.0759957583321\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_Q8CU99\t\t0.173070998557\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_P14491\t Protein rlx\t0.172105258916\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tUniRef50_P14491\t Protein rlx\t0.00010650270839\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tUniRef50_P18358\t Transposon Tn552 resolvase\t0.132196365122\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_P18358\t Transposon Tn552 resolvase\t0.0309505071873\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_Q5HRN3\t ISSep1 like transposase\t0.125576550449\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tUniRef50_Q5HRN3\t ISSep1 like transposase\t0.0183157071851\n-Propionibacterium\t0.36055\tPropionibacterium_acnes\t0.36055\tUniRef50_Q5HRN3\t ISSep1 like transposase\t0.00112799242136\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_Q4L351\t Staphylococcus haemolyticus JCSC1435 DNA, complete genome\t0.130782524407\n-Rhodobacter\t5.64659\tRhodobacter_sphaeroides\t5.64659\tUniRef50_Q3J5T4\t 50S ribosomal protein L11\t0.12410365529\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_N6A8S2\t\t0.113249904113\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_L7WXY9\t\t0.107571179124\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tUniRef50_P18357\t Regulatory protein BlaR1\t0.0712959295517\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_P18357\t Regulatory protein BlaR1\t0.0277440503984\n-Propionibacterium\t0.36055\tPropionibacterium_acnes\t0.36055\tUniRef50_P18357\t Regulatory protein BlaR1\t0.0084931424066\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tUniRef50_K0LDS3\t\t0.104070365649\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tUniRef50_I3U5U5\t Mobilization protein C\t0.0997088242247\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tUniRef50_I3U5U5\t Mobilization protein C\t0.00114228510186\n-Staphylococcus\t55.38558\tStap'..b'500697096e-05\n-Neisseria\t0.04343\tNeisseria_meningitidis\t0.04343\tUniRef50_E3D229\t Chromosome partition protein Smc\t3.18199078347e-05\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tUniRef50_G0LRQ0\t Serine aspartate repeat containing protein D\t3.14433408727e-05\n-Deinococcus\t0.30974\tDeinococcus_radiodurans\t0.15196\tUniRef50_Q9RUP8\t Isoleucine tRNA ligase\t3.12100672473e-05\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tUniRef50_C1DLW9\t\t3.09897383496e-05\n-Acinetobacter\t0.12091\tAcinetobacter_baumannii\t0.12091\tUniRef50_A3M2F1\t IcmB protein\t3.0951737447e-05\n-Neisseria\t0.04343\tNeisseria_meningitidis\t0.04343\tUniRef50_F0MM85\t Hemagglutinin hemolysin family protein\t3.06557363026e-05\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tUniRef50_P58402\t Sensor protein EvgS\t3.01027333145e-05\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tUniRef50_Q02GC2\t Type 4 fimbrial biogenesis protein PilY1\t3.00132483779e-05\n-Acinetobacter\t0.12091\tAcinetobacter_baumannii\t0.12091\tUniRef50_J4VP36\t DNA polymerase III, alpha subunit\t2.97216860599e-05\n-Neisseria\t0.04343\tNeisseria_meningitidis\t0.04343\tUniRef50_Q9JVX8\t DNA polymerase III subunit alpha\t2.94357339795e-05\n-Acinetobacter\t0.12091\tAcinetobacter_baumannii\t0.12091\tUniRef50_A0A009XXP0\t RecF RecN SMC N terminal domain protein\t2.92905620962e-05\n-Propionibacterium\t0.36055\tPropionibacterium_acnes\t0.36055\tUniRef50_F9YY53\t\t2.92566118618e-05\n-Acinetobacter\t0.12091\tAcinetobacter_baumannii\t0.12091\tUniRef50_B0V8Z8\t ATP dependent dsDNA exonuclease \t2.88552636616e-05\n-Helicobacter\t0.07678\tHelicobacter_pylori\t0.07678\tUniRef50_I9V7J9\t Outer membrane protein