| Next changeset 1:eb65ab160a10 (2020-09-23) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit d45eb2747cc58e1120b3935f10ab47c4e0f8f44a |
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added:
macros.xml metaquantome_expand.xml test-data/ec.tar test-data/ec_ttest.tab test-data/ec_ttest_tested.tab test-data/func_full_filt_out.tab test-data/func_full_test_out.tab test-data/go_expanded.tab test-data/go_filtered.tab test-data/int_737_test.tab test-data/int_ttest.tab test-data/multiple_func.tab test-data/multiple_int.tab test-data/multiple_tax.tab test-data/outfile.png test-data/rudney_samples.tab test-data/samples.tab test-data/samples0.tab test-data/samples_basic.tab test-data/tax_filt.tab test-data/tax_filt_out.tab test-data/tax_ns.png test-data/tax_test_out.tab test-data/tf_filt_out.tab test-data/wrapped_outfile.html |
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| diff -r 000000000000 -r 170b5fa2402d macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Apr 25 13:46:17 2019 -0400 |
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| @@ -0,0 +1,51 @@ +<macros> + <token name="@VERSION@">1.0.0</token> + <token name="@GVERSION@">1.0.0-0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">metaquantome</requirement> + <yield/> + </requirements> + </xml> + <xml name="db"> + <param argument="db_tar" type="data" label="Database Archive File"/> + </xml> + <xml name="ONTOLOGY_ARGS"> + <conditional name="ontology_args"> + <param name="ontology" type="select" label="Ontology"> + <option value="go">Gene Ontology (GO terms)</option> + <option value="ec">Enzyme Commission (EC) numbers</option> + <option value="cog">Clusters of Orthologous Groups (COG categories)</option> + </param> + <when value="go"> + <param argument="--slim_down" type="boolean" label="Use slim GO"/> + </when> + <when value="ec"> + <!-- do nothing --> + </when> + <when value="cog"> + <!-- do nothing --> + </when> + </conditional> + </xml> + <token name="@COMMON_PARAMS@"><![CDATA[ + --samps '$samps' + --mode '$mode_args.mode' + #if $mode_args.mode == 'f' + --ontology='$mode_args.ontology_args.ontology' + #end if + #if $mode_args.mode == 'ft' + --ontology='$mode_args.ontology_args.ontology' + #end if + ]]> + </token> + <xml name="SAMPS"> + <param name="samps" type="data" format="tabular" label="Samples file" + help="must be created by 'metaQuantome: create samples file'"/> + </xml> + <xml name="citations"> + <citations> + <yield /> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r 170b5fa2402d metaquantome_expand.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/metaquantome_expand.xml Thu Apr 25 13:46:17 2019 -0400 |
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| b'@@ -0,0 +1,234 @@\n+<tool id="metaquantome_expand" name="metaQuantome: expand" version="@GVERSION@">\n+ <description>a set of functional or taxonomy annotations</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ <xml name="FUNC_FILE">\n+ <param argument="--func_file" type="data" format="tabular" label="Functional file"\n+ help="Tabular file with a peptide sequence column and a functional assignment column with GO terms, EC number, or COG."/>\n+ <param argument="--pep_colname_func" type="text" label="Functional file: peptide column name" value="peptide"\n+ help="The column name within the function file that corresponds to the peptide sequences">\n+ <validator type="empty_field"/>\n+ </param>\n+ </xml>\n+ <xml name="FUNC_COLNAME">\n+ <param argument="--func_colname" type="text" label="Functional column name"\n+ help="The column name within the function file with the functional terms">\n+ <validator type="empty_field"/>\n+ </param>\n+ </xml>\n+ <xml name="TAX_FILE">\n+ <param argument="--tax_file" type="data" format="tabular" label="Taxonomy assignments file"/>\n+ <param argument="--pep_colname_tax" type="text" label="Taxonomy file: peptide column name" value="peptide"\n+ help="The column name within the taxonomy file that corresponds to the peptide sequences">\n+ <validator type="empty_field"/>\n+ </param>\n+ </xml>\n+ <xml name="TAX_COLNAME">\n+ <param argument="--tax_colname" type="text" label="Taxonomy column name">\n+ <help>\n+ Name of column in taxonomy annotation file that contains\n+ the lowest common ancestor (LCA) annotation. The annotations must\n+ be either NCBI taxids (strongly preferred) or taxonomy\n+ names.\n+ </help>\n+ <validator type="empty_field"/>\n+ </param>\n+ </xml>\n+ <xml name="FT_TAR_RANK">\n+ <param argument="--ft_tar_rank" type="select" label="rank at which to group taxonomy">\n+ <option value="species">species</option>\n+ <option value="genus" selected="true">genus</option>\n+ <option value="family">family</option>\n+ <option value="order">order</option>\n+ <option value="class">class</option>\n+ <option value="phylum">phylum</option>\n+ <option value="kingdom">kingdom</option>\n+ </param>\n+ </xml>\n+ <token name="@FUNC_FILE@">\n+ --func_file=\'$mode_args.func_file\'\n+ --pep_colname_func=\'$mode_args.pep_colname_func\'\n+ </token>\n+ <token name="@FUNC_COLNAME@">\n+ --func_colname=\'$mode_args.func_colname\'\n+ </token>\n+ <token name="@ONTOLOGY@">\n+ --ontology=\'$mode_args.ontology_args.ontology\'\n+ #if $mode_args.ontology_args.ontology == \'go\'\n+ #if $mode_args.ontology_args.slim_down\n+ --slim_down\n+ #end if\n+ #end if\n+ </token>\n+ <token name="@TAX_FILE@">\n+ --tax_file=\'$mode_args.tax_file\'\n+ --pep_colname_tax=\'$mode_args.pep_colname_tax\'\n+ </token>\n+ <token name="@TAX_COLNAME@">\n+ --tax_colname=\'$mode_args.tax_colname\'\n+ </token>\n+ <token name="@FT_TAR_RANK@">\n+ --ft_tar_rank=\'$mode_args.ft_tar_rank\'\n+ </token>\n+ </macros>\n+ <expand macro="requirements" />\n+ <command detect_errors="exit_code"><![CDATA[\n+ tar -xf \'$db_tar\' &&\n+ metaquantome expand\n+ --data_dir ./data\n+ --samps \'$samps\'\n+ --mode \'$mode_args.mode\'\n+ --int_file=\'$int_file\'\n+ --pep_colname_int=\'$pep_colname_int\'\n+ #if $mode_args.mode == \'f\'\n+ @FUNC_FILE@\n+ @FUNC_COLNAME@\n+ @ONTOLOGY@\n+ #elif $mode_args.mode ==\'t\'\n+ @TAX_FILE@\n+ @TAX_COLNAME@\n+ #elif $mode_args.mode == \'ft\'\n+ @FUNC_FILE@\n+ @FUNC_COLNAME@\n+ @ONTOLOGY@\n+ @TAX_FILE@\n+ @TAX_COLNAME@\n+ @FT_TAR_RANK@\n+ #end if\n+ --outfile=\'$outfile\'\n+ ]]></command>\n+ <inputs>\n+ <param name="db_tar" type="data" format="tar" label="Database Archive File'..b' module is the first analysis step in the metaQuantome analysis workflow,\n+and can be run to analyze function, taxonomy, or function and taxonomy together.\n+\n+To prepare to run this module, you must create your samples file with\n+"metaQuantome: create samples file" and download the necessary databases with\n+"metaQuantome: database".\n+\n+Some example analysis workflows are:\n+\n+1. Get the functional, taxonomic, or functional-taxonomic distribution: run expand, filter, and viz.\n+2. Cluster analysis: run expand, filter, and viz. The viz module has heatmaps and PCA plots for cluster analysis.\n+3. Differential expression: run expand, filter, stat, and viz.\n+\n+\n+The following information is required for all 3 analysis modes\n+(function, taxonomy, and function-taxonomy).\n+\n+- experimental design information.\n+- a tab-separated peptide intensity file.\n+- the name of the peptide column in the intensity file.\n+\n+Function mode\n+-------------\n+\n+In function mode, the following information is required:\n+\n+- the ontology being used: Gene Ontology (GO), Clusters of Orthologous Groups (COG), or Enzyme Commission (EC) numbers.\n+- a tab-separated functional annotation file, with a peptide column and a functional annotation column. An entry in the functional annotation column may contain multiple functional annotations separated by commas.\n+- the name of the peptide column in the functional annotation file.\n+- the name of the functional annotation column in the functional annotation file.\n+\n+Taxonomy mode\n+-------------\n+\n+In taxonomy mode, the following information is required:\n+\n+- a tab-separated taxonomy annotation file, with a peptide column and a taxonomy annotation column. The taxonomic annotations should be the lowest common ancestor (LCA) for each peptide, preferably given as NCBI taxonomy IDs.\n+- the name of the peptide column in the taxonomic annotation file.\n+- the name of the taxonomy annotation column in the taxonomy annotation file.\n+\n+Function-Taxonomy mode\n+----------------------\n+\n+In the combined mode, all of the above must be provided. In addition, the "target rank" must be provided, which is the desired taxonomic rank at which to summarize the function/taxonomy results.