| Next changeset 1:1e74cb2c8e67 (2020-09-14) |
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Commit message:
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/format_metaphlan2_output/ commit 36388cac89e4ffa55fe317d10cbf97346ab00a71-dirty |
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added:
format_metaphlan2_output.py format_metaphlan2_output.xml test-data/all_taxo_level_abundance.txt test-data/class_abundance.txt test-data/family_abundance.txt test-data/genus_abundance.txt test-data/kingdom_abundance.txt test-data/metaphlan2_output.txt test-data/order_abundance.txt test-data/phylum_abundance.txt test-data/species_abundance.txt test-data/strains_abundance.txt |
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| diff -r 000000000000 -r 2bfa9b200600 format_metaphlan2_output.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/format_metaphlan2_output.py Wed Apr 20 07:52:41 2016 -0400 |
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| @@ -0,0 +1,97 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +import sys +import os +import argparse +import re + +taxo_level_correspondance = {} +taxo_level_correspondance['k'] = 'kingdom' +taxo_level_correspondance['p'] = 'phylum' +taxo_level_correspondance['c'] = 'class' +taxo_level_correspondance['o'] = 'order' +taxo_level_correspondance['f'] = 'family' +taxo_level_correspondance['g'] = 'genus' +taxo_level_correspondance['s'] = 'species' +taxo_level_correspondance['t'] = 'strains' + +def write_taxo_abundance(output_files, level, taxo, abundance): + if not taxo_level_correspondance.has_key(level): + raise ValueError(level + ' is not a know taxonomic level') + output_files[taxo_level_correspondance[level]].write(taxo + '\t') + output_files[taxo_level_correspondance[level]].write(abundance + '\n') + +def format_metaphlan2_output(args): + taxo_levels_abundance_files = {} + taxo_levels_abundance_files['kingdom'] = open(args.kingdom_abundance_file, 'w') + taxo_levels_abundance_files['phylum'] = open(args.phylum_abundance_file, 'w') + taxo_levels_abundance_files['class'] = open(args.class_abundance_file, 'w') + taxo_levels_abundance_files['order'] = open(args.order_abundance_file, 'w') + taxo_levels_abundance_files['family'] = open(args.family_abundance_file, 'w') + taxo_levels_abundance_files['genus'] = open(args.genus_abundance_file, 'w') + taxo_levels_abundance_files['species'] = open(args.species_abundance_file, 'w') + taxo_levels_abundance_files['strains'] = open(args.strains_abundance_file, 'w') + + for taxo_level_file in taxo_levels_abundance_files: + taxo_levels_abundance_files[taxo_level_file].write(taxo_level_file + '\t') + taxo_levels_abundance_files[taxo_level_file].write('abundance\n') + + with open(args.metaphlan2_output, 'r') as input_file: + with open(args.all_taxo_level_abundance_file, 'w') as output_file: + output_file.write("kingdom\t") + output_file.write("phylum\t") + output_file.write("class\t") + output_file.write("order\t") + output_file.write("family\t") + output_file.write("genus\t") + output_file.write("species\t") + output_file.write("strains\t") + output_file.write("abundance\n") + levels_number = 8 + + for line in input_file.readlines(): + if line.startswith("#"): + continue + + split_line = line[:-1].split('\t') + all_taxo = split_line[0] + abundance = split_line[1] + + split_taxo = all_taxo.split('|') + for level in split_taxo: + taxo = level.split('__')[1] + taxo = taxo.replace("_"," ") + output_file.write(taxo + '\t') + + for i in range(len(split_taxo), levels_number): + output_file.write('\t') + + output_file.write(abundance + "\n") + + + last_taxo_level = split_taxo[-1].split('__') + taxo = last_taxo_level[1].replace("_"," ") + level = last_taxo_level[0] + write_taxo_abundance(taxo_levels_abundance_files, level, taxo, + abundance) + + for taxo_level_file in taxo_levels_abundance_files: + taxo_levels_abundance_files[taxo_level_file].close() + +if __name__ == '__main__': + parser = argparse.ArgumentParser() + parser.add_argument('--metaphlan2_output', required=True) + parser.add_argument('--all_taxo_level_abundance_file', required=True) + parser.add_argument('--kingdom_abundance_file', required=True) + parser.add_argument('--phylum_abundance_file', required=True) + parser.add_argument('--class_abundance_file', required=True) + parser.add_argument('--order_abundance_file', required=True) + parser.add_argument('--family_abundance_file', required=True) + parser.add_argument('--genus_abundance_file', required=True) + parser.add_argument('--species_abundance_file', required=True) + parser.add_argument('--strains_abundance_file', required=True) + + args = parser.parse_args() + + format_metaphlan2_output(args) \ No newline at end of file |
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| diff -r 000000000000 -r 2bfa9b200600 format_metaphlan2_output.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/format_metaphlan2_output.xml Wed Apr 20 07:52:41 2016 -0400 |
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| @@ -0,0 +1,67 @@ +<tool id="format_metaphlan2_output" name="Format MetaPhlAn2" version="0.1.0"> + <description>output to extract abundance at different taxonomic levels</description> + + <requirements> + </requirements> + + <stdio> + </stdio> + + <version_command></version_command> + + <command><![CDATA[ + python $__tool_directory__/format_metaphlan2_output.py + --metaphlan2_output $input_file + --all_taxo_level_abundance_file $all_taxo_level_abundance_file + --kingdom_abundance_file $kingdom_abundance_file + --phylum_abundance_file $phylum_abundance_file + --class_abundance_file $class_abundance_file + --order_abundance_file $order_abundance_file + --family_abundance_file $family_abundance_file + --genus_abundance_file $genus_abundance_file + --species_abundance_file $species_abundance_file + --strains_abundance_file $strains_abundance_file + ]]></command> + + <inputs> + <param name="input_file" type="data" format="tabular,tsv,csv" label="Input file" help="Output file of MetaPhlAN with all taxonomic levels (from kingdom to strains, --metaphlan2_output)"/> + </inputs> + + <outputs> + <data name="all_taxo_level_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Abundances for all taxonomic levels" /> + <data name="kingdom_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Kingdom abundances" /> + <data name="phylum_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Phylum abundances" /> + <data name="class_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Class abundances" /> + <data name="order_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Order abundances" /> + <data name="family_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Family abundances" /> + <data name="genus_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Genus abundances" /> + <data name="species_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Species abundances" /> + <data name="strains_abundance_file" format="tabular" label="${tool.name} on ${on_string}: Stain abundances" /> + </outputs> + + <tests> + <test> + <param name="input_file" value="metaphlan2_output.txt"/> + <output name="all_taxo_level_abundance_file" file="all_taxo_level_abundance.txt"/> + <output name="kingdom_abundance_file" file="kingdom_abundance.txt"/> + <output name="phylum_abundance_file" file="phylum_abundance.txt"/> + <output