| Previous changeset 1:4dc76dcbd1e7 (2016-12-05) Next changeset 3:28d579fa1718 (2018-10-03) |
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Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/tool-bank-golm-lib_search.git commit a2892b221abe5a68ef271266a36b66894fcf9bde |
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modified:
golm_ws_lib_search.pl golm_ws_lib_search.xml lib/golm_ws_api.pm test-data/output01.html test-data/output01.tabular test-data/output01.txt test-data/output02.html test-data/output02.tabular test-data/output02.txt test-data/output03.html test-data/output03.tabular test-data/output03.txt |
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removed:
planemo_test.sh |
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| diff -r 4dc76dcbd1e7 -r 11779b6402bc golm_ws_lib_search.pl --- a/golm_ws_lib_search.pl Mon Dec 05 08:41:00 2016 -0500 +++ b/golm_ws_lib_search.pl Wed Feb 22 07:37:36 2017 -0500 |
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| @@ -242,7 +242,7 @@ $default_ri, $default_ri_window, $default_gc_column) ; push (@hits , $limited_hits) ; } - + ############# -------------- Build outputs -------------- ############# : |
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| diff -r 4dc76dcbd1e7 -r 11779b6402bc golm_ws_lib_search.xml --- a/golm_ws_lib_search.xml Mon Dec 05 08:41:00 2016 -0500 +++ b/golm_ws_lib_search.xml Wed Feb 22 07:37:36 2017 -0500 |
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| @@ -1,15 +1,15 @@ -<tool id="golm_ws_lib_search" name="Golm Metabolome Database search spectrum" version="2016-11-28"> +<tool id="golm_ws_lib_search" name="Golm Metabolome Database search spectrum" version="2016-12-05"> <description> : GC-MS Mass Spectral Database. </description> - <!--<requirements> + <requirements> <requirement type="package" version="0.413">perl-list-moreutils</requirement> <requirement type="package" version="1.19">perl-soap-lite</requirement> <requirement type="package" version="0.95">perl-excel-writer-xlsx</requirement> <requirement type="package" version="2.90">perl-json</requirement> <requirement type="package" version="2.95">perl-html-template</requirement> - </requirements>--> + </requirements> <stdio> <exit_code range="1" level="fatal" /> @@ -22,7 +22,7 @@ -output_tabular "$GolmOutTab" -output_html "$GolmOutWeb" -output_xls "$GolmOutXlsx" #else: -inputMasses "${input_type.mass}" - -output_tabular "$GolmOutTab2" -output_html "$GolmOutWeb2" -output_xls "$GolmResXlsx2" + -output_tabular "$GolmOutTab2" -output_html "$GolmOutWeb2" -output_xls "$GolmOutXlsx2" #end if -ri "$ri" -riWindow "$riWindow" @@ -84,13 +84,13 @@ </data> <data name="GolmOutTab2" label="GOLM.tabular" format="tabular" > <filter>input_type['choice'] == "NO"</filter> - </data - <data name="GolmOutWeb2" label="HMDB_WEB.html" format="html"> + </data> + <data name="GolmOutWeb2" label="GOLM_WEB.html" format="html"> <filter>input_type['choice'] == "NO"</filter> - </data - <data name="GolmOutXlsx2" label="HMDB.txt" format="tabular"> + </data> + <data name="GolmOutXlsx2" label="GOLM.txt" format="tabular"> <filter>input_type['choice'] == "NO"</filter> - </data + </data> </outputs> <tests> @@ -154,6 +154,8 @@ <output name="GolmOutWeb" file="output03.html"/> <output name="GolmOutTab" file="output03.tabular"/> </test> + + </tests> <help><![CDATA[ |