\n+\n+Output of the expand module\n+---------------------------\n+\n+The structure of the output file depends on the analysis mode and the experimental design,\n+but the columns generally look like this, with one row for each term:\n+\n+======= ======================= ======================= ====================== ========================= ==========================\n+term id info about term. mean term intensity term intensity number of unique peptides number of sample children\n+ (one or more columns) (by sample group) (by sample) (by sample) in each sample\n+======= ======================= ======================= ====================== ========================= ==========================\n+term1 name, rank, etc. note that this this is the log2 integer. 0 is coded as NA integer. 0 is coded as NA\n+ is the log2 of the mean of term intensity\n+ intensity in each sample.\n+ Missing data is coded\n+ as NA.\n+======= ======================= ======================= ====================== ========================= ==========================\n+\n+The next step in the metaQuantome workflow is "filter", which\n+filters out rows that don\'t meet certain conditions on the intensity,\n+the number of unique peptides annotated with each term, and the\n+number of sample children.\n+\n+Questions, Comments, Problems, Kudos\n+------------------------------------\n+\n+Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.\n+]]></help>\n+ <expand macro="citations" />\n+</tool>\n' |
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| diff -r 000000000000 -r 170b5fa2402d test-data/ec.tar |
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| Binary file test-data/ec.tar has changed |
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| diff -r 000000000000 -r 170b5fa2402d test-data/ec_ttest.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ec_ttest.tab Thu Apr 25 13:46:17 2019 -0400 |
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| @@ -0,0 +1,8 @@ +id description s1_mean s2_mean int1 int2 int3 int4 int5 int6 int1_n_peptide int2_n_peptide int3_n_peptide int4_n_peptide int5_n_peptide int6_n_peptide int1_n_samp_children int2_n_samp_children int3_n_samp_children int4_n_samp_children int5_n_samp_children int6_n_samp_children +1.-.-.- Oxidoreductases. 10.013089999440444 3.5443205162238103 9.965784284662087 10.228818690495881 9.813781191217037 3.584962500721156 3.700439718141092 3.321928094887362 1 1 1 1 1 1 1.0 1.0 1.0 1.0 1.0 1.0 +1.2.-.- Acting on the aldehyde or oxo group of donors. 10.013089999440444 3.5443205162238103 9.965784284662087 10.228818690495881 9.813781191217037 3.584962500721156 3.700439718141092 3.321928094887362 1 1 1 1 1 1 NA NA NA NA NA NA +3.-.-.- Hydrolases. 5.285402218862249 11.475564566327487 5.0 5.643856189774724 5.129283016944966 11.778077129535358 10.980853606379736 11.555547771647065 2 2 2 2 2 2 1.0 1.0 1.0 1.0 1.0 1.0 +3.4.-.- Acting on peptide bonds (peptidases). 5.285402218862249 11.475564566327487 5.0 5.643856189774724 5.129283016944966 11.778077129535358 10.980853606379736 11.555547771647065 2 2 2 2 2 2 2.0 2.0 2.0 2.0 2.0 2.0 +3.4.11.- Aminopeptidases. 3.969626350956481 3.841302253980942 3.584962500721156 4.321928094887363 3.9068905956085187 3.584962500721156 4.392317422778761 3.321928094887362 1 1 1 1 1 1 NA NA NA NA NA NA +3.4.21.- Serine endopeptidases. 4.54432051622381 11.46828462519127 4.321928094887363 4.906890595608519 4.321928094887363 11.77313920671969 10.965784284662087 11.550746785383243 1 1 1 1 1 1 1.0 1.0 1.0 1.0 1.0 1.0 +3.4.21.70 Pancreatic endopeptidase E. 4.54432051622381 11.46828462519127 4.321928094887363 4.906890595608519 4.321928094887363 11.77313920671969 10.965784284662087 11.550746785383243 1 1 1 1 1 1 NA NA NA NA NA NA |
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| diff -r 000000000000 -r 170b5fa2402d test-data/ec_ttest_tested.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ec_ttest_tested.tab Thu Apr 25 13:46:17 2019 -0400 |
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| @@ -0,0 +1,8 @@ +id description s1_mean s2_mean int1 int2 int3 int4 int5 int6 int1_n_peptide int2_n_peptide int3_n_peptide int4_n_peptide int5_n_peptide int6_n_peptide int1_n_samp_children int2_n_samp_children int3_n_samp_children int4_n_samp_children int5_n_samp_children int6_n_samp_children log2fc_s1_over_s2 p corrected_p +1.-.-.- Oxidoreductases. 10.013089999440444 3.5443205162238103 9.965784284662089 10.228818690495881 9.813781191217037 3.584962500721156 3.700439718141092 3.3219280948873617 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 6.468769483216634 2.70286875006428e-06 9.46004062522498e-06 +1.2.-.- Acting on the aldehyde or oxo group of donors. 10.013089999440444 3.5443205162238103 9.965784284662089 10.228818690495881 9.813781191217037 3.584962500721156 3.700439718141092 3.3219280948873617 1.0 1.0 1.0 1.0 1.0 1.0 NA NA NA NA NA NA 6.468769483216634 2.70286875006428e-06 9.46004062522498e-06 +3.-.-.- Hydrolases. 5.28540221886225 11.475564566327488 5.0 5.6438561897747235 5.1292830169449655 11.778077129535358 10.980853606379736 11.555547771647065 2.0 2.0 2.0 2.0 2.0 2.0 1.0 1.0 1.0 1.0 1.0 1.0 -6.190162347465239 4.742887028677606e-05 5.533368200123874e-05 +3.4.-.- Acting on peptide bonds (peptidases). 5.28540221886225 11.475564566327488 5.0 5.6438561897747235 5.1292830169449655 11.778077129535358 10.980853606379736 11.555547771647065 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 -6.190162347465239 4.742887028677606e-05 5.533368200123874e-05 +3.4.11.- Aminopeptidases. 3.9696263509564815 3.841302253980942 3.584962500721156 4.3219280948873635 3.906890595608519 3.584962500721156 4.392317422778762 3.3219280948873617 1.0 1.0 1.0 1.0 1.0 1.0 NA NA NA NA NA NA 0.1283240969755397 0.6832561051460733 0.6832561051460733 +3.4.21.- Serine endopeptidases. 4.544320516223809 11.468284625191268 4.3219280948873635 4.906890595608519 4.3219280948873635 11.773139206719689 10.965784284662087 11.550746785383243 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 -6.923964108967459 3.349508567404191e-05 5.533368200123874e-05 +3.4.21.70 Pancreatic endopeptidase E. 4.544320516223809 11.468284625191268 4.3219280948873635 4.906890595608519 4.3219280948873635 11.773139206719689 10.965784284662087 11.550746785383243 1.0 1.0 1.0 1.0 1.0 1.0 NA NA NA NA NA NA -6.923964108967459 3.349508567404191e-05 5.533368200123874e-05 |
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| diff -r 000000000000 -r 170b5fa2402d test-data/func_full_filt_out.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/func_full_filt_out.tab Thu Apr 25 13:46:17 2019 -0400 |
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| b'@@ -0,0 +1,1249 @@\n+id\tname\tnamespace\tNS_mean\tWS_mean\tX730NS\tX730WS\tX733NS\tX733WS\tX734NS\tX734WS\tX737NS\tX737WS\tX760NS\tX760WS\tX769NS\tX769WS\tX781NS\tX781WS\tX795NS\tX795WS\tX852NS\tX852WS\tX861NS\tX861WS\tX866NS\tX866WS\tX867NS\tX867WS\tX730NS_n_peptide\tX730WS_n_peptide\tX733NS_n_peptide\tX733WS_n_peptide\tX734NS_n_peptide\tX734WS_n_peptide\tX737NS_n_peptide\tX737WS_n_peptide\tX760NS_n_peptide\tX760WS_n_peptide\tX769NS_n_peptide\tX769WS_n_peptide\tX781NS_n_peptide\tX781WS_n_peptide\tX795NS_n_peptide\tX795WS_n_peptide\tX852NS_n_peptide\tX852WS_n_peptide\tX861NS_n_peptide\tX861WS_n_peptide\tX866NS_n_peptide\tX866WS_n_peptide\tX867NS_n_peptide\tX867WS_n_peptide\tX730NS_n_samp_children\tX730WS_n_samp_children\tX733NS_n_samp_children\tX733WS_n_samp_children\tX734NS_n_samp_children\tX734WS_n_samp_children\tX737NS_n_samp_children\tX737WS_n_samp_children\tX760NS_n_samp_children\tX760WS_n_samp_children\tX769NS_n_samp_children\tX769WS_n_samp_children\tX781NS_n_samp_children\tX781WS_n_samp_children\tX795NS_n_samp_children\tX795WS_n_samp_children\tX852NS_n_samp_children\tX852WS_n_samp_children\tX861NS_n_samp_children\tX861WS_n_samp_children\tX866NS_n_samp_children\tX866WS_n_samp_children\tX867NS_n_samp_children\tX867WS_n_samp_children\n+GO:0000015\tphosphopyruvate hydratase complex\tcellular_component\t25.886058501686048\t27.75998767351391\t26.063085341729952\t26.75868414835451\t26.872321573535828\t27.714535507520914\t25.66138683343686\t26.91922948200433\t24.56792307320876\t27.02361179346473\t26.027647781700303\t28.016086841596714\t26.02628222102915\t27.691319718917903\t26.16224176931668\t28.14922479286621\t25.589356591442357\t28.605803973702113\t24.96556438729523\t27.182932679501942\t26.61887047167179\t28.06289719214795\t23.98035185379387\t28.471187733625282\t25.803186314724897\t26.966628159317192\t9.0\t12.0\t9.0\t21.0\t7.0\t12.0\t12.0\t15.0\t9.0\t16.0\t6.0\t10.0\t20.0\t15.0\t12.0\t16.0\t9.0\t13.0\t9.0\t19.0\t13.0\t12.0\t11.0\t16.