name="class_abundance_file" file="class_abundance.txt"/> + <output name="order_abundance_file" file="order_abundance.txt"/> + <output name="family_abundance_file" file="family_abundance.txt"/> + <output name="genus_abundance_file" file="genus_abundance.txt"/> + <output name="species_abundance_file" file="species_abundance.txt"/> + <output name="strains_abundance_file" file="strains_abundance.txt"/> + </test> + </tests> + + <help><![CDATA[ +**What it does** + +This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains). + +9 files are generated: one file per taxonomic levels with abundance for corresponding clades and one file combining all taxonomic levels and corresponding abundances. + ]]></help> + + <citations> + </citations> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r 2bfa9b200600 test-data/all_taxo_level_abundance.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_taxo_level_abundance.txt Wed Apr 20 07:52:41 2016 -0400 |
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| b'@@ -0,0 +1,108 @@\n+kingdom\tphylum\tclass\torder\tfamily\tgenus\tspecies\tstrains\tabundance\n+Bacteria\t\t\t\t\t\t\t\t99.20573\n+Archaea\t\t\t\t\t\t\t\t0.79427\n+Bacteria\tDeinococcus Thermus\t\t\t\t\t\t\t45.20297\n+Bacteria\tFirmicutes\t\t\t\t\t\t\t19.15406\n+Bacteria\tProteobacteria\t\t\t\t\t\t\t16.57369\n+Bacteria\tActinobacteria\t\t\t\t\t\t\t10.37863\n+Bacteria\tBacteroidetes\t\t\t\t\t\t\t7.89639\n+Archaea\tEuryarchaeota\t\t\t\t\t\t\t0.79427\n+Bacteria\tDeinococcus Thermus\tDeinococci\t\t\t\t\t\t45.20297\n+Bacteria\tFirmicutes\tBacilli\t\t\t\t\t\t17.33469\n+Bacteria\tActinobacteria\tActinobacteria\t\t\t\t\t\t10.37863\n+Bacteria\tProteobacteria\tGammaproteobacteria\t\t\t\t\t\t8.28554\n+Bacteria\tBacteroidetes\tBacteroidia\t\t\t\t\t\t7.89639\n+Bacteria\tProteobacteria\tEpsilonproteobacteria\t\t\t\t\t\t4.03024\n+Bacteria\tProteobacteria\tBetaproteobacteria\t\t\t\t\t\t3.73739\n+Bacteria\tFirmicutes\tClostridia\t\t\t\t\t\t1.81937\n+Archaea\tEuryarchaeota\tMethanobacteria\t\t\t\t\t\t0.79427\n+Bacteria\tProteobacteria\tAlphaproteobacteria\t\t\t\t\t\t0.52051\n+Bacteria\tDeinococcus Thermus\tDeinococci\tDeinococcales\t\t\t\t\t45.20297\n+Bacteria\tActinobacteria\tActinobacteria\tActinomycetales\t\t\t\t\t10.37863\n+Bacteria\tFirmicutes\tBacilli\tBacillales\t\t\t\t\t9.19153\n+Bacteria\tFirmicutes\tBacilli\tLactobacillales\t\t\t\t\t8.14315\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\t\t\t\t\t7.89639\n+Bacteria\tProteobacteria\tGammaproteobacteria\tPseudomonadales\t\t\t\t\t6.58945\n+Bacteria\tProteobacteria\tEpsilonproteobacteria\tCampylobacterales\t\t\t\t\t4.03024\n+Bacteria\tProteobacteria\tBetaproteobacteria\tNeisseriales\t\t\t\t\t3.73739\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\t\t\t\t\t1.81937\n+Bacteria\tProteobacteria\tGammaproteobacteria\tEnterobacteriales\t\t\t\t\t1.6961\n+Archaea\tEuryarchaeota\tMethanobacteria\tMethanobacteriales\t\t\t\t\t0.79427\n+Bacteria\tProteobacteria\tAlphaproteobacteria\tRhodobacterales\t\t\t\t\t0.52051\n+Bacteria\tDeinococcus Thermus\tDeinococci\tDeinococcales\tDeinococcaceae\t\t\t\t45.20297\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tBacteroidaceae\t\t\t\t7.89639\n+Bacteria\tFirmicutes\tBacilli\tBacillales\tStaphylococcaceae\t\t\t\t7.4516\n+Bacteria\tActinobacteria\tActinobacteria\tActinomycetales\tPropionibacteriaceae\t\t\t\t6.71696\n+Bacteria\tFirmicutes\tBacilli\tLactobacillales\tStreptococcaceae\t\t\t\t6.43313\n+Bacteria\tProteobacteria\tGammaproteobacteria\tPseudomonadales\tMoraxellaceae\t\t\t\t5.88648\n+Bacteria\tProteobacteria\tEpsilonproteobacteria\tCampylobacterales\tHelicobacteraceae\t\t\t\t4.03024\n+Bacteria\tProteobacteria\tBetaproteobacteria\tNeisseriales\tNeisseriaceae\t\t\t\t3.