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| diff -r 4dc76dcbd1e7 -r 11779b6402bc lib/golm_ws_api.pm --- a/lib/golm_ws_api.pm Mon Dec 05 08:41:00 2016 -0500 +++ b/lib/golm_ws_api.pm Wed Feb 22 07:37:36 2017 -0500 |
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| @@ -200,7 +200,7 @@ ## Limitate number of hits returned according to user's $maxHit ## and filter hits on specific values with thresholds my @results = @$results ; - + ### Return all hits my $oapi = lib::golm_ws_api->new() ; if ($maxHits == 100 && $status eq 'success') { @@ -235,7 +235,7 @@ } else { carp "The spectrum for query is undef, Golm soap will stop.\n" ; } - return \@filtered_limited_res ; +# return \@filtered_limited_res ; } ### END of SUB @@ -261,12 +261,25 @@ my @results = @$results ; my @filtered_res = () ; + ## Adjust threshold + $JaccardDistanceThreshold = sprintf("%.6f", $JaccardDistanceThreshold) ; + $s12GowerLegendreDistanceThreshold = sprintf("%.6f", $s12GowerLegendreDistanceThreshold) ; + $DotproductDistanceThreshold = sprintf("%.6f", $DotproductDistanceThreshold) ; +# $HammingDistanceThreshold = sprintf("%.6f", $HammingDistanceThreshold); + $EuclideanDistanceThreshold = sprintf("%.6f", $EuclideanDistanceThreshold); + foreach my $res (@results){ + + $res->{'JaccardDistance'} = sprintf("%.6f", $res->{'JaccardDistance'}) ; + $res->{'s12GowerLegendreDistance'} = sprintf("%.6f", $res->{'s12GowerLegendreDistance'}) ; + $res->{'DotproductDistance'} = sprintf("%.6f", $res->{'DotproductDistance'}) ; +# $res->{'HammingDistance'} = sprintf("%.6f", $res->{'HammingDistance'}) ; + $res->{'EuclideanDistance'} = sprintf("%.6f", $res->{'EuclideanDistance'}) ; if ($res->{'JaccardDistance'} <= $JaccardDistanceThreshold && $res->{'s12GowerLegendreDistance'} <= $s12GowerLegendreDistanceThreshold - && $res->{'DotproductDistance' } <= $DotproductDistanceThreshold && $res->{'HammingDistance'} <= $HammingDistanceThreshold && - $res->{'EuclideanDistance' } <= $EuclideanDistanceThreshold) { - + && $res->{'DotproductDistance'} <= $DotproductDistanceThreshold && $res->{'HammingDistance'} <= $HammingDistanceThreshold && + $res->{'EuclideanDistance'} <= $EuclideanDistanceThreshold) { + push (@filtered_res , $res) ; } } |
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| diff -r 4dc76dcbd1e7 -r 11779b6402bc planemo_test.sh --- a/planemo_test.sh Mon Dec 05 08:41:00 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,3 +0,0 @@ -planemo conda_init --conda_prefix /tmp/mc/ -planemo conda_install --conda_prefix /tmp/mc/ . -planemo test --install_galaxy --conda_dependency_resolution --conda_prefix /tmp/mc/ --no_cleanup |
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| diff -r 4dc76dcbd1e7 -r 11779b6402bc test-data/output01.html --- a/test-data/output01.html Mon Dec 05 08:41:00 2016 -0500 +++ b/test-data/output01.html Wed Feb 22 07:37:36 2017 -0500 |