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+GO:0000027\tribosomal large subunit assembly\tbiological_process\t24.93071577771554\t25.59199706393845\t24.79502406577661\t24.90569362782595\t24.98653026336489\t25.54103884489353\t23.235856648559913\t25.931788552669857\t25.039623407494012\t25.45976392090486\t24.544491045410794\t25.52182426968223\t25.141851834365102\t25.289466690231773\t25.900937208609022\t25.935471942444728\t24.03595672520859\t26.011397107654144\t24.664753825097794\t25.849804449449888\t24.843398416694487\t25.350436246047447\t25.804646284613423\t25.501822202499124\t24.281786470078014\t25.41548110918182\t14.0\t6.0\t12.0\t32.0\t12.0\t12.0\t20.0\t11.0\t24.0\t15.0\t21.0\t13.0\t25.0\t15.0\t17.0\t16.0\t26.0\t17.0\t19.0\t11.0\t26.0\t12.0\t15.0\t15.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+GO:0000036\tacyl carrier activity\tmolecular_function\t25.957124762066027\t26.279571177686467\t26.5301700656991\t25.713248274935196\t23.51705029509677\t23.162225189828625\t25.71677865632887\t27.34753252356737\t24.762495943469332\t27.104656358315633\t25.695589715923877\t27.215607058954525\t25.964407715885855\t25.376217309281692\t24.710785124891835\t24.769491577313733\t26.583389308611466\t26.855652944530483\t27.299615071207107\t26.21417524637679\t25.987672484095224\t25.62275900338784\t25.498246974021807\t25.479528439599648\t25.891370301559785\t26.106957744939113\t8.0\t5.0\t4.0\t6.0\t9.0\t8.0\t9.0\t6.0\t7.0\t8.0\t8.0\t5.0\t5.0\t5.0\t11.0\t6.0\t9.0\t8.0\t8.0\t7.0\t9.0\t6.0\t8.0\t10.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+GO:0000049\ttRNA binding\tmolecular_function\t29.334384670306477\t29.866410348871714\t29.34869846467857\t29.421655277196997\t29.2837931122148\t29.981729378140212\t28.84739681956653\t29.861138275832506\t29.511822916465768\t29.5789021928085\t29.26397852161527\t29.849840976877704\t29.19847063527141\t29.680573984412536\t29.78160947364881\t30.14265486546316\t28.836974946568535\t29.77400766267598\t29.84406783531248\t29.98304230286376\t29.04660382106465\t29.921153355794505\t29.468392401488643\t30.227909688052133\t29.19134574545442\t29.780293851199517\t249.0\t200.0\t202.0\t317.0\t265.0\t303.0\t358.0\t'..b'\t5.0\t3.0\t4.0\t5.0\t4.0\t4.0\t5.0\t4.0\t4.0\t5.0\t3.0\t5.0\t5.0\t5.0\t4.0\t7.0\t2.0\t4.0\t4.0\t4.0\t5.0\t5.0\n+GO:2000112\tregulation of cellular macromolecule biosynthetic process\tbiological_process\t28.079891651623925\t28.790202097835518\t28.26915640698684\t28.40919311526568\t28.304349960869413\t28.72065470341578\t27.703615179375\t29.07974724242657\t27.72573130808365\t28.94447930691111\t27.98123342119566\t28.925853440725582\t28.070327450767127\t28.64378840898086\t28.0412330956282\t28.717095722191754\t27.542977117183128\t28.691346823804523\t28.63541965303673\t29.17655748772289\t28.259425342329425\t28.545245875488934\t27.939341483560987\t28.581495264653373\t28.135415728928514\t28.84866809360601\t163.0\t179.0\t156.0\t192.0\t165.0\t248.0\t167.0\t246.0\t214.0\t241.0\t214.0\t211.0\t177.0\t228.0\t150.0\t232.0\t325.0\t268.0\t198.0\t176.0\t162.0\t231.0\t211.0\t261.0\t3.0\t3.0\t3.0\t3.0\t4.0\t3.0\t3.0\t3.0\t4.0\t4.0\t4.0\t3.0\t3.0\t3.0\t4.0\t3.0\t4.0\t3.0\t4.0\t3.0\t4.0\t4.0\t4.0\t4.0\n+GO:2000113\tnegative regulation of cellular macromolecule biosynthetic process\tbiological_process\t22.60266741107676\t22.236837972385544\t21.30030518237217\t22.047478426541858\t23.27970856165999\t21.464966997040502\t22.68300308242573\t21.403375515281333\t20.941315544901308\t23.20906481771488\t23.110740747879433\t21.784612522231637\t23.234225562341464\t22.03786639857234\t21.433366644229807\t20.233594686557442\t21.522695545358385\t21.07809661598035\t22.89397308126998\t23.721564622589497\t23.42759588328258\t21.680974100515922\t22.096908708542376\t21.55145677527049\t22.65052395817018\t22.92760386629374\t10.0\t13.0\t15.0\t7.0\t14.0\t13.0\t11.0\t17.0\t16.0\t11.0\t21.0\t11.0\t7.0\t8.0\t7.0\t11.0\t20.0\t22.0\t17.0\t13.0\t10.0\t11.0\t17.0\t21.0\t1.0\t2.0\t2.0\t1.0\t3.0\t1.0\t2.0\t1.0\t3.0\t3.0\t3.0\t2.0\t1.0\t1.0\t3.0\t1.0\t3.0\t1.0\t2.0\t2.0\t3.0\t2.0\t2.0\t2.0\n+GO:2001059\tD-tagatose 6-phosphate catabolic process\tbiological_process\t23.511656222915654\t24.98449088822721\t24.58628517759067\t24.912876342135274\t25.061871229539328\t24.283061735179054\t23.405696302068467\t25.63328576980955\t17.829756253830322\t25.040481875405426\t19.691261902405127\t25.311348757482648\t22.64895131639827\t25.07592700325359\t24.957240657266393\t25.395341204296265\t22.223531971764206\t24.759006753308693\t24.25004185139378\t24.47573296436818\t21.889494052794266\t24.7374192095463\t19.94916118927913\t24.89935198902975\t21.075907601073208\t24.721609809672685\t27.0\t33.0\t30.0\t28.0\t12.0\t42.0\t2.0\t36.0\t5.0\t36.0\t11.0\t23.0\t26.0\t38.0\t12.0\t41.0\t23.0\t30.0\t10.0\t34.0\t4.0\t27.0\t10.0\t33.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n+GO:2001141\tregulation of RNA biosynthetic process\tbiological_process\t26.34205256788306\t27.635435307439774\t26.651512126434778\t27.28352201899168\t26.948655423347923\t27.05700592789492\t25.51291335182695\t27.923407315980626\t26.27982855783693\t28.042422307734395\t26.20815926277268\t27.76388853668417\t26.412683613973726\t27.38663485129848\t26.03647283004182\t27.59377882498742\t25.126784640686463\t27.58471360291358\t26.947624030309463\t28.17369718937304\t26.68520714216416\t27.23792387977294\t25.86321781865529\t27.403800793482624\t26.354142491094432\t27.72650496536477\t108.0\t134.0\t103.0\t122.0\t105.0\t176.0\t99.0\t181.0\t134.0\t150.0\t147.0\t155.0\t111.0\t148.0\t87.0\t159.0\t195.0\t198.0\t131.0\t123.0\t93.0\t161.0\t142.0\t184.0\t3.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t3.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\n+GO:2001295\tmalonyl-CoA biosynthetic process\tbiological_process\t24.041767189026174\t23.368503914625965\t21.869190774106308\t22.091623247786497\t22.35226996419096\t23.63067388937766\t23.95004243777072\t23.428428821209547\t24.81066402548795\t22.344982692352076\t24.884545910598035\t22.33349522393337\t24.3377404391613\t23.13908510884377\t23.65652105389825\t24.35531641248085\t24.302973205450648\t23.68292928714755\t23.659012427821196\t23.030970680176765\t23.41822612657516\t23.591034950731125\t23.797385759933352\t24.254723130459904\t24.70188938490118\t22.31230963978653\t7.0\t11.0\t16.0\t15.0\t21.0\t21.0\t23.0\t11.0\t24.0\t15.0\t24.0\t8.0\t22.0\t24.0\t13.0\t19.0\t25.0\t23.0\t16.0\t20.0\t18.0\t16.0\t23.0\t13.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n' |
| b |
| diff -r 000000000000 -r 170b5fa2402d test-data/func_full_test_out.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/func_full_test_out.tab Thu Apr 25 13:46:17 2019 -0400 |
| b |
| b'@@ -0,0 +1,1249 @@\n+id\tname\tnamespace\tNS_mean\tWS_mean\tX730NS\tX730WS\tX733NS\tX733WS\tX734NS\tX734WS\tX737NS\tX737WS\tX760NS\tX760WS\tX769NS\tX769WS\tX781NS\tX781WS\tX795NS\tX795WS\tX852NS\tX852WS\tX861NS\tX861WS\tX866NS\tX866WS\tX867NS\tX867WS\tX730NS_n_peptide\tX730WS_n_peptide\tX733NS_n_peptide\tX733WS_n_peptide\tX734NS_n_peptide\tX734WS_n_peptide\tX737NS_n_peptide\tX737WS_n_peptide\tX760NS_n_peptide\tX760WS_n_peptide\tX769NS_n_peptide\tX769WS_n_peptide\tX781NS_n_peptide\tX781WS_n_peptide\tX795NS_n_peptide\tX795WS_n_peptide\tX852NS_n_peptide\tX852WS_n_peptide\tX861NS_n_peptide\tX861WS_n_peptide\tX866NS_n_peptide\tX866WS_n_peptide\tX867NS_n_peptide\tX867WS_n_peptide\tX730NS_n_samp_children\tX730WS_n_samp_children\tX733NS_n_samp_children\tX733WS_n_samp_children\tX734NS_n_samp_children\tX734WS_n_samp_children\tX737NS_n_samp_children\tX737WS_n_samp_children\tX760NS_n_samp_children\tX760WS_n_samp_children\tX769NS_n_samp_children\tX769WS_n_samp_children\tX781NS_n_samp_children\tX781WS_n_samp_children\tX795NS_n_samp_children\tX795WS_n_samp_children\tX852NS_n_samp_children\tX852WS_n_samp_children\tX861NS_n_samp_children\tX861WS_n_samp_children\tX866NS_n_samp_children\tX866WS_n_samp_children\tX867NS_n_samp_children\tX867WS_n_samp_children\tlog2fc_NS_over_WS\tp\tcorrected_p\n+GO:0000015\tphosphopyruvate hydratase complex\tcellular_component\t25.886058501686048\t27.75998767351391\t26.063085341729952\t26.75868414835451\t26.872321573535828\t27.714535507520914\t25.66138683343686\t26.91922948200433\t24.56792307320876\t27.02361179346473\t26.027647781700306\t28.016086841596714\t26.02628222102915\t27.691319718917903\t26.16224176931668\t28.14922479286621\t25.58935659144236\t28.605803973702113\t24.96556438729523\t27.182932679501942\t26.61887047167179\t28.06289719214795\t23.98035185379387\t28.471187733625282\t25.803186314724893\t26.966628159317192\t9.0\t12.0\t9.0\t21.0\t7.0\t12.0\t12.0\t15.0\t9.0\t16.0\t6.0\t10.0\t20.0\t15.0\t12.0\t16.0\t9.0\t13.0\t9.0\t19.0\t13.0\t12.0\t11.0\t16.0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t-1.8739291718278608\t4.146041132679973e-05\t0.0005099643033035255\n+GO:0000027\tribosomal