73739\n+Bacteria\tActinobacteria\tActinobacteria\tActinomycetales\tActinomycetaceae\t\t\t\t3.66166\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tClostridiaceae\t\t\t\t1.81937\n+Bacteria\tFirmicutes\tBacilli\tLactobacillales\tEnterococcaceae\t\t\t\t1.71002\n+Bacteria\tProteobacteria\tGammaproteobacteria\tEnterobacteriales\tEnterobacteriaceae\t\t\t\t1.6961\n+Bacteria\tFirmicutes\tBacilli\tBacillales\tListeriaceae\t\t\t\t1.58307\n+Archaea\tEuryarchaeota\tMethanobacteria\tMethanobacteriales\tMethanobacteriaceae\t\t\t\t0.79427\n+Bacteria\tProteobacteria\tGammaproteobacteria\tPseudomonadales\tPseudomonadaceae\t\t\t\t0.70297\n+Bacteria\tProteobacteria\tAlphaproteobacteria\tRhodobacterales\tRhodobacteraceae\t\t\t\t0.52051\n+Bacteria\tFirmicutes\tBacilli\tBacillales\tBacillaceae\t\t\t\t0.15687\n+Bacteria\tDeinococcus Thermus\tDeinococci\tDeinococcales\tDeinococcaceae\tDeinococcus\t\t\t45.20297\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tBacteroidaceae\tBacteroides\t\t\t7.89639\n+Bacteria\tFirmicutes\tBacilli\tBacillales\tStaphylococcaceae\tStaphylococcus\t\t\t7.4516\n+Bacteria\tActinobacteria\tActinobacteria\tActinomycetales\tPropionibacteriaceae\tPropionibacterium\t\t\t6.71696\n+Bacteria\tFirmicutes\tBacilli\tLactobacillales\tStreptococcaceae\tStreptococcus\t\t\t6.43313\n+Bacteria\tProteobacteria\tGammaproteobacteria\tPseudomonadales\tMoraxellaceae\tAcinetobacter\t\t\t5.88648\n+Bacteria\tProteobacteria\tEpsilonproteobacteria\tCampylobacterales\tHelicobacteraceae\tHelicobacter\t\t\t4.03024\n+Bacteria\tProteobacteria\tBetaproteobacteria\tNeisseriales\tNeisseriaceae\tNeisseria\t\t\t3.73739\n+Bacteria\tActinobacteria\tActinobacteria\tActinomycetales\tActinomycetaceae\tActinomyces\t\t\t3.66166\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tClostridiaceae\tClostridium\t\t\t1.81937\n+Bact'..b'bacteriaceae\tEscherichia\tEscherichia coli\t\t0.89751\n+Bacteria\tProteobacteria\tGammaproteobacteria\tEnterobacteriales\tEnterobacteriaceae\tEscherichia\tEscherichia unclassified\t\t0.79859\n+Bacteria\tProteobacteria\tGammaproteobacteria\tPseudomonadales\tPseudomonadaceae\tPseudomonas\tPseudomonas unclassified\t\t0.55542\n+Archaea\tEuryarchaeota\tMethanobacteria\tMethanobacteriales\tMethanobacteriaceae\tMethanobrevibacter\tMethanobrevibacter smithii\t\t0.55066\n+Bacteria\tProteobacteria\tAlphaproteobacteria\tRhodobacterales\tRhodobacteraceae\tRhodobacter\tRhodobacter sphaeroides\t\t0.52051\n+Archaea\tEuryarchaeota\tMethanobacteria\tMethanobacteriales\tMethanobacteriaceae\tMethanobrevibacter\tMethanobrevibacter unclassified\t\t0.24361\n+Bacteria\tFirmicutes\tBacilli\tBacillales\tBacillaceae\tBacillus\tBacillus cereus thuringiensis\t\t0.15687\n+Bacteria\tProteobacteria\tGammaproteobacteria\tPseudomonadales\tPseudomonadaceae\tPseudomonas\tPseudomonas aeruginosa\t\t0.14755\n+Bacteria\tFirmicutes\tBacilli\tLactobacillales\tStreptococcaceae\tStreptococcus\tStreptococcus agalactiae\t\t0.05124\n+Bacteria\tDeinococcus Thermus\tDeinococci\tDeinococcales\tDeinococcaceae\tDeinococcus\tDeinococcus radiodurans\tGCF 000008565\t45.20297\n+Bacteria\tBacteroidetes\tBacteroidia\tBacteroidales\tBacteroidaceae\tBacteroides\tBacteroides vulgatus\tGCF 000012825\t7.89639\n+Bacteria\tActinobacteria\tActinobacteria\tActinomycetales\tPropionibacteriaceae\tPropionibacterium\tPropionibacterium acnes\tPropionibacterium acnes unclassified\t6.71696\n+Bacteria\tProteobacteria\tGammaproteobacteria\tPseudomonadales\tMoraxellaceae\tAcinetobacter\tAcinetobacter baumannii\tAcinetobacter baumannii unclassified\t5.88648\n+Bacteria\tFirmicutes\tBacilli\tBacillales\tStaphylococcaceae\tStaphylococcus\tStaphylococcus epidermidis\tStaphylococcus epidermidis