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| b'@@ -6,6 +6,6 @@\n $(\'.buttons-copy\').each(function(){$(this).attr("id","mytooltip2");})\n $(\'.buttons-collection\').each(function(){$(this).attr("id","mytooltip3");})\n for(var i=0;i<12;i++){$($($("table.display.stripe.dataTable")[2]).find("th")[i]).css(\'width\',$($($("table.display.stripe.dataTable")[0]).find("th")[i]).css(\'width\'));}});$(document).on(\'click\',\'.ripple\',function(e){var $rippleElement=$(\'<span class="ripple-effect" />\'),$buttonElement=$(this),btnOffset=$buttonElement.offset(),xPos=e.pageX-btnOffset.left,yPos=e.pageY-btnOffset.top,size=parseInt(Math.min($buttonElement.height(),$buttonElement.width())*0.5),animateSize=parseInt(Math.max($buttonElement.width(),$buttonElement.height())*Math.PI);$rippleElement.css({top:yPos,left:xPos,width:size,height:size,backgroundColor:$buttonElement.data("ripple-color")}).appendTo($buttonElement).animate({width:animateSize,height:animateSize,opacity:0},700,function(){$(this).remove();});});\n-</script><title>Golm Search Results</title></head><body><div class=\'mdl-layout mdl-js-layout mdl-layout--fixed-header\'> <header class=\'mdl-layout__header\'><div class=\'mdl-layout__header-row\'> <span class=\'mdl-layout-title\'><h3><b>Visualization of Golm Database Results</b></h3></span></div><div class=\'mdl-layout__tab-bar mdl-js-ripple-effect\'> <a href=\'#fixed-tab-1\' class=\'mdl-layout__tab is-active\'><b>Table</b></a> <a href=\'#fixed-tab-2\' class=\'mdl-layout__tab\'><b>Help</b></a></div> </header> <main class=\'mdl-layout__content\'> <section class=\'mdl-layout__tab-panel is-active\' id=\'fixed-tab-1\'><div class=\'page-content\'><table id=\'table_id\' class=\'display stripe\' cellspacing=\'0\' width=\'100%\' ><thead><tr><th colspan=\'1\'></th><th colspan=\'2\' style=\'text-align:center\'>NAMES</th><th colspan=\'2\' style=\'text-align:center\'>RETENTION INFOS</th><th colspan=\'5\' style=\'text-align:center\'>DISTANCE SCORES</th><th colspan=\'3\' style=\'text-align:center\'>IDs</th></tr><tr><th style=\'text-align:center;border-left: 1px solid #A7A7A7;\'>N\xc2\xb0 Spectres</th><th style=\'text-align:center;border-left: 1px solid #A7A7A7;\'>Spectrum</th><th style=\'text-align:center;border-right: 1px solid #A7A7A7;\'>Analyte</th><th style=\'text-align:center\'>Retention Index</th><th style=\'text-align:center;border-right: 1px solid #A7A7A7;\'>RI Discrepancy</th><th style=\'text-align:center\'>Dot product</th><th style=\'text-align:center\'>Euclidean</th><th style=\'text-align:center\'>Jaccard</th><th style=\'text-align:center\'>Hamming</th><th style=\'text-align:center;border-right: 1px solid #A7A7A7;\'>s12 Gower-Legendre</th><th style=\'text-align:center\'>Spectrum id</th><th style=\'text-align:center\'>Metabolite id</th><th style=\'text-align:center;border-right: 1px solid #A7A7A7;\'>Analyte id</th></tr></thead><tfoot><tr><th style=\'text-align:center\'>N\xc2\xb0 Spectre</th><th style=\'text-align:center\'>Spectrum</th><th style=\'text-align:center\'>Analyte</th><th style=\'text-align:center\'>Retention Index</th><th style=\'text-align:center\'>RI Discrepancy</th><th style=\'text-align:center\'>Dot product</th><th style=\'text-align:center\'>Euclidean</th><th