large subunit assembly\tbiological_process\t24.93071577771554\t25.59199706393845\t24.79502406577661\t24.90569362782595\t24.98653026336489\t25.54103884489353\t23.235856648559913\t25.931788552669854\t25.039623407494012\t25.45976392090486\t24.544491045410794\t25.52182426968223\t25.141851834365106\t25.289466690231773\t25.900937208609022\t25.935471942444728\t24.03595672520859\t26.011397107654144\t24.664753825097794\t25.84980444944989\t24.843398416694487\t25.350436246047447\t25.80464628461343\t25.501822202499124\t24.28178647007801\t25.41548110918182\t14.0\t6.0\t12.0\t32.0\t12.0\t12.0\t20.0\t11.0\t24.0\t15.0\t21.0\t13.0\t25.0\t15.0\t17.0\t16.0\t26.0\t17.0\t19.0\t11.0\t26.0\t12.0\t15.0\t15.0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t-0.6612812862229092\t0.00268017172806849\t0.006910856026093958\n+GO:0000036\tacyl carrier activity\tmolecular_function\t25.95712476206603\t26.279571177686467\t26.5301700656991\t25.713248274935196\t23.51705029509677\t23.162225189828625\t25.71677865632887\t27.34753252356737\t24.76249594346933\t27.104656358315633\t25.695589715923877\t27.215607058954525\t25.964407715885855\t25.376217309281692\t24.710785124891835\t24.76949157731373\t26.583389308611466\t26.855652944530483\t27.299615071207107\t26.21417524637679\t25.987672484095224\t25.62275900338784\t25.498246974021807\t25.479528439599648\t25.891370301559785\t26.106957744939113\t8.0\t5.0\t4.0\t6.0\t9.0\t8.0\t9.0\t6.0\t7.0\t8.0\t8.0\t5.0\t5.0\t5.0\t11.0\t6.0\t9.0\t8.0\t8.0\t7.0\t9.0\t6.0\t8.0\t10.0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t-0.32244641562043697\t0.6033317722918665\t0.6716842567531217\n+GO:0000049\ttRNA binding\tmolecular_function\t29.33438467030648\t29.866410348871714\t29.34869846467857\t29.421655277196997\t29.2837931122148\t29.981729378140212\t28.84739681956653\t29.861138275832506\t29.511822916465768\t29.5789021928085\t29.26397852161527\t29.849840976877704\t29.19847063527141\t29.680573984412536\t29.78160947364881\t30.14265486546316\t28.83697494656853\t29.77400766267598\t29.84406783531248\t29.98304230286376\t29.04660382106465\t2'..b'304349960869413\t28.72065470341578\t27.703615179375\t29.07974724242657\t27.72573130808365\t28.94447930691111\t27.98123342119566\t28.925853440725582\t28.07032745076713\t28.64378840898086\t28.0412330956282\t28.717095722191754\t27.542977117183128\t28.691346823804523\t28.63541965303673\t29.176557487722892\t28.259425342329425\t28.54524587548893\t27.939341483560987\t28.581495264653373\t28.135415728928514\t28.84866809360601\t163.0\t179.0\t156.0\t192.0\t165.0\t248.0\t167.0\t246.0\t214.0\t241.0\t214.0\t211.0\t177.0\t228.0\t150.0\t232.0\t325.0\t268.0\t198.0\t176.0\t162.0\t231.0\t211.0\t261.0\t3.0\t3.0\t3.0\t3.0\t4.0\t3.0\t3.0\t3.0\t4.0\t4.0\t4.0\t3.0\t3.0\t3.0\t4.0\t3.0\t4.0\t3.0\t4.0\t3.0\t4.0\t4.0\t4.0\t4.0\t-0.7103104462115972\t6.784570247173055e-05\t0.0005498145239267514\n+GO:2000113\tnegative regulation of cellular macromolecule biosynthetic process\tbiological_process\t22.60266741107676\t22.236837972385544\t21.30030518237217\t22.047478426541858\t23.27970856165999\t21.464966997040502\t22.68300308242573\t21.403375515281333\t20.941315544901308\t23.20906481771488\t23.110740747879433\t21.78461252223164\t23.234225562341464\t22.03786639857234\t21.433366644229807\t20.233594686557442\t21.522695545358385\t21.07809661598035\t22.89397308126998\t23.721564622589497\t23.42759588328258\t21.680974100515922\t22.096908708542376\t21.55145677527049\t22.65052395817018\t22.92760386629374\t10.0\t13.0\t15.0\t7.0\t14.0\t13.0\t11.0\t17.0\t16.0\t11.0\t21.0\t11.0\t7.0\t8.0\t7.0\t11.0\t20.0\t22.0\t17.0\t13.0\t10.0\t11.0\t17.0\t21.0\t1.0\t2.0\t2.0\t1.0\t3.0\t1.0\t2.0\t1.0\t3.0\t3.0\t3.0\t2.0\t1.0\t1.0\t3.0\t1.0\t3.0\t1.0\t2.0\t2.0\t3.0\t2.0\t2.0\t2.0\t0.36582943869121465\t0.3263484733220724\t0.4012639356708831\n+GO:2001059\tD-tagatose 6-phosphate catabolic process\tbiological_process\t23.51165622291565\t24.98449088822721\t24.58628517759067\t24.912876342135274\t25.061871229539328\t24.283061735179054\t23.405696302068467\t25.63328576980955\t17.829756253830322\t25.040481875405426\t19.691261902405127\t25.311348757482648\t22.648951316398268\t25.07592700325359\t24.957240657266393\t25.395341204296265\t22.223531971764206\t24.759006753308693\t24.25004185139378\t24.47573296436818\t21.889494052794266\t24.7374192095463\t19.94916118927913\t24.89935198902975\t21.075907601073208\t24.721609809672685\t27.0\t33.0\t30.0\t28.0\t12.0\t42.0\t2.0\t36.0\t5.0\t36.0\t11.0\t23.0\t26.0\t38.0\t12.0\t41.0\t23.0\t30.0\t10.0\t34.0\t4.0\t27.0\t10.0\t33.0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t-1.4728346653115594\t0.0014961642897455532\t0.004424675435076897\n+GO:2001141\tregulation of RNA biosynthetic process\tbiological_process\t26.34205256788306\t27.63543530743977\t26.651512126434774\t27.28352201899168\t26.948655423347926\t27.05700592789492\t25.51291335182695\t27.923407315980626\t26.27982855783693\t28.042422307734395\t26.20815926277268\t27.76388853668417\t26.412683613973734\t27.38663485129848\t26.03647283004182\t27.59377882498742\t25.126784640686463\t27.58471360291358\t26.947624030309463\t28.17369718937304\t26.68520714216416\t27.23792387977294\t25.86321781865529\t27.403800793482624\t26.354142491094432\t27.72650496536477\t108.0\t134.0\t103.0\t122.0\t105.0\t176.0\t99.0\t181.0\t134.0\t150.0\t147.0\t155.0\t111.0\t148.0\t87.0\t159.0\t195.0\t198.0\t131.0\t123.0\t93.0\t161.0\t142.0\t184.0\t3.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t3.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t-1.2933827395567121\t3.225641456243767e-05\t0.0005099643033035255\n+GO:2001295\tmalonyl-CoA biosynthetic process\tbiological_process\t24.04176718902617\t23.368503914625965\t21.869190774106308\t22.091623247786497\t22.35226996419096\t23.63067388937766\t23.95004243777072\t23.42842882120955\t24.81066402548795\t22.34498269235208\t24.884545910598035\t22.333495223933372\t24.3377404391613\t23.13908510884377\t23.65652105389825\t24.35531641248085\t24.302973205450648\t23.68292928714755\t23.659012427821196\t23.030970680176765\t23.41822612657516\t23.591034950731125\t23.797385759933352\t24.254723130459904\t24.70188938490118\t22.31230963978653\t7.0\t11.0\t16.0\t15.0\t21.0\t21.0\t23.0\t11.0\t24.0\t15.0\t24.0\t8.0\t22.0\t24.0\t13.0\t19.0\t25.0\t23.0\t16.0\t20.0\t18.0\t16.0\t23.0\t13.0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t0.6732632744002061\t0.04964722965745621\t0.07872902492059129\n' |
| b |
| diff -r 000000000000 -r 170b5fa2402d test-data/go_expanded.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/go_expanded.tab Thu Apr 25 13:46:17 2019 -0400 |
| b |
| @@ -0,0 +1,5 @@ +id name namespace s1_mean s2_mean int1 int2 int3 int4 int5 int6 int1_n_peptide int2_n_peptide int3_n_peptide int4_n_peptide int5_n_peptide int6_n_peptide int1_n_samp_children int2_n_samp_children int3_n_samp_children int4_n_samp_children int5_n_samp_children int6_n_samp_children +GO:0000003 reproduction biological_process 10.013089999440444 3.5443205162238103 9.965784284662089 10.228818690495881 9.813781191217037 3.584962500721156 3.700439718141092 3.3219280948873617 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 +GO:0008150 biological_process biological_process 10.066537719931583 11.4814630999144 10.011227255423254 10.287712379549447 9.868822554774999 11.782998208920414 10.9901039638575 11.560332834212446 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 +GO:0008152 metabolic process biological_process 3.9696263509564815 3.841302253980942 3.584962500721156 4.321928094887364 3.9068905956085187 3.584962500721156 4.392317422778762 3.3219280948873617 1.0 1.0 1.0 1.0 1.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 +GO:0032505 reproduction of a single-celled organism biological_process 10.013089999440444 3.5443205162238103 9.965784284662089 10.228818690495881 9.813781191217037 3.584962500721156 3.700439718141092 3.3219280948873617 1.0 1.0 1.0 1.0 1.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 |
| b |
| diff -r 000000000000 -r 170b5fa2402d test-data/go_filtered.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/go_filtered.tab Thu Apr 25 13:46:17 2019 -0400 |
| b |
| @@ -0,0 +1,2 @@ +id name namespace s1_mean s2_mean int1 int2 int3 int4 int5 int6 int1_n_peptide int2_n_peptide int3_n_peptide int4_n_peptide int5_n_peptide int6_n_peptide int1_n_samp_children int2_n_samp_children int3_n_samp_children int4_n_samp_children int5_n_samp_children int6_n_samp_children +GO:0008150 biological_process biological_process 10.066537719931583 11.4814630999144 10.011227255423254 10.287712379549447 9.868822554774999 11.782998208920414 10.9901039638575 11.560332834212446 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 3.0 |