unclassified\t4.54517\n+Bacteria\tProteobacteria\tEpsilonproteobacteria\tCampylobacterales\tHelicobacteraceae\tHelicobacter\tHelicobacter pylori\tHelicobacter pylori unclassified\t4.03024\n+Bacteria\tFirmicutes\tBacilli\tLactobacillales\tStreptococcaceae\tStreptococcus\tStreptococcus mitis oralis pneumoniae\tStreptococcus mitis oralis pneumoniae unclassified\t4.02995\n+Bacteria\tProteobacteria\tBetaproteobacteria\tNeisseriales\tNeisseriaceae\tNeisseria\tNeisseria meningitidis\tNeisseria meningitidis unclassified\t3.73739\n+Bacteria\tActinobacteria\tActinobacteria\tActinomycetales\tActinomycetaceae\tActinomyces\tActinomyces odontolyticus\tActinomyces odontolyticus unclassified\t3.66166\n+Bacteria\tFirmicutes\tBacilli\tBacillales\tStaphylococcaceae\tStaphylococcus\tStaphylococcus aureus\tStaphylococcus aureus unclassified\t2.90642\n+Bacteria\tFirmicutes\tBacilli\tLactobacillales\tStreptococcaceae\tStreptococcus\tStreptococcus mutans\tStreptococcus mutans unclassified\t2.35195\n+Bacteria\tFirmicutes\tClostridia\tClostridiales\tClostridiaceae\tClostridium\tClostridium beijerinckii\tClostridium beijerinckii unclassified\t1.81937\n+Bacteria\tFirmicutes\tBacilli\tLactobacillales\tEnterococcaceae\tEnterococcus\tEnterococcus faecalis\tEnterococcus faecalis unclassified\t1.71002\n+Bacteria\tFirmicutes\tBacilli\tBacillales\tListeriaceae\tListeria\tListeria monocytogenes\tListeria monocytogenes unclassified\t1.58307\n+Bacteria\tProteobacteria\tGammaproteobacteria\tEnterobacteriales\tEnterobacteriaceae\tEscherichia\tEscherichia coli\tEscherichia coli unclassified\t0.89751\n+Archaea\tEuryarchaeota\tMethanobacteria\tMethanobacteriales\tMethanobacteriaceae\tMethanobrevibacter\tMethanobrevibacter smithii\tMethanobrevibacter smithii unclassified\t0.55066\n+Bacteria\tProteobacteria\tAlphaproteobacteria\tRhodobacterales\tRhodobacteraceae\tRhodobacter\tRhodobacter sphaeroides\tRhodobacter sphaeroides unclassified\t0.52051\n+Bacteria\tFirmicutes\tBacilli\tBacillales\tBacillaceae\tBacillus\tBacillus cereus thuringiensis\tBacillus cereus thuringiensis unclassified\t0.15687\n+Bacteria\tProteobacteria\tGammaproteobacteria\tPseudomonadales\tPseudomonadaceae\tPseudomonas\tPseudomonas aeruginosa\tPseudomonas aeruginosa unclassified\t0.14755\n+Bacteria\tFirmicutes\tBacilli\tLactobacillales\tStreptococcaceae\tStreptococcus\tStreptococcus agalactiae\tStreptococcus agalactiae unclassified\t0.05124\n' |
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| diff -r 000000000000 -r 2bfa9b200600 test-data/class_abundance.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/class_abundance.txt Wed Apr 20 07:52:41 2016 -0400 |
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| @@ -0,0 +1,11 @@ +class abundance +Deinococci 45.20297 +Bacilli 17.33469 +Actinobacteria 10.37863 +Gammaproteobacteria 8.28554 +Bacteroidia 7.89639 +Epsilonproteobacteria 4.03024 +Betaproteobacteria 3.73739 +Clostridia 1.81937 +Methanobacteria 0.79427 +Alphaproteobacteria 0.52051 |
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| diff -r 000000000000 -r 2bfa9b200600 test-data/family_abundance.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/family_abundance.txt Wed Apr 20 07:52:41 2016 -0400 |
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| @@ -0,0 +1,18 @@ +family abundance +Deinococcaceae 45.20297 +Bacteroidaceae 7.89639 +Staphylococcaceae 7.4516 +Propionibacteriaceae 6.71696 +Streptococcaceae 6.43313 +Moraxellaceae 5.88648 +Helicobacteraceae 4.03024 +Neisseriaceae 3.73739 +Actinomycetaceae 3.66166 +Clostridiaceae 1.81937 +Enterococcaceae 1.71002 +Enterobacteriaceae 1.6961 +Listeriaceae 1.58307 +Methanobacteriaceae 0.79427 +Pseudomonadaceae 0.70297 +Rhodobacteraceae 0.52051 +Bacillaceae 0.15687 |