HopL\t2.85775736026e-05\n-Propionibacterium\t0.36055\tPropionibacterium_acnes\t0.36055\tUniRef50_Q6ABR7\t Cobalamin biosynthesis protein CobN\t2.8553327931e-05\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tUniRef50_A6V8C8\t\t2.82972442692e-05\n-Propionibacterium\t0.36055\tPropionibacterium_acnes\t0.36055\tUniRef50_G8VL08\t ATP dependent helicase HrpA\t2.82418370752e-05\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tUniRef50_W1C828\t Molybdate metabolism regulator\t2.79757737727e-05\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tUniRef50_I3GYQ4\t\t2.73839347839e-05\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tUniRef50_Q8FJC7\t DNA translocase FtsK\t2.65486635693e-05\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tUniRef50_G9W1N9\t Enterobactin synthetase component F\t2.6238193233e-05\n-Neisseria\t0.04343\tNeisseria_meningitidis\t0.04343\tUniRef50_F0N1G5\t Transcription repair coupling factor\t2.58949903961e-05\n-Neisseria\t0.04343\tNeisseria_meningitidis\t0.04343\tUniRef50_C9WZ56\t Transcription repair coupling factor\t2.48987836093e-05\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tUniRef50_E2QDF8\t Phage lambda related protein, Side tail fiber protein homolog\t2.4770502341e-05\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tUniRef50_L4JUW1\t Adhesin invasin\t2.44170659171e-05\n-Neisseria\t0.04343\tNeisseria_meningitidis\t0.04343\tUniRef50_R0UE42\t Filamentous hemagglutinin family N terminal domain protein\t2.43934688419e-05\n-Deinococcus\t0.30974\tDeinococcus_radiodurans\t0.15196\tUniRef50_Q9RWI1\t\t2.27141884239e-05\n-Propionibacterium\t0.36055\tPropionibacterium_acnes\t0.36055\tUniRef50_F9NYB1\t RHS repeat associated core domain protein\t2.15782362763e-05\n-Methanobrevibacter\t6.51285\tMethanobrevibacter_smithii\t6.51285\tUniRef50_A5UKU3\t Adhesin like protein\t1.83906316145e-05\n-Acinetobacter\t0.12091\tAcinetobacter_baumannii\t0.12091\tUniRef50_V5VA04\t Hemolysin type calcium binding domain containing protein\t1.83471865409e-05\n-Neisseria\t0.04343\tNeisseria_meningitidis\t0.04343\tUniRef50_R0YL20\t Filamentous hemagglutinin family N terminal domain protein\t1.82246511863e-05\n-Acinetobacter\t0.12091\tAcinetobacter_baumannii\t0.12091\tUniRef50_A3M865\t\t1.69091555151e-05\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tUniRef50_A0A024L957\t\t1.60746007854e-05\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tUniRef50_U6ANV5\t\t1.52169657171e-05\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tUniRef50_M4JLP2\t\t1.50648414743e-05\n' |
| b |
| diff -r 31394a0c0242 -r e25efca0a49c test-data/pathways_output.tabular --- a/test-data/pathways_output.tabular Fri Apr 15 09:15:21 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1533 +0,0 @@\n-genus\tgenus_abundance\tspecies\tspecies_abundance\tpathways_id\tpathways_name\tpathways_abundance\n-Rhodobacter\t5.64659\tRhodobacter_sphaeroides\t5.64659\tPWY-3781\t aerobic respiration I \t0.368556895131\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tPWY-3781\t aerobic respiration I \t0.253147232386\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tPWY-3781\t aerobic respiration I \t0.233475601635\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tPWY-3781\t aerobic respiration I \t0.0918554879572\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tPWY-3781\t aerobic respiration I \t0.0602129571868\n-Helicobacter\t0.07678\tHelicobacter_pylori\t0.07678\tPWY-3781\t aerobic respiration I \t0.00382462905467\n-Propionibacterium\t0.36055\tPropionibacterium_acnes\t0.36055\tPWY-3781\t aerobic respiration I \t0.00247237718207\n-Deinococcus\t0.30974\tDeinococcus_radiodurans\t0.15196\tPWY-3781\t aerobic