| b |
| diff -r 000000000000 -r 170b5fa2402d test-data/int_737_test.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/int_737_test.tab Thu Apr 25 13:46:17 2019 -0400 |
| b |
| @@ -0,0 +1,8 @@ +peptide X737WS X737NS X852WS X852NS X867WS X867NS +LPGQQHGTPSAK 160259.916175029 334347.666958984 NA NA 564647.63540584 402888.904269133 +ELPGLAALTDK 9640246.8931187 NA 6379355.00041968 1842766.95005539 5491673.68230822 NA +ELADASVSTIEIER 3957112.96196795 NA 238529.022661759 NA 1277833.76064831 165964.15109473 +QISAGELR 17929965.5310232 774077.154902849 18109620.3255319 2481987.05852403 6576851.39343382 NA +VPAILADATK NA 202338.16108319 447102.130728772 1892303.72241057 1049044.6751075 1696422.39796239 +TVAWYDNEMSYTAQLVR 312188.928912629 145755.448008399 NA NA 236226.302935237 101927.343240103 +NYLSPIFTPINER 584412.175442185 NA 640797.879601609 73945.5784882333 689197.378565154 118069.439027697 |
| b |
| diff -r 000000000000 -r 170b5fa2402d test-data/int_ttest.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/int_ttest.tab Thu Apr 25 13:46:17 2019 -0400 |
| b |
| @@ -0,0 +1,4 @@ +peptide int1 int2 int3 int4 int5 int6 +A 12 20 15 12 21 10 +B 20 30 20 3500 2000 3000 +C 1000 1200 900 12 13 10 |
| b |
| diff -r 000000000000 -r 170b5fa2402d test-data/multiple_func.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multiple_func.tab Thu Apr 25 13:46:17 2019 -0400 |
| b |
| @@ -0,0 +1,4 @@ +peptide cog go ec +A C GO:0008152 1.-.-.- +B N GO:0022610 1.2.7.10 +C D GO:0000003,GO:0032505 3.1.8.1 |
| b |
| diff -r 000000000000 -r 170b5fa2402d test-data/multiple_int.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multiple_int.tab Thu Apr 25 13:46:17 2019 -0400 |
| b |
| @@ -0,0 +1,4 @@ +peptide int1 int2 int3 +A 10 20 70 +B 40 30 30 +C 50 50 0 |
| b |
| diff -r 000000000000 -r 170b5fa2402d test-data/multiple_tax.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multiple_tax.tab Thu Apr 25 13:46:17 2019 -0400 |
| b |
| @@ -0,0 +1,4 @@ +peptide lca +A 210 +B 1496 +C 1870884 |
| b |
| diff -r 000000000000 -r 170b5fa2402d test-data/outfile.png |
| b |
| Binary file test-data/outfile.png has changed |
| b |
| diff -r 000000000000 -r 170b5fa2402d test-data/rudney_samples.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rudney_samples.tab Thu Apr 25 13:46:17 2019 -0400 |
| b |
| @@ -0,0 +1,3 @@ +group colnames +NS X730NS,X733NS,X734NS,X737NS,X760NS,X769NS,X781NS,X795NS,X852NS,X861NS,X866NS,X867NS +WS X730WS,X733WS,X734WS,X737WS,X760WS,X769WS,X781WS,X795WS,X852WS,X861WS,X866WS,X867WS \ No newline at end of file |
| b |
| diff -r 000000000000 -r 170b5fa2402d test-data/samples.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samples.tab Thu Apr 25 13:46:17 2019 -0400 |
| b |
| @@ -0,0 +1,3 @@ +group colnames +NS X737NS,X852NS,X867NS +WS X737WS,X852WS,X867WS |
| b |
| diff -r 000000000000 -r 170b5fa2402d test-data/samples0.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samples0.tab Thu Apr 25 13:46:17 2019 -0400 |
| b |
| @@ -0,0 +1,3 @@ +group colnames +NS X737NS,X852NS,X867NS +WS X737WS,X852WS,X867WS |
| b |
| diff -r 000000000000 -r 170b5fa2402d test-data/samples_basic.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samples_basic.tab Thu Apr 25 13:46:17 2019 -0400 |
| b |
| @@ -0,0 +1,3 @@ +group colnames +s1 int1,int2,int3 +s2 int4,int5,int6 |
| b |
| diff -r 000000000000 -r 170b5fa2402d test-data/tax_filt.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tax_filt.tab Thu Apr 25 13:46:17 2019 -0400 |
| b |
| @@ -0,0 +1,15 @@ +id taxon_name rank NS_mean WS_mean X737NS X737WS X852NS X852WS X867NS X867WS X737NS_n_peptide X737WS_n_peptide X852NS_n_peptide X852WS_n_peptide X867NS_n_peptide X867WS_n_peptide X737NS_n_samp_children X737WS_n_samp_children X852NS_n_samp_children X852WS_n_samp_children X867NS_n_samp_children X867WS_n_samp_children +712 Pasteurellaceae family 26.45508515455985 24.240760984631766 24.965005542520593 22.218244926365948 0.0 17.341365183225566 27.1723016809798 25.697827115441516 12.0 12.0 0.0 1.0 12.0 12.0 1.0 1.0 0.0 0.0 1.0 1.0 +724 Haemophilus genus 26.043545589333238 24.308669239875652 23.49238493402781 21.57274687722112 0.0 0.0 26.91490217583963 25.19610989120677 5.0 5.0 0.0 0.0 5.0 5.0 1.0 1.0 0.0 0.0 1.0 1.0 +729 Haemophilus parainfluenzae species 23.516051135977808 21.837453207025035 22.113077280032016 20.132830444840515 0.0 0.0 24.21369255243491 22.597204359627263 4.0 4.0 0.0 0.0 4.0 4.0 0.0 0.0 0.0 0.0 0.0 0.0 +1224 Proteobacteria phylum 26.506407720117732 26.405669726384243 25.647561843048845 25.684049762573892 25.572526514273356 26.02079872568725 27.451384780869606 27.10853680624065 18.0 18.0 3.0 4.0 17.0 17.0 2.0 2.0 2.0 2.0 2.0 2.0 +1239 Firmicutes phylum 28.512385596646148 30.091433318476454 28.16821189186139 29.85860894014845 28.689295147943678 29.902989443795985 28.625794429436656 30.43794314029389 247.0 362.0 325.0 366.0 317.0 354.0 3.0 2.0 3.0 3.0 3.0 2.0 +1301 Streptococcus genus 26.867617254051414 28.85011386863358 26.46624241376839 28.05891048314316 26.560458646377878 29.13539355848514 27.388297546047863 29.117339967272912 67.0 124.0 96.0 127.0 111.0 124.0 2.0 3.0 3.0 3.0 2.0 3.0 +1302 Streptococcus gordonii species 24.686370636745576 27.653507330007766 23.762400434698712 26.151624056996113 24.539475551766014 27.515752990669643 25.336906564014722 28.450914623490767 24.0 43.0 29.0 44.0 44.0 45.0 0.0 0.0 0.0 0.0 0.0 0.0 +28216 Betaproteobacteria class 23.29428542923752 24.791799066973446 22.374889513201293 21.402137416070087 24.544202571791207 23.84100698984557 19.8675358581728 26.047141520330538 2.0 2.0 2.0 2.0 1.0 1.0 2.0 2.0 2.0 2.0 1.0 1.0 +29465 Veillonella genus 27.14677305830786 28.768830375331426 27.034861383116564 28.980840680293607 27.47904567128595 27.71387087737904 26.85278433596802 29.212848758443123 134.0 167.0 149.0 156.0 126.0 156.0 3.0 2.0 3.0 2.0 2.0 3.0 +29466 Veillonella parvula species 18.832221452467913 23.646622731934286 18.99584905472981 22.846993959159153 18.647632848343047 21.527044665274683 0.0 24.781099201499504 3.0 4.0 2.0 4.0 0.0 4.0 0.0 0.0 0.0 0.0 0.0 0.0 +39778 Veillonella dispar species 20.06805764601431 21.234364824902784 18.873358040924337 21.41636590750601 18.430484676034965 0.0 21.232667529959397 21.02604333055197 4.0 4.0 1.0 0.0 4.0 4.0 0.0 0.0 0.0 0.0 0.0 0.0 +40674 Mammalia class 18.71423436046836 17.946348342079197 17.822232855425355 17.738850060395933 18.41771660331577 18.769965187049696 19.43400368663769 16.48885357307721 1.0 1.0 2.0 2.0 2.0 1.0 0.0 0.0 1.0 1.0 1.0 1.0 +46124 Granulicatella adiacens species 25.44795951209062 24.095117178766355 22.413021529130273 23.066852858599482 26.121087214932714 23.994120320785946 25.808003124552783 24.75258507306872 12.0 25.0 31.0 31.0 33.0 29.0 0.0 0.0 0.0 0.0 0.0 0.0 +186826 Lactobacillales order 27.515198585571607 29.11785831796523 26.715706855135487 28.32187712752904 27.586822118206747 29.36333727974101 27.974157758353318 29.426524865028252 92.0 171.0 151.0 183.0 167.0 176.0 2.0 3.0 3.0 3.0 2.0 3.0 |
| b |
| diff -r 000000000000 -r 170b5fa2402d test-data/tax_filt_out.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tax_filt_out.tab Thu Apr 25 13:46:17 2019 -0400 |
| b |
| b'@@ -0,0 +1,93 @@\n+id\ttaxon_name\trank\tNS_mean\tWS_mean\tX730NS\tX730WS\tX733NS\tX733WS\tX734NS\tX734WS\tX737NS\tX737WS\tX760NS\tX760WS\tX769NS\tX769WS\tX781NS\tX781WS\tX795NS\tX795WS\tX852NS\tX852WS\tX861NS\tX861WS\tX866NS\tX866WS\tX867NS\tX867WS\tX730NS_n_peptide\tX730WS_n_peptide\tX733NS_n_peptide\tX733WS_n_peptide\tX734NS_n_peptide\tX734WS_n_peptide\tX737NS_n_peptide\tX737WS_n_peptide\tX760NS_n_peptide\tX760WS_n_peptide\tX769NS_n_peptide\tX769WS_n_peptide\tX781NS_n_peptide\tX781WS_n_peptide\tX795NS_n_peptide\tX795WS_n_peptide\tX852NS_n_peptide\tX852WS_n_peptide\tX861NS_n_peptide\tX861WS_n_peptide\tX866NS_n_peptide\tX866WS_n_peptide\tX867NS_n_peptide\tX867WS_n_peptide\tX730NS_n_samp_children\tX730WS_n_samp_children\tX733NS_n_samp_children\tX733WS_n_samp_children\tX734NS_n_samp_children\tX734WS_n_samp_children\tX737NS_n_samp_children\tX737WS_n_samp_children\tX760NS_n_samp_children\tX760WS_n_samp_children\tX769NS_n_samp_children\tX769WS_n_samp_children\tX781NS_n_samp_children\tX781WS_n_samp_children\tX795NS_n_samp_children\tX795WS_n_samp_children\tX852NS_n_samp_children\tX852WS_n_samp_children\tX861NS_n_samp_children\tX861WS_n_samp_children\tX866NS_n_samp_children\tX866WS_n_samp_children\tX867NS_n_samp_children\tX867WS_n_samp_children\n+157\tTreponema\tgenus\t22.4592368471399\t23.251641665456614\t21.782210