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| diff -r 000000000000 -r 2bfa9b200600 test-data/genus_abundance.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genus_abundance.txt Wed Apr 20 07:52:41 2016 -0400 |
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| @@ -0,0 +1,18 @@ +genus abundance +Deinococcus 45.20297 +Bacteroides 7.89639 +Staphylococcus 7.4516 +Propionibacterium 6.71696 +Streptococcus 6.43313 +Acinetobacter 5.88648 +Helicobacter 4.03024 +Neisseria 3.73739 +Actinomyces 3.66166 +Clostridium 1.81937 +Enterococcus 1.71002 +Escherichia 1.6961 +Listeria 1.58307 +Methanobrevibacter 0.79427 +Pseudomonas 0.70297 +Rhodobacter 0.52051 +Bacillus 0.15687 |
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| diff -r 000000000000 -r 2bfa9b200600 test-data/kingdom_abundance.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kingdom_abundance.txt Wed Apr 20 07:52:41 2016 -0400 |
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| @@ -0,0 +1,3 @@ +kingdom abundance +Bacteria 99.20573 +Archaea 0.79427 |
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| diff -r 000000000000 -r 2bfa9b200600 test-data/metaphlan2_output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/metaphlan2_output.txt Wed Apr 20 07:52:41 2016 -0400 |
| b |
| b'@@ -0,0 +1,108 @@\n+#SampleID\tMetaphlan2_Analysis\n+k__Bacteria\t99.20573\n+k__Archaea\t0.79427\n+k__Bacteria|p__Deinococcus_Thermus\t45.20297\n+k__Bacteria|p__Firmicutes\t19.15406\n+k__Bacteria|p__Proteobacteria\t16.57369\n+k__Bacteria|p__Actinobacteria\t10.37863\n+k__Bacteria|p__Bacteroidetes\t7.89639\n+k__Archaea|p__Euryarchaeota\t0.79427\n+k__Bacteria|p__Deinococcus_Thermus|c__Deinococci\t45.20297\n+k__Bacteria|p__Firmicutes|c__Bacilli\t17.33469\n+k__Bacteria|p__Actinobacteria|c__Actinobacteria\t10.37863\n+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria\t8.28554\n+k__Bacteria|p__Bacteroidetes|c__Bacteroidia\t7.89639\n+k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria\t4.03024\n+k__Bacteria|p__Proteobacteria|c__Betaproteobacteria\t3.73739\n+k__Bacteria|p__Firmicutes|c__Clostridia\t1.81937\n+k__Archaea|p__Euryarchaeota|c__Methanobacteria\t0.79427\n+k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria\t0.52051\n+k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Deinococcales\t45.20297\n+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales\t10.37863\n+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales\t9.19153\n+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales\t8.14315\n+k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales\t7.89639\n+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales\t6.58945\n+k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales\t4.03024\n+k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales\t3.73739\n+k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales\t1.81937\n+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales\t1.6961\n+k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales\t0.79427\n+k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales\t0.52051\n+k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Deinococcales|f__Deinococcaceae\t45.20297\n+k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae\t7.89639\n+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae\t7.4516\n+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Propionibacteriaceae\t6.71696\n+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae\t6.43313\n+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae\t5.88648\n+k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae\t4.03024\n+k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae\t3.73739\n+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Actinomycetaceae\t3.66166\n+k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiaceae\t1.81937\n+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae\t1.71002\n+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae\t1.6961\n+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Listeriaceae\t1.58307\n+k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae\t0.79427\n+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae\t0.70297\n+k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae\t0.52051\n+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae\t0.15687\n+k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus\t45.20297\n+k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides\t7.89639\n+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus\t7.4516\n+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Propionibacteriaceae|g__Propionibacterium\t6.71696\n+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus\t6.43313\n+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Acinetobac'..b'k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter_unclassified\t0.24361\n+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus_cereus_thuringiensis\t0.15687\n+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas_aeruginosa\t0.14755\n+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus_agalactiae\t0.05124\n+k__Bacteria|p__Deinococcus_Thermus|c__Deinococci|o__Deinococcales|f__Deinococcaceae|g__Deinococcus|s__Deinococcus_radiodurans|t__GCF_000008565\t45.20297\n+k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_vulgatus|t__GCF_000012825\t7.89639\n+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Propionibacteriaceae|g__Propionibacterium|s__Propionibacterium_acnes|t__Propionibacterium_acnes_unclassified\t6.71696\n+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Acinetobacter|s__Acinetobacter_baumannii|t__Acinetobacter_baumannii_unclassified\t5.88648\n+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus_epidermidis|t__Staphylococcus_epidermidis_unclassified\t4.54517\n+k__Bacteria|p__Proteobacteria|c__Epsilonproteobacteria|o__Campylobacterales|f__Helicobacteraceae|g__Helicobacter|s__Helicobacter_pylori|t__Helicobacter_pylori_unclassified\t4.03024\n+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus_mitis_oralis_pneumoniae|t__Streptococcus_mitis_oralis_pneumoniae_unclassified\t4.02995\n+k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Neisseriales|f__Neisseriaceae|g__Neisseria|s__Neisseria_meningitidis|t__Neisseria_meningitidis_unclassified\t3.73739\n+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces_odontolyticus|t__Actinomyces_odontolyticus_unclassified\t3.66166\n+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus|s__Staphylococcus_aureus|t__Staphylococcus_aureus_unclassified\t2.90642\n+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus_mutans|t__Streptococcus_mutans_unclassified\t2.35195\n+k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiaceae|g__Clostridium|s__Clostridium_beijerinckii|t__Clostridium_beijerinckii_unclassified\t1.81937\n+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus|s__Enterococcus_faecalis|t__Enterococcus_faecalis_unclassified\t1.71002\n+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Listeriaceae|g__Listeria|s__Listeria_monocytogenes|t__Listeria_monocytogenes_unclassified\t1.58307\n+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli|t__Escherichia_coli_unclassified\t0.89751\n+k__Archaea|p__Euryarchaeota|c__Methanobacteria|o__Methanobacteriales|f__Methanobacteriaceae|g__Methanobrevibacter|s__Methanobrevibacter_smithii|t__Methanobrevibacter_