respiration I \t0.00196076982686\n-Neisseria\t0.04343\tNeisseria_meningitidis\t0.04343\tPWY-3781\t aerobic respiration I \t0.00114299428398\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tPWY66-389\t phytol degradation\t0.249553035467\n-Rhodobacter\t5.64659\tRhodobacter_sphaeroides\t5.64659\tPWY66-389\t phytol degradation\t0.237125038432\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tPWY66-389\t phytol degradation\t0.106059732351\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tPWY66-389\t phytol degradation\t0.0290622837557\n-Acinetobacter\t0.12091\tAcinetobacter_baumannii\t0.12091\tPWY66-389\t phytol degradation\t0.0138467548757\n-Clostridium\t0.93894\tClostridium_beijerinckii\t0.93894\tPWY66-389\t phytol degradation\t0.0054086128391\n-Propionibacterium\t0.36055\tPropionibacterium_acnes\t0.36055\tPWY66-389\t phytol degradation\t0.00343336868651\n-Deinococcus\t0.30974\tDeinococcus_radiodurans\t0.15196\tPWY66-389\t phytol degradation\t0.00256960762473\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tPWY-5173\t superpathway of acetyl CoA biosynthesis\t0.296752306253\n-Rhodobacter\t5.64659\tRhodobacter_sphaeroides\t5.64659\tPWY-5173\t superpathway of acetyl CoA biosynthesis\t0.148537093411\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tPWY-5173\t superpathway of acetyl CoA biosynthesis\t0.125379958848\n-Streptococcus\t17.12842\tStreptococcus_mutans\t16.30896\tPWY-5173\t superpathway of acetyl CoA biosynthesis\t0.106650295398\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tPWY-5173\t superpathway of acetyl CoA biosynthesis\t0.0485906161711\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tPWY-5173\t superpathway of acetyl CoA biosynthesis\t0.00859504489919\n-Streptococcus\t17.12842\tStreptococcus_agalactiae\t0.81946\tPWY-5173\t superpathway of acetyl CoA biosynthesis\t0.00389664869866\n-Acinetobacter\t0.12091\tAcinetobacter_baumannii\t0.12091\tPWY-5173\t superpathway of acetyl CoA biosynthesis\t0.00112889604332\n-Propionibacterium\t0.36055\tPropionibacterium_acnes\t0.36055\tPWY-5173\t superpathway of acetyl CoA biosynthesis\t0.000963588944608\n-Staphylococcus\t55.38558\tStaphylococcus_epidermidis\t27.10796\tPWY-7111\t pyruvate fermentation to isobutanol \t0.204215296434\n-Rhodobacter\t5.64659\tRhodobacter_sphaeroides\t5.64659\tPWY-7111\t pyruvate fermentation to isobutanol \t0.176397583599\n-Staphylococcus\t55.38558\tStaphylococcus_aureus\t28.27762\tPWY-7111\t pyruvate fermentation to isobutanol \t0.14789632153\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tPWY-7111\t pyruvate fermentation to isobutanol \t0.108168322976\n-Streptococcus\t17.12842\tStreptococcus_mutans\t16.30896\tPWY-7111\t pyruvate fermentation to isobutanol \t0.0846845592441\n-Methanobrevibacter\t6.51285\tMethanobrevibacter_smithii\t6.51285\tPWY-7111\t pyruvate fermentation to isobutanol \t0.0294822118253\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tPWY-7111\t pyruvate fermentation to isobutanol \t0.0135584729954\n-Clostridium\t0.93894\tClostridium_beijerinckii\t0.93894\tPWY-7111\t pyruvate fermentation to isobutanol \t0.0129564304194\n-Acinetobacter\t0.12091\tAcinetobacter_baumannii\t0.12091\tPWY-7111\t pyruvate fermentation to isobutanol \t0.00466772463498\n-Streptococcus\t17.12'..b'371335506\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tPWY-5656\t mannosylglycerate biosynthesis I\t0.0189326674698\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tPWY-7165\t L ascorbate biosynthesis VI \t0.00330800105556\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tLPSSYN-PWY\t superpathway of lipopolysaccharide biosynthesis\t0.018571618591\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tFUCCAT-PWY\t