style=\'text-align:center\'>Jaccard</th><th style=\'text-align:center\'>Hamming</th><th style=\'text-align:center\'>s12 Gower-Legendre</th><th style=\'text-align:center\'>Spectrum id</th><th style=\'text-align:center\'>Metabolite id</th><th style=\'text-align:center\'>Analyte id</th></tr></tfoot><tbody> <tr><td>1</td><td><a href=\'http://gmd.mpimp-golm.mpg.de/Spectrums/833ab58c-a8fa-4389-8b42-95e618cafb91.aspx\' target=\'_blank\'>Glucose (1MEOX) (5TMS) BP [A191001-ambient-na-12]</a></td><td><a href=\'http://gmd.mpimp-golm.mpg.de/Analytes/0a2b3536-2245-4c0e-bdbc-495766eeec67.aspx\' target=\'_blank\'>Glucose (1MEOX) (5TMS) BP</a></td><td>1899.05493</td><td>1.054953</td><td>0.4861827</td><td>0.0871585</td><td>0.8515625</td><td>109</td><td>0.784043431</td><td>833ab58c-a8fa-4389-8b42-95e618cafb91</td><td><a href=\'http://gmd.mpimp-golm.mpg.de/Metabolites/68513255-fc44-4041-bc4b-4fd2fae7541d.aspx\' target=\'_blank\'>68513255-fc44-4041-bc4b-4fd2fae7541d</a></td'..b'ard__title\'><h1 class=\'mdl-card__title-text\'>What can the table do ?</h1></div><div class=\'mdl-card__supporting-text\'><ul class=\'list-icon mdl-list\'><li class=\'mdl-list__item\'> <span class=\'mdl-list__item-primary-content\'> <i class=\'material-icons mdl-list__item-icon\'>filter_list</i> By default, the spectra numbers (N\xc2\xb0 Spectra) are ordered by ascending values. You can manage your data ordering as you wish. You can even order data according to multiple columns: SHIFT + LEFT CLICK on column headers. This will order by the first column clicked, then the second, etc. You can sort data specifically by clicking on any entry in boxes under each columns. </span></li><li class=\'mdl-list__item\'> <span class=\'mdl-list__item-primary-content\'> <i class=\'material-icons mdl-list__item-icon\'>delete_sweep</i> You can delete multiple entries that are selected: Select wanted entries and click on the button DELETE SELECTED ROWS. </span></li><li class=\'mdl-list__item\'> <span class=\'mdl-list__item-primary-content\'> <i class=\'material-icons mdl-list__item-icon\'>remove_red_eye</i> You have the possibility to toggle columns by clicking on SHOW MORE. </span></li><li class=\'mdl-list__item\'> <span class=\'mdl-list__item-primary-content\'> <i class=\'material-icons mdl-list__item-icon\'>save</i> You can print, copy, or export to excel and csv the table on its actual state, with the three buttons right above the table. </span></li></ul></div></div> </br><div id="large_card" class=\'card-wide mdl-card mdl-shadow--3dp\'> <figure class=\'mdl-card__media\' style=\'background-color: white\'> <img src=\'http://image005.flaticon.com/1/svg/125/125279.svg\' style=\'height: 60px; width: 60px;\'> </figure><div class=\'mdl-card__title\'><h1 class=\'mdl-card__title-text\'>Distances scores</h1></div><div class=\'mdl-card__supporting-text\'><table id="dist_table" style="color: rgba(0,0,0,.87);"><tr><td style="padding-right:10px;><b style="white-space: nowrap;"><b>S12Gower-Legendre Distance</b></td><td> The distance measure S12GowLeg = sqrt(1 - s12) is derived from the S12 coefficient of Gower & Legendre defined as s12 = a / sqrt((a + b)(a + c)), with "a" representing the number of positions at which both spectra are in "on-state" and "b" respectively "c" representing the number of positions at which only the query spectrum or the hit spectrum are in "on-state".