465654984\t22.293663201701612\t19.506474847066862\t18.393389679254238\t21.31060467932299\t21.728055628093554\t20.480986062363687\t22.602867980613627\t23.203993721974225\t23.566696765176243\t22.313857374707805\t25.335612959036755\t24.564206593926965\t23.758132985051397\t21.865153582932077\t21.378622826723475\t22.004619704258204\t23.01330290131711\t21.929889350172612\t22.77047366650371\t22.145836211855425\t22.482730706742693\t22.080359413733433\t23.436551973678235\t9.0\t3.0\t2.0\t2.0\t6.0\t11.0\t8.0\t10.0\t10.0\t10.0\t7.0\t5.0\t15.0\t9.0\t4.0\t6.0\t8.0\t13.0\t12.0\t6.0\t5.0\t5.0\t14.0\t8.0\t5.0\t2.0\t2.0\t1.0\t4.0\t6.0\t4.0\t4.0\t5.0\t5.0\t4.0\t2.0\t4.0\t3.0\t3.0\t1.0\t4.0\t3.0\t5.0\t3.0\t3.0\t2.0\t6.0\t4.0\n+194\tCampylobacter\tgenus\t22.737726781977898\t23.402014527754694\t19.374983778535537\t20.606446832930114\t22.374052312423657\t22.175914745445667\t20.710711088017703\t21.497720060388442\t21.935778024142905\t21.360868814816588\t19.67510328882646\t18.442382745355207\t21.21818802567592\t18.98249372666148\t25.95861986611441\t24.365465047288765\t19.540072068600086\t22.271211580494718\t17.998259192791753\t26.353858284366478\t18.911902395646823\t20.233239126385538\t19.83361162568149\t19.261402979800614\t20.129527247691183\t22.479579021998745\t3.0\t5.0\t2.0\t5.0\t2.0\t7.0\t25.0\t5.0\t7.0\t4.0\t17.0\t3.0\t209.0\t8.0\t4.0\t9.0\t4.0\t8.0\t3.0\t5.0\t7.0\t4.0\t7.0\t6.0\t2.0\t2.0\t2.0\t3.0\t2.0\t4.0\t2.0\t3.0\t2.0\t2.0\t3.0\t2.0\t4.0\t4.0\t2.0\t3.0\t2.0\t4.0\t2.0\t3.0\t2.0\t2.0\t2.0\t4.0\n+286\tPseudomonas\tgenus\t22.84530963528067\t20.941262344966102\t19.390653532195216\t21.257892314732068\t23.40900039680405\t21.249447306145736\t22.85533086446144\t17.189270329854693\t21.43373289557238\t18.940290665716923\t21.2755581152792\t21.78465732920301\t19.42254043551283\t17.888724701002317\t22.016714341281943\t20.86953224363516\t18.685241717022148\t22.54333528743205\t20.234005329853034\t18.807506861121887\t23.765290496984004\t16.805950901945454\t25.39397860675149\t22.523625447598253\t19.404033335324762\t14.425011898222733\t2.0\t4.0\t2.0\t7.0\t11.0\t3.0\t4.0\t6.0\t7.0\t4.0\t4.0\t2.0\t16.0\t8.0\t2.0\t7.0\t5.0\t5.0\t6.0\t3.0\t6.0\t4.0\t5.0\t1.0\t1.0\t1.0\t1.0\t2.0\t3.0\t0.0\t2.0\t2.0\t2.0\t2.0\t2.0\t0.0\t3.0\t3.0\t2.0\t3.0\t3.0\t1.0\t2.0\t0.0\t3.0\t0.0\t2.0\t1.0\n+356\tRhizobiales\torder\t24.69225559146653\t24.47928415080033\t24.213805954712\t26.19612910182332\t23.852474395772273\t20.88389298705434\t24.072293206158825\t24.6359011866213\t23.253772028711925\t23.84124611127577\t25.211843229277033\t23.37465798633904\t24.971694694445382\t23.732993264497427\t25.466853125051237\t22.51337324493513\t23.333984301104184\t22.80206380634942\t24.48437767254155\t26.428256133544647\t25.06992046020705\t22.354137707550283\t23.963063933116196\t23.69000244474017\t25.821578844423875\t23.678835807279214\t18.0\t10.0\t13.0\t10.0\t12.0\t24.0\t14.0\t11.0\t12.0\t15.0\t20.0\t7.0\t21.0\t13.0\t17.0\t17.0\t18.0\t17.0\t16.0\t11.0\t15.0\t10.0\t21.0\t9.0\t5.0\t4.0\t5.0\t4.0\t5.0\t5.0\t4.0\t5.0\t4.0\t5.0\t5.0\t4.0\t4.0\t4.0\t5.0\t5.0\t5.0\t5.0\t3.0\t4.0'..b'\t16.378181817066846\t24.00350903786073\t17.7667506724018\t20.87439115632514\t19.272291498679323\t24.40326724487193\t0.0\t23.155822634831036\t15.8378395946466\t23.165629190009927\t21.236082242783827\t3.0\t4.0\t2.0\t2.0\t5.0\t3.0\t364.0\t9.0\t41.0\t12.0\t18.0\t5.0\t493.0\t2.0\t29.0\t2.0\t3.0\t3.0\t27.0\t0.0\t14.0\t2.0\t9.0\t8.0\t1.0\t2.0\t1.0\t1.0\t2.0\t1.0\t3.0\t2.0\t3.0\t3.0\t3.0\t3.0\t3.0\t1.0\t3.0\t1.0\t2.0\t1.0\t3.0\t0.0\t3.0\t2.0\t2.0\t3.0\n+649777\tSynergistaceae\tfamily\t21.34410870483268\t20.342481859790933\t12.722775191402784\t18.92833567189773\t20.513630556865273\t0.0\t21.123541056925603\t16.633712993437534\t17.439985048901242\t19.296406260651942\t20.62546717088497\t22.722314508599528\t18.941545335029307\t12.558719922528866\t23.26590054186841\t18.81660458896966\t20.71863709736182\t21.23783558474517\t20.577158921964482\t19.019500051140387\t23.284148568284248\t21.194625956766988\t20.366267968252497\t17.258831083285212\t19.802895038657333\t18.718863384956276\t1.0\t3.0\t3.0\t0.0\t4.0\t2.0\t3.0\t4.0\t3.0\t3.0\t2.0\t1.0\t9.0\t4.0\t1.0\t4.0\t2.0\t4.0\t2.0\t3.0\t4.0\t2.0\t2.0\t1.0\t1.0\t3.0\t2.0\t0.0\t2.0\t2.0\t2.0\t3.0\t2.0\t2.0\t2.0\t1.0\t3.0\t2.0\t1.0\t2.0\t2.0\t3.0\t2.0\t3.0\t3.0\t2.0\t2.0\t0.0\n+909932\tNegativicutes\tclass\t31.642194031354713\t32.13468762235439\t31.544314244694014\t22.26107368410749\t23.403415372397927\t25.274630134164894\t30.995174586086407\t32.534383226499486\t31.221607191441215\t33.416289115554946\t31.007758003630567\t32.812479432123524\t32.3657796226359\t31.27982807466682\t31.50580897261089\t31.419980035372852\t31.73676675760914\t32.46689932493384\t31.90335373250952\t32.01991155162215\t32.440506546087626\t31.624366871994567\t32.376633329293604\t30.77201116376389\t31.324387306077984\t33.27525557843209\t2112.0\t24.0\t13.0\t22.0\t1858.0\t4415.0\t2187.0\t6539.0\t2047.0\t4470.0\t3786.0\t2718.0\t2281.0\t2701.0\t2355.0\t4257.0\t2365.0\t3164.0\t3391.0\t2649.0\t3465.0\t1957.0\t2384.0\t5655.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t3.0\t2.0\t2.0\t2.0\t2.0\n+1570339\tPeptoniphilaceae\tfamily\t23.376192221156746\t21.9233285218442\t21.530370272488227\t18.080746778833426\t22.069344119853483\t21.69336496273765\t24.224440757757648\t23.248488219093908\t22.70511207327184\t20.87440581741395\t22.21077750839318\t21.90605373227633\t20.779175868793548\t20.912271401897566\t25.86972432971436\t21.05424678262083\t21.751447218169673\t22.82055468109171\t22.872969174097605\t22.769851569191083\t22.94097984639506\t22.587358803525447\t21.898503869358407\t20.8124661881928\t22.427603428836107\t20.403651221891238\t8.0\t4.0\t5.0\t7.0\t9.0\t15.0\t16.0\t11.0\t20.0\t11.0\t13.0\t8.0\t28.0\t9.0\t16.0\t17.0\t10.0\t13.0\t8.0\t5.0\t7.0\t9.0\t9.0\t8.0\t4.0\t2.0\t4.0\t3.0\t4.0\t4.0\t4.0\t4.0\t4.0\t3.0\t3.0\t3.0\t4.0\t3.0\t4.0\t4.0\t4.0\t3.0\t3.0\t2.0\t4.0\t3.0\t4.0\t3.0\n+1643824\tAtopobiaceae\tfamily\t23.095961409992302\t23.208563169782163\t24.915226695607878\t21.298333283010308\t24.201904039997398\t23.93953836973515\t21.588480102781343\t22.589064661598893\t22.67860039633661\t22.386543718617833\t23.38407466541362\t19.904829849577574\t22.032654192647296\t22.494976060551032\t21.97127765348275\t23.91618649632667\t23.087297488120807\t23.709595883268843\t21.94359747287084\t22.81282029308393\t22.48415692721951\t22.29631653248385\t21.844043109426398\t23.250123815558876\t22.211599792157088\t24.682377093999648\t6.0\t2.0\t8.0\t7.0\t5.0\t5.0\t10.0\t10.0\t7.0\t3.0\t3.0\t3.0\t9.0\t8.0\t4.0\t5.0\t5.0\t6.0\t5.0\t3.0\t2.0\t8.0\t6.0\t7.0\t2.0\t1.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t1.0\t2.0\t2.0\t2.0\n+1843491\tSelenomonadaceae\tfamily\t23.23864639783701\t22.8728938280295\t22.15215088671252\t17.208137383583722\t21.598185771677297\t22.661543465600804\t23.015096873655523\t22.531134703617262\t22.68649736015477\t23.24016576883264\t23.96621462793578\t21.778565860399933\t24.31621982642957\t21.414594274785475\t23.418189249072828\t20.40663564024541\t23.612216055685572\t22.864012545765014\t22.747995432652267\t22.521151691407837\t22.712049747539854\t24.22506609220036\t23.83919133820257\t24.50800705913742\t22.384756810701738\t22.106172333873914\t9.0\t2.0\t10.0\t10.0\t14.0\t13.0\t15.0\t10.0\t15.0\t7.0\t18.0\t6.0\t16.0\t9.0\t8.0\t12.0\t12.0\t12.0\t13.0\t9.0\t16.0\t9.0\t10.0\t9.0\t2.0\t1.0\t2.0\t3.0\t2.0\t2.0\t2.0\t2.0\t2.0\t1.0\t3.0\t1.0\t3.0\t3.0\t3.0\t2.0\t2.0\t2.0\t3.0\t2.0\t3.0\t2.0\t2.0\t3.0\n' |
| b |
| diff -r 000000000000 -r 170b5fa2402d test-data/tax_ns.png |
| b |
| Binary file test-data/tax_ns.png has changed |
| b |
| diff -r 000000000000 -r 170b5fa2402d test-data/tax_test_out.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tax_test_out.tab Thu Apr 25 13:46:17 2019 -0400 |
| b |