smithii_unclassified\t0.55066\n+k__Bacteria|p__Proteobacteria|c__Alphaproteobacteria|o__Rhodobacterales|f__Rhodobacteraceae|g__Rhodobacter|s__Rhodobacter_sphaeroides|t__Rhodobacter_sphaeroides_unclassified\t0.52051\n+k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillaceae|g__Bacillus|s__Bacillus_cereus_thuringiensis|t__Bacillus_cereus_thuringiensis_unclassified\t0.15687\n+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Pseudomonadaceae|g__Pseudomonas|s__Pseudomonas_aeruginosa|t__Pseudomonas_aeruginosa_unclassified\t0.14755\n+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus|s__Streptococcus_agalactiae|t__Streptococcus_agalactiae_unclassified\t0.05124\n' |
| b |
| diff -r 000000000000 -r 2bfa9b200600 test-data/order_abundance.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/order_abundance.txt Wed Apr 20 07:52:41 2016 -0400 |
| b |
| @@ -0,0 +1,13 @@ +order abundance +Deinococcales 45.20297 +Actinomycetales 10.37863 +Bacillales 9.19153 +Lactobacillales 8.14315 +Bacteroidales 7.89639 +Pseudomonadales 6.58945 +Campylobacterales 4.03024 +Neisseriales 3.73739 +Clostridiales 1.81937 +Enterobacteriales 1.6961 +Methanobacteriales 0.79427 +Rhodobacterales 0.52051 |
| b |
| diff -r 000000000000 -r 2bfa9b200600 test-data/phylum_abundance.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phylum_abundance.txt Wed Apr 20 07:52:41 2016 -0400 |
| b |
| @@ -0,0 +1,7 @@ +phylum abundance +Deinococcus Thermus 45.20297 +Firmicutes 19.15406 +Proteobacteria 16.57369 +Actinobacteria 10.37863 +Bacteroidetes 7.89639 +Euryarchaeota 0.79427 |
| b |
| diff -r 000000000000 -r 2bfa9b200600 test-data/species_abundance.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/species_abundance.txt Wed Apr 20 07:52:41 2016 -0400 |
| b |
| @@ -0,0 +1,24 @@ +species abundance +Deinococcus radiodurans 45.20297 +Bacteroides vulgatus 7.89639 +Propionibacterium acnes 6.71696 +Acinetobacter baumannii 5.88648 +Staphylococcus epidermidis 4.54517 +Helicobacter pylori 4.03024 +Streptococcus mitis oralis pneumoniae 4.02995 +Neisseria meningitidis 3.73739 +Actinomyces odontolyticus 3.66166 +Staphylococcus aureus 2.90642 +Streptococcus mutans 2.35195 +Clostridium beijerinckii 1.81937 +Enterococcus faecalis 1.71002 +Listeria monocytogenes 1.58307 +Escherichia coli 0.89751 +Escherichia unclassified 0.79859 +Pseudomonas unclassified 0.55542 +Methanobrevibacter smithii 0.55066 +Rhodobacter sphaeroides 0.52051 +Methanobrevibacter unclassified 0.24361 +Bacillus cereus thuringiensis 0.15687 +Pseudomonas aeruginosa 0.14755 +Streptococcus agalactiae 0.05124 |
| b |
| diff -r 000000000000 -r 2bfa9b200600 test-data/strains_abundance.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/strains_abundance.txt Wed Apr 20 07:52:41 2016 -0400 |
| b |
| @@ -0,0 +1,21 @@ +strains abundance +GCF 000008565 45.20297 +GCF 000012825 7.89639 +Propionibacterium acnes unclassified 6.71696 +Acinetobacter baumannii unclassified 5.88648 +Staphylococcus epidermidis unclassified 4.54517 +Helicobacter pylori unclassified 4.03024 +Streptococcus mitis oralis pneumoniae unclassified 4.02995 +Neisseria meningitidis unclassified 3.73739 +Actinomyces odontolyticus unclassified 3.66166 +Staphylococcus aureus unclassified 2.90642 +Streptococcus mutans unclassified 2.35195 +Clostridium beijerinckii unclassified 1.81937 +Enterococcus faecalis unclassified 1.71002 +Listeria monocytogenes unclassified 1.58307 +Escherichia coli unclassified 0.89751 +Methanobrevibacter smithii unclassified 0.55066 +Rhodobacter sphaeroides unclassified 0.52051 +Bacillus cereus thuringiensis unclassified 0.15687 +Pseudomonas aeruginosa unclassified 0.14755 +Streptococcus agalactiae unclassified 0.05124 |