</td></tr><tr><td style="padding-right:10px;"><b style="white-space: nowrap;">Hamming Distance</b></td><td> In information theory, the Hamming distance between two strings of equal length is the number of positions for which the corresponding symbols are different. Put another way, it measures the minimum number of substitutions required to change one into the other, or the number of errors that transformed one string into the other.</td></tr><tr><td style="padding-right:10px;"><b style="white-space: nowrap;">Jaccard Distance</b></td><td>Number of matches (a mass with appropriate intensity in both spectra) divided by the sum of matches and mismatches (a mass where only one of both spectra has a intensity). The jaccard distance is a binary distance.</td></tr><tr><td style="padding-right:10px;"><b style="white-space: nowrap;padding-right:60px;">Dotproduct Distance</b></td><td>The Dotproduct distance is summing the multiplied intensities over all matching peaks within both spectra. Here, to satisfy the conditions of a metric I) non-negativity, II) identity of indiscernibles, III) symmetry and IV) subadditivity / triangle inequality, we use 1-Dotproduct. Both spectra are normalised prior to the spectral vector norm in that way, that the absolute value of the squared intensities is equal to 1.</td></tr><tr><td style="padding-right:10px;"><b style="white-space: nowrap;padding-right:60px;">Euclidean Distance</b></td><td>The Euclid is the square root of the sum of the squared differences over all matching peaks.</td></tr></table></div></div></div> </br></br></center> </section> </main></div></body></html>\n \t\t\n \t\n\\ No newline at end of file\n' |
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| diff -r 4dc76dcbd1e7 -r 11779b6402bc test-data/output01.tabular --- a/test-data/output01.tabular Mon Dec 05 08:41:00 2016 -0500 +++ b/test-data/output01.tabular Wed Feb 22 07:37:36 2017 -0500 |
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| @@ -1,13 +1,13 @@ "Num Spectre" "Analyte Name" "Spectrum Name" "Retention Index" "RI Discrepancy" "DotproductDistance" "EuclideanDistance" "JaccardDistance" "HammingDistance" "s12GowerLegendreDistance" "Spectrum ID" "Metabolite ID" "Analyte ID" -"1" "Glucose (1MEOX) (5TMS) BP" "Glucose (1MEOX) (5TMS) BP [A191001-ambient-na-12]" "1899.05493" "1.054953" "0.4861827" "0.0871585" "0.8515625" "109" "0.784043431" "833ab58c-a8fa-4389-8b42-95e618cafb91" "68513255-fc44-4041-bc4b-4fd2fae7541d" "0a2b3536-2245-4c0e-bdbc-495766eeec67" -"1" "Galactose (1MEOX) (5TMS) BP" "Galactose (1MEOX) (5TMS) BP [A191002-ambient-DL--6]" "1902.42212" "4.422119" "0.4875465" "0.0869417042" "0.852713168" "110" "0.784997046" "6e056b61-4da9-46e3-970b-680a22e4afd0" "dd3ea070-54a6-4ea7-b99b-a6e975fdd204" "1c3ad0aa-ee78-4542-93b3-aa9fdf07add1" -"1" "Idose (1MEOX) (5TMS) BP" "Idose (1MEOX) (5TMS) BP [A191005-ambient-na-1]" "1897.25439" "0.745605469" "0.4901554" "0.0861777" "0.8560606" "113" "0.7877858" "d00de57d-6fab-49d0-9aee-25e259da9180" "ab025068-f464-4bc6-9c92-994c29387db2" "6f4e926f-d7ef-47b6-a52c-91ff88ca567a" -"1" "Allantoin (5TMS)" "Allantoin (5TMS) [A188009-ambient-na-5]" "1896.99829" "1.001709" "0.4914575" "0.09410148" "0.8558559" "95" "0.804233432" "817f2a03-9df5-46e3-973c-b2a9675109cf" "a999f0d6-0285-41d9-a6ba-b705987b663c" "65bb54d2-6bf7-4a53-aa22-8abf71240005" -"1" "Glucose, U-13C- (1MEOX) (5TMS) BP" "Glucose, U-13C- (1MEOX) (5TMS) BP [A191001-13C-na-2]" "1901.63" "3.63" "0.497226775" "0.0910335854" "0.85" "102" "0.788321555" "27d4dcdd-d351-4976-8ef9-76a0cc53f631" "441faccb-2631-4e7d-b6ca-99437265ccb8" "96441b61-2891-4e81-93dc-d0fc0ad175d4" +"1" "Glucose (1MEOX) (5TMS) BP" "Glucose (1MEOX) (5TMS) BP [A191001-ambient-na-12]" "1899.05493" "1.054953" "0.486183" "0.087158" "0.851562" "109" "0.784043" "833ab58c-a8fa-4389-8b42-95e618cafb91" "68513255-fc44-4041-bc4b-4fd2fae7541d" "0a2b3536-2245-4c0e-bdbc-495766eeec67" +"1" "Galactose (1MEOX) (5TMS) BP" "Galactose (1MEOX) (5TMS) BP [A191002-ambient-DL--6]" "1902.42212" "4.422119" "0.487546" "0.086942" "0.852713" "110" "0.784997" "6e056b61-4da9-46e3-970b-680a22e4afd0" "dd3ea070-54a6-4ea7-b99b-a6e975fdd204" "1c3ad0aa-ee78-4542-93b3-aa9fdf07add1" +"1" "Idose (1MEOX) (5TMS) BP" "Idose (1MEOX) (5TMS) BP [A191005-ambient-na-1]" "1897.25439" "0.745605469" "0.490155" "0.086178" "0.856061" "113" "0.787786" "d00de57d-6fab-49d0-9aee-25e259da9180" "ab025068-f464-4bc6-9c92-994c29387db2" "6f4e926f-d7ef-47b6-a52c-91ff88ca567a" +"1" "Allantoin (5TMS)" "Allantoin (5TMS) [A188009-ambient-na-5]" "1896.99829" "1.001709" "0.491457" "0.094101" "0.855856" "95" "0.804233" "817f2a03-9df5-46e3-973c-b2a9675109cf" "a999f0d6-0285-41d9-a6ba-b705987b663c" "65bb54d2-6bf7-4a53-aa22-8abf71240005" +"1" "Glucose, U-13C- (1MEOX) (5TMS) BP" "Glucose, U-13C- (1MEOX) (5TMS) BP [A191001-13C-na-2]" "1901.63" "3.63" "0.497227" "0.091034" "0.850000" "102" "0.788322" "27d4dcdd-d351-4976-8ef9-76a0cc53f631" "441faccb-2631-4e7d-b6ca-99437265ccb8" "96441b61-2891-4e81-93dc-d0fc0ad175d4" "2" "" "no results" "" "" "" "" "" "" "" "" "" "" -"3" "Glucose (1MEOX) (5TMS) BP" "Glucose (1MEOX) (5TMS) BP [A191001-ambient-na-12]" "1899.05493" "1.054953" "0.487051964" "0.0868976042" "0.8604651" "111" "0.79687" "833ab58c-a8fa-4389-8b42-95e618cafb91" "68513255-fc44-4041-bc4b-4fd2fae7541d" "0a2b3536-2245-4c0e-bdbc-495766eeec67" -"3" "Galactose (1MEOX) (5TMS) BP" "Galactose (1MEOX) (5TMS) BP [A191002-ambient-DL--6]" "1902.42212" "4.422119" "0.4883618" "0.08667906" "0.86153847" "112" "0.797758937" "6e056b61-4da9-46e3-970b-680a22e4afd0" "dd3ea070-54a6-4ea7-b99b-a6e975fdd204" "1c3ad0aa-ee78-4542-93b3-aa9fdf07add1" -"3" "Idose (1MEOX) (5TMS) BP" "Idose (1MEOX) (5TMS) BP [A191005-ambient-na-1]" "1897.25439" "0.745605469" "0.491137743" "0.0859391" "0.864661634" "115" "0.8003591" "d00de57d-6fab-49d0-9aee-25e259da9180" "ab025068-f464-4bc6-9c92-994c29387db2" "6f4e926f-d7ef-47b6-a52c-91ff88ca567a" -"3" "Allantoin (5TMS)" "Allantoin (5TMS) [A188009-ambient-na-5]" "1896.99829" "1.001709" "0.4918884" "0.09372151" "0.8660714" "97" "0.817842841" "817f2a03-9df5-46e3-973c-b2a9675109cf" "a999f0d6-0285-41d9-a6ba-b705987b663c" "65bb54d2-6bf7-4a53-aa22-8abf71240005" -"3" "Glucose, U-13C- (1MEOX) (5TMS) BP" "Glucose, U-13C- (1MEOX) (5TMS) BP [A191001-13C-na-2]" "1901.63" "3.63" "0.49828127" "0.0907527059" "0.8595041" "104" "0.8015494" "27d4dcdd-d351-4976-8ef9-76a0cc53f631" "441faccb-2631-4e7d-b6ca-99437265ccb8" "96441b61-2891-4e81-93dc-d0fc0ad175d4" +"3" "Glucose (1MEOX) (5TMS) BP" "Glucose (1MEOX) (5TMS) BP [A191001-ambient-na-12]" "1899.05493" "1.054953" "0.487052" "0.086898" "0.860465" "111" "0.796870" "833ab58c-a8fa-4389-8b42-95e618cafb91" "68513255-fc44-4041-bc4b-4fd2fae7541d" "0a2b3536-2245-4c0e-bdbc-495766eeec67" +"3" "Galactose (1MEOX) (5TMS) BP" "Galactose (1MEOX) (5TMS) BP [A191002-ambient-DL--6]" "1902.42212" "4.422119" "0.488362" "0.086679" "0.861538" "112" "0.797759" "6e056b61-4da9-46e3-970b-680a22e4afd0" "dd3ea070-54a6-4ea7-b99b-a6e975fdd204" "1c3ad0aa-ee78-4542-93b3-aa9fdf07add1" +"3" "Idose (1MEOX) (5TMS) BP" "Idose (1MEOX) (5TMS) BP [A191005-ambient-na-1]" "1897.25439" "0.745605469" "0.491138" "0.085939" "0.864662" "115" "0.800359" "d00de57d-6fab-49d0-9aee-25e259da9180" "ab025068-f464-4bc6-9c92-994c29387db2" "6f4e926f-d7ef-47b6-a52c-91ff88ca567a" +"3" "Allantoin (5TMS)" "Allantoin (5TMS) [A188009-ambient-na-5]" "1896.99829" "1.001709" "0.491888" "0.093722" "0.866071" "97" "0.817843" "817f2a03-9df5-46e3-973c-b2a9675109cf" "a999f0d6-0285-41d9-a6ba-b705987b663c" "65bb54d2-6bf7-4a53-aa22-8abf71240005" +"3" "Glucose, U-13C- (1MEOX) (5TMS) BP" "Glucose, U-13C- (1MEOX) (5TMS) BP [A191001-13C-na-2]" "1901.63" "3.63" "0.498281" "0.090753" "0.859504" "104" "0.801549" "27d4dcdd-d351-4976-8ef9-76a0cc53f631" "441faccb-2631-4e7d-b6ca-99437265ccb8" "96441b61-2891-4e81-93dc-d0fc0ad175d4" "4" "" "no results" "" "" "" "" "" "" "" "" "" "" |
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| diff -r 4dc76dcbd1e7 -r 11779b6402bc test-data/output01.txt --- a/test-data/output01.txt Mon Dec 05 08:41:00 2016 -0500 +++ b/test-data/output01.txt Wed Feb 22 07:37:36 2017 -0500 |
| [ |
| @@ -1,13 +1,13 @@ Num Spectre Analyte Name Spectrum Name Retention Index RI Discrepancy DotproductDistance EuclideanDistance JaccardDistance HammingDistance s12GowerLegendreDistance Spectrum ID Metabolite ID Analyte ID -1 Glucose (1MEOX) (5TMS) BP Glucose (1MEOX) (5TMS) BP [A191001-ambient-na-12] 1899.05493 1.054953 0.4861827 0.0871585 0.8515625 109 0.784043431 833ab58c-a8fa-4389-8b42-95e618cafb91 68513255-fc44-4041-bc4b-4fd2fae7541d 0a2b3536-2245-4c0e-bdbc-495766eeec67 -1 Galactose (1MEOX) (5TMS) BP Galactose (1MEOX) (5TMS) BP [A191002-ambient-DL--6] 1902.42212 4.422119 0.4875465 0.0869417042 0.852713168 110 0.784997046 6e056b61-4da9-46e3-970b-680a22e4afd0 dd3ea070-54a6-4ea7-b99b-a6e975fdd204 1c3ad0aa-ee78-4542-93b3-aa9fdf07add1 -1 Idose (1MEOX) (5TMS) BP Idose (1MEOX) (5TMS) BP [A191005-ambient-na-1] 1897.25439 0.745605469 0.4901554 0.0861777 0.8560606 113 0.7877858 d00de57d-6fab-49d0-9aee-25e259da9180 ab025068-f464-4bc6-9c92-994c29387db2 6f4e926f-d7ef-47b6-a52c-91ff88ca567a -1 Allantoin (5TMS) Allantoin (5TMS) [A188009-ambient-na-5] 1896.99829 1.001709 0.4914575 0.09410148 0.8558559 95 0.804233432 817f2a03-9df5-46e3-973c-b2a9675109cf