fucose degradation\t0.0258996873857\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tPWY-7446\t sulfoglycolysis\t0.0275758331758\n-Methanobrevibacter\t6.51285\tMethanobrevibacter_smithii\t6.51285\tP241-PWY\t coenzyme B biosynthesis\t0.0254264295134\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tPWY-6948\t sitosterol degradation to androstenedione\t0.00329315802192\n-Clostridium\t0.93894\tClostridium_beijerinckii\t0.93894\tCENTFERM-PWY\t pyruvate fermentation to butanoate\t0.0077654210394\n-Clostridium\t0.93894\tClostridium_beijerinckii\t0.93894\tPWY-5367\t petroselinate biosynthesis\t0.00470335180994\n-Streptococcus\t17.12842\tStreptococcus_agalactiae\t0.81946\tPWY-5367\t petroselinate biosynthesis\t0.00385663493416\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tPWY0-41\t allantoin degradation IV \t0.0222930161173\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tPWY-6731\t starch degradation III\t0.016278474061\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tFUC-RHAMCAT-PWY\t superpathway of fucose and rhamnose degradation\t0.0214779190288\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tPWY-7409\t phospholipid remodeling \t0.0186794588374\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\t0.0202085072369\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tRHAMCAT-PWY\t L rhamnose degradation I\t0.0188827745801\n-Clostridium\t0.93894\tClostridium_beijerinckii\t0.93894\tRHAMCAT-PWY\t L rhamnose degradation I\t0.00223834731648\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tKDO-NAGLIPASYN-PWY\t superpathway of 2 lipid A biosynthesis\t0.012366617493\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tPWY0-1338\t polymyxin resistance\t0.0203425769976\n-Methanobrevibacter\t6.51285\tMethanobrevibacter_smithii\t6.51285\tP261-PWY\t coenzyme M biosynthesis I\t0.0184374760723\n-Methanobrevibacter\t6.51285\tMethanobrevibacter_smithii\t6.51285\tPWY-5198\t factor 420 biosynthesis\t0.0165329714607\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tHCAMHPDEG-PWY\t 3 phenylpropanoate and 3 propanoate degradation to 2 oxopent 4 enoate\t0.0112800262634\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tPWY-6690\t cinnamate and 3 hydroxycinnamate degradation to 2 oxopent 4 enoate\t0.0112800262634\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tPWY-7090\t UDP 2,3 diacetamido 2,3 dideoxy α D mannuronate biosynthesis\t0.00812186950085\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tPWY-6467\t Kdo transfer to lipid IVA III \t0.00739415124056\n-Escherichia\t11.54704\tEscherichia_coli\t6.69956\tPWY-6309\t L tryptophan degradation XI \t0.00644240092358\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tPWY-6309\t L tryptophan degradation XI \t0.00336506734394\n-Clostridium\t0.93894\tClostridium_beijerinckii\t0.93894\tP562-PWY\t myo inositol degradation I\t0.00411946456846\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tPWY-6660\t 2 heptyl 3 hydroxy 4 quinolone biosynthesis\t0.00736993141727\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tPWY66-388\t fatty acid α oxidation III\t0.00731134431452\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tPWY-6662\t superpathway of quinolone and alkylquinolone biosynthesis\t0.00706261848576\n-Pseudomonas\t1.92917\tPseudomonas_aeruginosa\t0.81333\tPWY-6672\t cis genanyl CoA degradation\t0.00198318684357\n-Acinetobacter\t0.12091\tAcinetobacter_baumannii\t0.12091\tPWY-6672\t cis genanyl CoA degradation\t0.00159085944767\n-Propionibacterium\t0.36055\tPropionibacterium_acnes\t0.36055\tUDPNACETYLGALSYN-PWY\t UDP N acetyl D glucosamine biosynthesis II\t0.000844180685352\n' |