| b'@@ -0,0 +1,93 @@\n+id\ttaxon_name\trank\tNS_mean\tWS_mean\tX730NS\tX730WS\tX733NS\tX733WS\tX734NS\tX734WS\tX737NS\tX737WS\tX760NS\tX760WS\tX769NS\tX769WS\tX781NS\tX781WS\tX795NS\tX795WS\tX852NS\tX852WS\tX861NS\tX861WS\tX866NS\tX866WS\tX867NS\tX867WS\tX730NS_n_peptide\tX730WS_n_peptide\tX733NS_n_peptide\tX733WS_n_peptide\tX734NS_n_peptide\tX734WS_n_peptide\tX737NS_n_peptide\tX737WS_n_peptide\tX760NS_n_peptide\tX760WS_n_peptide\tX769NS_n_peptide\tX769WS_n_peptide\tX781NS_n_peptide\tX781WS_n_peptide\tX795NS_n_peptide\tX795WS_n_peptide\tX852NS_n_peptide\tX852WS_n_peptide\tX861NS_n_peptide\tX861WS_n_peptide\tX866NS_n_peptide\tX866WS_n_peptide\tX867NS_n_peptide\tX867WS_n_peptide\tX730NS_n_samp_children\tX730WS_n_samp_children\tX733NS_n_samp_children\tX733WS_n_samp_children\tX734NS_n_samp_children\tX734WS_n_samp_children\tX737NS_n_samp_children\tX737WS_n_samp_children\tX760NS_n_samp_children\tX760WS_n_samp_children\tX769NS_n_samp_children\tX769WS_n_samp_children\tX781NS_n_samp_children\tX781WS_n_samp_children\tX795NS_n_samp_children\tX795WS_n_samp_children\tX852NS_n_samp_children\tX852WS_n_samp_children\tX861NS_n_samp_children\tX861WS_n_samp_children\tX866NS_n_samp_children\tX866WS_n_samp_children\tX867NS_n_samp_children\tX867WS_n_samp_children\tlog2fc_NS_over_WS\tp\tcorrected_p\n+157\tTreponema\tgenus\t22.4592368471399\t23.25164166545661\t21.782210465654984\t22.29366320170161\t19.506474847066862\t18.393389679254238\t21.31060467932299\t21.728055628093554\t20.480986062363687\t22.602867980613627\t23.203993721974225\t23.566696765176243\t22.313857374707805\t25.335612959036755\t24.564206593926965\t23.758132985051397\t21.865153582932077\t21.378622826723475\t22.004619704258204\t23.01330290131711\t21.929889350172612\t22.77047366650371\t22.145836211855425\t22.482730706742693\t22.080359413733433\t23.436551973678235\t9.0\t3.0\t2.0\t2.0\t6.0\t11.0\t8.0\t10.0\t10.0\t10.0\t7.0\t5.0\t15.0\t9.0\t4.0\t6.0\t8.0\t13.0\t12.0\t6.0\t5.0\t5.0\t14.0\t8.0\t5.0\t2.0\t2.0\t1.0\t4.0\t6.0\t4.0\t4.0\t5.0\t5.0\t4.0\t2.0\t4.0\t3.0\t3.0\t1.0\t4.0\t3.0\t5.0\t3.0\t3.0\t2.0\t6.0\t4.0\t-0.7924048183167116\t0.10596880912720232\t0.22157114635687755\n+194\tCampylobacter\tgenus\t22.737726781977898\t23.402014527754694\t19.374983778535537\t20.606446832930114\t22.374052312423657\t22.175914745445667\t20.710711088017703\t21.497720060388442\t21.935778024142905\t21.360868814816588\t19.67510328882646\t18.442382745355207\t21.21818802567592\t18.98249372666148\t25.95861986611441\t24.365465047288765\t19.540072068600086\t22.271211580494718\t17.998259192791753\t26.353858284366478\t18.911902395646823\t20.233239126385538\t19.83361162568149\t19.261402979800614\t20.129527247691183\t22.479579021998745\t3.0\t5.0\t2.0\t5.0\t2.0\t7.0\t25.0\t5.0\t7.0\t4.0\t17.0\t3.0\t209.0\t8.0\t4.0\t9.0\t4.0\t8.0\t3.0\t5.0\t7.0\t4.0\t7.0\t6.0\t2.0\t2.0\t2.0\t3.0\t2.0\t4.0\t2.0\t3.0\t2.0\t2.0\t3.0\t2.0\t4.0\t4.0\t2.0\t3.0\t2.0\t4.0\t2.0\t3.0\t2.0\t2.0\t2.0\t4.0\t-0.6642877457767966\t0.27265646879500405\t0.41807325215233954\n+286\tPseudomonas\tgenus\t22.84530963528067\t20.941262344966106\t19.390653532195216\t21.257892314732068\t23.40900039680405\t21.249447306145736\t22.85533086446144\t17.189270329854693\t21.43373289557238\t18.940290665716926\t21.2755581152792\t21.78465732920301\t19.42254043551283\t17.888724701002317\t22.016714341281943\t20.86953224363516\t18.685241717022148\t22.54333528743205\t20.234005329853034\t18.807506861121887\t23.765290496984004\t16.805950901945454\t25.39397860675149\t22.523625447598253\t19.404033335324762\t14.425011898222733\t2.0\t4.0\t2.0\t7.0\t11.0\t3.0\t4.0\t6.0\t7.0\t4.0\t4.0\t2.0\t16.0\t8.0\t2.0\t7.0\t5.0\t5.0\t6.0\t3.0\t6.0\t4.0\t5.0\t1.0\t1.0\t1.0\t1.0\t2.0\t3.0\tNA\t2.0\t2.0\t2.0\t2.0\t2.0\tNA\t3.0\t3.0\t2.0\t3.0\t3.0\t1.0\t2.0\tNA\t3.0\tNA\t2.0\t1.0\t1.9040472903145655\t0.06467168750236378\t0.15657355921624916\n+356\tRhizobiales\torder\t24.69225559146653\t24.47928415080033\t24.213805954712\t26.19612910182332\t23.852474395772273\t20.88389298705434\t24.072293206158825\t24.6359011866213\t23.253772028711925\t23.84124611127577\t25.211843229277033\t23.37465798633904\t24.971694694445386\t23.732993264497427\t25.466853125051237\t22.51337324493513\t23.333984301104184\t22.80206380634942\t24.48437767254155\t26.42825613354465\t25.06992046020705\t22.354137707550287\t23.963063933116196\t23.69000244474017\t25.821578844423875\t23.678835807'..b'0\t3.0\t1.0\t3.0\t1.0\t2.0\t1.0\t3.0\tNA\t3.0\t2.0\t2.0\t3.0\t4.064428054212016\t0.031232244921543854\t0.09268924299296886\n+649777\tSynergistaceae\tfamily\t21.34410870483268\t20.342481859790933\t12.722775191402786\t18.92833567189773\t20.513630556865273\tNA\t21.123541056925603\t16.633712993437534\t17.439985048901242\t19.296406260651946\t20.62546717088497\t22.722314508599528\t18.941545335029307\t12.558719922528866\t23.26590054186841\t18.81660458896966\t20.71863709736182\t21.23783558474517\t20.577158921964482\t19.019500051140387\t23.284148568284248\t21.194625956766988\t20.366267968252497\t17.258831083285212\t19.802895038657333\t18.718863384956283\t1.0\t3.0\t3.0\tNA\t4.0\t2.0\t3.0\t4.0\t3.0\t3.0\t2.0\t1.0\t9.0\t4.0\t1.0\t4.0\t2.0\t4.0\t2.0\t3.0\t4.0\t2.0\t2.0\t1.0\t1.0\t3.0\t2.0\tNA\t2.0\t2.0\t2.0\t3.0\t2.0\t2.0\t2.0\t1.0\t3.0\t2.0\t1.0\t2.0\t2.0\t3.0\t2.0\t3.0\t3.0\t2.0\t2.0\tNA\t1.0016268450417485\t0.17573433564422514\t0.3233511775853743\n+909932\tNegativicutes\tclass\t31.642194031354713\t32.13468762235439\t31.544314244694014\t22.26107368410749\t23.403415372397927\t25.27463013416489\t30.99517458608641\t32.534383226499486\t31.221607191441212\t33.416289115554946\t31.00775800363057\t32.812479432123524\t32.3657796226359\t31.27982807466682\t31.50580897261089\t31.419980035372852\t31.73676675760914\t32.46689932493384\t31.90335373250952\t32.01991155162215\t32.440506546087626\t31.62436687199457\t32.376633329293604\t30.77201116376389\t31.324387306077984\t33.27525557843209\t2112.0\t24.0\t13.0\t22.0\t1858.0\t4415.0\t2187.0\t6539.0\t2047.0\t4470.0\t3786.0\t2718.0\t2281.0\t2701.0\t2355.0\t4257.0\t2365.0\t3164.0\t3391.0\t2649.0\t3465.0\t1957.0\t2384.0\t5655.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t3.0\t2.0\t2.0\t2.0\t2.0\t-0.49249359099967904\t0.3864762307712327\t0.4969091373099221\n+1570339\tPeptoniphilaceae\tfamily\t23.376192221156746\t21.9233285218442\t21.530370272488227\t18.080746778833426\t22.069344119853483\t21.693364962737647\t24.224440757757648\t23.248488219093908\t22.70511207327184\t20.87440581741395\t22.21077750839318\t21.90605373227633\t20.779175868793548\t20.912271401897566\t25.86972432971436\t21.05424678262083\t21.751447218169673\t22.82055468109171\t22.872969174097605\t22.769851569191083\t22.94097984639506\t22.587358803525447\t21.898503869358407\t20.8124661881928\t22.427603428836107\t20.403651221891238\t8.0\t4.0\t5.0\t7.0\t9.0\t15.0\t16.0\t11.0\t20.0\t11.0\t13.0\t8.0\t28.0\t9.0\t16.0\t17.0\t10.0\t13.0\t8.0\t5.0\t7.0\t9.0\t9.0\t8.0\t4.0\t2.0\t4.0\t3.0\t4.0\t4.0\t4.0\t4.0\t4.0\t3.0\t3.0\t3.0\t4.0\t3.0\t4.0\t4.0\t4.0\t3.0\t3.0\t2.0\t4.0\t3.0\t4.0\t3.0\t1.4528636993125446\t0.0940685547103812\t0.2012629542640714\n+1643824\tAtopobiaceae\tfamily\t23.095961409992302\t23.208563169782163\t24.915226695607878\t21.298333283010308\t24.201904039997398\t23.93953836973515\t21.588480102781343\t22.589064661598893\t22.67860039633661\t22.386543718617833\t23.38407466541362\t19.904829849577574\t22.032654192647296\t22.494976060551032\t21.97127765348275\t23.91618649632667\t23.087297488120807\t23.709595883268843\t21.94359747287084\t22.81282029308393\t22.48415692721951\t22.29631653248385\t21.844043109426398\t23.250123815558876\t22.211599792157088\t24.682377093999648\t6.0\t2.0\t8.0\t7.0\t5.0\t5.0\t10.0\t10.0\t7.0\t3.0\t3.0\t3.0\t9.0\t8.0\t4.0\t5.0\t5.0\t6.0\t5.0\t3.0\t2.0\t8.0\t6.0\t7.0\t2.0\t1.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t2.0\t1.0\t2.0\t2.0\t2.0\t-0.11260175978986098\t0.4884223166225936\t0.5991313750570482\n+1843491\tSelenomonadaceae\tfamily\t23.23864639783701\t22.8728938280295\t22.15215088671252\t17.208137383583722\t21.598185771677297\t22.661543465600804\t23.015096873655523\t22.53113470361727\t22.68649736015477\t23.24016576883264\t23.96621462793578\t21.778565860399933\t24.31621982642957\t21.414594274785475\t23.418189249072828\t20.40663564024541\t23.612216055685572\t22.864012545765014\t22.747995432652267\t22.521151691407837\t22.71204974753985\t24.22506609220036\t23.83919133820257\t24.50800705913742\t22.38475681070173\t22.106172333873914\t9.0\t2.0\t10.0\t10.0\t14.0\t13.0\t15.0\t10.0\t15.0\t7.0\t18.0\t6.0\t16.0\t9.0\t8.0\t12.0\t12.0\t12.0\t13.0\t9.0\t16.0\t9.0\t10.0\t9.0\t2.0\t1.0\t2.0\t3.0\t2.0\t2.0\t2.0\t2.0\t2.0\t1.0\t3.0\t1.0\t3.0\t3.0\t3.0\t2.0\t2.0\t2.0\t3.0\t2.0\t3.0\t2.0\t2.0\t3.0\t0.36575256980750837\t0.14891467317876572\t0.2914925517541797\n' |
| b |
| diff -r 000000000000 -r 170b5fa2402d test-data/tf_filt_out.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tf_filt_out.tab Thu Apr 25 13:46:17 2019 -0400 |
| b |
| b'@@ -0,0 +1,195 @@\n+go_id\tname\tnamespace\ttax_id\ttaxon_name\trank\tNS_mean\tWS_mean\tX730NS\tX730WS\tX733NS\tX733WS\tX734NS\tX734WS\tX737NS\tX737WS\tX760NS\tX760WS\tX769NS\tX769WS\tX781NS\tX781WS\tX795NS\tX795WS\tX852NS\tX852WS\tX861NS\tX861WS\tX866NS\tX866WS\tX867NS\tX867WS\tX730NS_n_peptide\tX730WS_n_peptide\tX733NS_n_peptide\tX733WS_n_peptide\tX734NS_n_peptide\tX734WS_n_peptide\tX737NS_n_peptide\tX737WS_n_peptide\tX760NS_n_peptide\tX760WS_n_peptide\tX769NS_n_peptide\tX769WS_n_peptide\tX781NS_n_peptide\tX781WS_n_peptide\tX795NS_n_peptide\tX795WS_n_peptide\tX852NS_n_peptide\tX852WS_n_peptide\tX861NS_n_peptide\tX861WS_n_peptide\tX866NS_n_peptide\tX866WS_n_peptide\tX867NS_n_peptide\tX867WS_n_peptide\n+GO:0000166\tnucleotide binding\tmolecular_function\t1301\tStreptococcus\tgenus\t23.30473651409458\t26.548612184308638\t23.469319528833342\t24.7382759122065\t25.555924940970954\t26.638659151994535\t19.389738778451733\t26.641124760139174\t23.21396920345138\t26.25209508256927\t19.95805429931315\t24.977003986496424\t23.18662389945245\t25.822526630314737\t21.242631199315323\t27.21066416016841\t19.189672167395045\t27.4189579238358\t21.90159227429199\t25.349443551980176\t24.62573002453793\t27.207659326313976\t20.325458678389854\t27.524097432181115\t22.97000793114937\t25.356803912239922\t19.0\t39.0\t37.0\t69.0\t2.0\t47.0\t4.0\t41.0\t1.0\t36.0\t6.0\t23.0\t12.0\t80.0\t4.0\t74.0\t5.0\t37.0\t12.0\t50.0\t4.0\t51.0\t5.0\t44.0\n+GO:0000166\tnucleotide binding\tmolecular_function\t29465\tVeillonella\tgenus\t25.061382835641886\t25.413140921517357\t25.182980714582033\t0.0\t0.0\t0.0\t23.84783230965444\t25.954093563676754\t24.47189750298385\t26.47990470144072\t23.31018946572931\t25.673785960186528\t25.526821726449107\t24.40788278890973\t24.878194280627323\t24.4978172691651\t25.790196506866693\t26.457431198243547\t25.206034591897694\t25.08453705764599\t26.08715490399581\t24.857420426791197\t25.231858222246238\t24.198738798089927\t25.476611215806788\t26.585622413772803\t24.0\t0.0\t0.0\t0.0\t19.0\t41.0\t31.0\t89.0\t23.0\t59.0\t50.0\t51.0\t33.0\t26.0\t28.0\t40.0\t40.0\t46.0\t40.0\t27.0\t42.0\t26.0\t39.0\t73.0\n+GO:0003674\tmolecular_function\tmolecular_function\t848\tFusobacterium\tgenus\t28.11951718676351\t22.86520267660315\t20.329170797503192\t0.0\t0.0\t15.024037079358726\t28.32967721965599\t17.392119432799262\t29.29633271109983\t19.135077784899664\t29.07092254978022\t16.59358146251789\t28.457321331078692\t0.0\t28.689881092715343\t0.0\t27.944216326982474\t0.0\t26.9747543674305\t26.43625153656205\t21.69481319084998\t0.0\t28.03359789877866\t0.0\t28.800955533598604\t0.0\t2.0\t0.0\t0.0\t1.0\t253.0\t2.0\t495.0\t1.0\t370.0\t1.0\t309.0\t0.0\t340.0\t0.0\t218.0\t0.0\t169.0\t151.0\t14.0\t0.0\t327.0\t0.0\t342.0\t0.0\n+GO:0003674\tmolecular_function\tmolecular_function\t1301\tStreptococcus\tgenus\t24.17749078971571\t27.19240926722064\t25.00536657619239\t26.43181828778861\t26.267064167585012\t28.304036489686922\t23.176162407246885\t27.227650085451693\t22.31501654089106\t26.015140769225468\t20.973588081830002\t26.356756258599738\t23.876746050504387\t26.34229757090562\t24.52556954029224\t27.86988957773961\t23.65472647404589\t28.020945805277695\t22.696778984577822\t26.697344428895306\t24.52551571803027\t26.66995033821489\t18.131289261738054\t27.42533767082077\t23.57506016193438\t26.699736352863823\t49.0\t110.0\t104.0\t201.0\t32.0\t160.0\t21.0\t115.0\t7.0\t79.0\t35.0\t113.0\t41.0\t245.0\t28.0\t226.0\t18.0\t107.0\t51.0\t151.0\t1.0\t158.0\t32.0\t137.0\n+GO:0003674\tmolecular_function\tmolecular_function\t29465\tVeillonella\tgenus\t25.93722399321307\t26.314247777963637\t25.709601572027978\t0.0\t0.0\t0.0\t25.02242940625912\t26.398086419196463\t25.03679385999819\t27.62435530533861\t25.446910164978362\t27.371571993928388\t26.952331228853694\t25.978072011068967\t25.56633594374977\t25.016910767501468\t25.896066676196\t26.269920138379554\t26.273868323349934\t26.08235242500588\t26.863076793039014\t25.342501795056748\t26.629362410766387\t25.59683041932128\t25.656903997318274\t27.47848803217556\t50.0\t0.0\t0.0\t0.0\t43.0\t107.0\t59.0\t192.0\t47.0\t155.0\t117.0\t88.0\t51.0\t50.0\t64.0\t94.0\t93.0\t98.0\t120.0\t56.0\t122.0\t82.0\t84.0\t160.0\n+GO:0003674\tmolecular_function\tmolecular_function\t117563\tGranulicatella\tgenus\t18.901345185090822\t16.74568294784119\t20.19942142370727\t16.51475103911933\t20.89029598149793\t'..b'2\t0.0\t18.94067497176566\t18.4806722846698\t19.14133148086633\t17.21054951006002\t21.344089663101013\t0.0\t22.411171288147322\t1.0\t1.0\t4.0\t7.0\t0.0\t1.0\t0.0\t0.0\t0.0\t2.0\t0.0\t4.0\t0.0\t8.0\t0.0\t4.0\t0.0\t2.0\t2.0\t4.0\t2.0\t11.0\t0.0\t3.0\n+GO:0071103\tDNA conformation change\tbiological_process\t29465\tVeillonella\tgenus\t22.87124269025797\t24.2585148099511\t23.669369834355532\t0.0\t0.0\t0.0\t24.401265363442803\t25.730618255768036\t21.825068496324388\t25.501765042904516\t23.44100927831922\t23.42472437254513\t23.088814286474804\t18.692094591961858\t21.67848569171658\t24.078521915299646\t21.98838566126453\t25.46748107120349\t16.921693875375762\t18.612821701851047\t23.058381199606405\t23.97483651939533\t19.457805036261412\t17.69892906240016\t23.88105434544159\t25.4154122051635\t1.0\t0.0\t0.0\t0.0\t1.0\t2.0\t1.0\t2.0\t1.0\t3.0\t1.0\t2.0\t1.0\t1.0\t1.0\t1.0\t1.0\t2.0\t2.0\t1.0\t2.0\t1.0\t1.0\t5.0\n+GO:0071840\tcellular component organization or biogenesis\tbiological_process\t1301\tStreptococcus\tgenus\t23.36931070865711\t24.721234639267717\t23.214112725619877\t25.222660044465798\t25.60430670963775\t24.450217718226728\t20.612896964619733\t24.499369252445863\t22.2412481050996\t24.16558347824425\t21.306188337086507\t24.554230527406734\t23.569525654358724\t25.051474067430238\t23.70668160397436\t24.96099281159652\t22.28197046606773\t24.574747083875604\t22.85856154793457\t24.85097034670341\t23.672315384320868\t25.179956921584967\t17.334673670897438\t23.909218989841328\t22.886908951336306\t24.643721802564322\t19.0\t32.0\t41.0\t28.0\t4.0\t30.0\t8.0\t29.0\t6.0\t21.0\t18.0\t32.0\t15.0\t33.0\t6.0\t38.0\t7.0\t32.0\t25.0\t49.0\t2.0\t21.0\t21.0\t33.0\n+GO:0071840\tcellular component organization or biogenesis\tbiological_process\t29465\tVeillonella\tgenus\t24.097348812911477\t24.637755457084594\t24.351184254733386\t0.0\t0.0\t0.0\t24.180523356547976\t24.870641359316657\t23.906371561747516\t25.867956023729683\t23.714766029463487\t25.524988863394555\t24.087075945684518\t24.036441617178927\t23.677110119598144\t23.969556463382226\t23.70567091769716\t24.633916794640783\t24.400852524711308\t24.837313965399453\t24.809943268517042\t23.546744521039894\t25.037078294286733\t23.461853550794412\t23.796371143471536\t25.82869938736789\t8.0\t0.0\t0.0\t0.0\t8.0\t16.0\t9.0\t15.0\t7.0\t16.0\t14.0\t10.0\t13.0\t14.0\t10.0\t11.0\t9.0\t11.0\t12.0\t6.0\t15.0\t10.0\t13.0\t18.0\n+GO:0098796\tmembrane protein complex\tcellular_component\t1301\tStreptococcus\tgenus\t19.31403457379215\t24.45702636411511\t17.792993945984726\t22.306527125247868\t22.1763444493302\t26.01308822536041\t17.697296528266712\t24.65400944698547\t0.0\t22.78075181061697\t14.27685011398016\t21.61874746879364\t15.451243733640421\t22.418464849517303\t0.0\t24.93971753338989\t0.0\t24.535178058478014\t0.0\t23.502136007085014\t21.166689366268905\t25.23080938877911\t0.0\t24.741645992530664\t17.769786625557195\t24.588105806371953\t1.0\t10.0\t9.0\t18.0\t2.0\t19.0\t0.0\t15.0\t1.0\t10.0\t1.0\t8.0\t0.0\t14.0\t0.0\t22.0\t0.0\t12.0\t9.0\t24.0\t0.0\t17.0\t2.0\t21.0\n+GO:0098796\tmembrane protein complex\tcellular_component\t29465\tVeillonella\tgenus\t20.687321205051425\t21.031905660730022\t21.244896270905162\t0.0\t0.0\t0.0\t20.31938965940495\t21.48816335772356\t21.347724264625754\t22.914580151950407\t20.813023310157554\t22.332056737078872\t20.54181700530028\t0.0\t20.13924967928026\t18.94819855494045\t21.032866092684017\t21.22278153658437\t19.86184840048016\t14.119792935624705\t21.77051225750943\t20.546332311343974\t20.48735440221516\t18.31497074377935\t20.10855979453269\t22.186305533186427\t3.0\t0.0\t0.0\t0.0\t3.0\t4.0\t3.0\t4.0\t3.0\t4.0\t4.0\t0.0\t3.0\t1.0\t3.0\t2.0\t2.0\t1.0\t5.0\t2.0\t3.0\t1.0\t4.0\t2.0\n+GO:1902494\tcatalytic complex\tcellular_component\t29465\tVeillonella\tgenus\t21.12332288217632\t21.370496892516858\t20.692925428588058\t0.0\t0.0\t0.0\t20.85873065770146\t21.187603040292192\t19.808103372439547\t22.742662284967327\t19.676578790516746\t22.314140505391073\t22.432794666476656\t19.233519486788925\t21.598930991842714\t19.011890747676965\t20.699493362489285\t22.20298218139625\t19.8584855550306\t20.62501181575648\t21.908335367926746\t20.10093312257102\t22.408930034510973\t21.85194041996485\t20.019372695664032\t22.368056850115337\t6.0\t0.0\t0.0\t0.0\t7.0\t11.0\t4.0\t21.0\t4.0\t9.0\t10.0\t4.0\t11.0\t4.0\t7.0\t15.0\t6.0\t4.0\t11.0\t7.0\t13.0\t7.0\t8.0\t15.0\n' |
| b |
| diff -r 000000000000 -r 170b5fa2402d test-data/wrapped_outfile.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/wrapped_outfile.html Thu Apr 25 13:46:17 2019 -0400 |
| b |
| @@ -0,0 +1,1 @@ +<!DOCTYPE html> <html> <head> <link rel="stylesheet" type="text/css" href="style.css"/> </head> <body> <h1>Output Figure</h1> <br> <img src="outfile.png" width=600 height=600> <br> <p>To download the image, right-click and choose "Save image as..."</p> <br> <p>OR</p> <br> <p><a href="outfile.png">Click Here</a></p> </body> </html> |