a999f0d6-0285-41d9-a6ba-b705987b663c 65bb54d2-6bf7-4a53-aa22-8abf71240005 -1 Glucose, U-13C- (1MEOX) (5TMS) BP Glucose, U-13C- (1MEOX) (5TMS) BP [A191001-13C-na-2] 1901.63 3.63 0.497226775 0.0910335854 0.85 102 0.788321555 27d4dcdd-d351-4976-8ef9-76a0cc53f631 441faccb-2631-4e7d-b6ca-99437265ccb8 96441b61-2891-4e81-93dc-d0fc0ad175d4 +1 Glucose (1MEOX) (5TMS) BP Glucose (1MEOX) (5TMS) BP [A191001-ambient-na-12] 1899.05493 1.054953 0.486183 0.087158 0.851562 109 0.784043 833ab58c-a8fa-4389-8b42-95e618cafb91 68513255-fc44-4041-bc4b-4fd2fae7541d 0a2b3536-2245-4c0e-bdbc-495766eeec67 +1 Galactose (1MEOX) (5TMS) BP Galactose (1MEOX) (5TMS) BP [A191002-ambient-DL--6] 1902.42212 4.422119 0.487546 0.086942 0.852713 110 0.784997 6e056b61-4da9-46e3-970b-680a22e4afd0 dd3ea070-54a6-4ea7-b99b-a6e975fdd204 1c3ad0aa-ee78-4542-93b3-aa9fdf07add1 +1 Idose (1MEOX) (5TMS) BP Idose (1MEOX) (5TMS) BP [A191005-ambient-na-1] 1897.25439 0.745605469 0.490155 0.086178 0.856061 113 0.787786 d00de57d-6fab-49d0-9aee-25e259da9180 ab025068-f464-4bc6-9c92-994c29387db2 6f4e926f-d7ef-47b6-a52c-91ff88ca567a +1 Allantoin (5TMS) Allantoin (5TMS) [A188009-ambient-na-5] 1896.99829 1.001709 0.491457 0.094101 0.855856 95 0.804233 817f2a03-9df5-46e3-973c-b2a9675109cf a999f0d6-0285-41d9-a6ba-b705987b663c 65bb54d2-6bf7-4a53-aa22-8abf71240005 +1 Glucose, U-13C- (1MEOX) (5TMS) BP Glucose, U-13C- (1MEOX) (5TMS) BP [A191001-13C-na-2] 1901.63 3.63 0.497227 0.091034 0.850000 102 0.788322 27d4dcdd-d351-4976-8ef9-76a0cc53f631 441faccb-2631-4e7d-b6ca-99437265ccb8 96441b61-2891-4e81-93dc-d0fc0ad175d4 2 no results -3 Glucose (1MEOX) (5TMS) BP Glucose (1MEOX) (5TMS) BP [A191001-ambient-na-12] 1899.05493 1.054953 0.487051964 0.0868976042 0.8604651 111 0.79687 833ab58c-a8fa-4389-8b42-95e618cafb91 68513255-fc44-4041-bc4b-4fd2fae7541d 0a2b3536-2245-4c0e-bdbc-495766eeec67 -3 Galactose (1MEOX) (5TMS) BP Galactose (1MEOX) (5TMS) BP [A191002-ambient-DL--6] 1902.42212 4.422119 0.4883618 0.08667906 0.86153847 112 0.797758937 6e056b61-4da9-46e3-970b-680a22e4afd0 dd3ea070-54a6-4ea7-b99b-a6e975fdd204 1c3ad0aa-ee78-4542-93b3-aa9fdf07add1 -3 Idose (1MEOX) (5TMS) BP Idose (1MEOX) (5TMS) BP [A191005-ambient-na-1] 1897.25439 0.745605469 0.491137743 0.0859391 0.864661634 115 0.8003591 d00de57d-6fab-49d0-9aee-25e259da9180 ab025068-f464-4bc6-9c92-994c29387db2 6f4e926f-d7ef-47b6-a52c-91ff88ca567a -3 Allantoin (5TMS) Allantoin (5TMS) [A188009-ambient-na-5] 1896.99829 1.001709 0.4918884 0.09372151 0.8660714 97 0.817842841 817f2a03-9df5-46e3-973c-b2a9675109cf a999f0d6-0285-41d9-a6ba-b705987b663c 65bb54d2-6bf7-4a53-aa22-8abf71240005 -3 Glucose, U-13C- (1MEOX) (5TMS) BP Glucose, U-13C- (1MEOX) (5TMS) BP [A191001-13C-na-2] 1901.63 3.63 0.49828127 0.0907527059 0.8595041 104 0.8015494 27d4dcdd-d351-4976-8ef9-76a0cc53f631 441faccb-2631-4e7d-b6ca-99437265ccb8 96441b61-2891-4e81-93dc-d0fc0ad175d4 +3 Glucose (1MEOX) (5TMS) BP Glucose (1MEOX) (5TMS) BP [A191001-ambient-na-12] 1899.05493 1.054953 0.487052 0.086898 0.860465 111 0.796870 833ab58c-a8fa-4389-8b42-95e618cafb91 68513255-fc44-4041-bc4b-4fd2fae7541d 0a2b3536-2245-4c0e-bdbc-495766eeec67 +3 Galactose (1MEOX) (5TMS) BP Galactose (1MEOX) (5TMS) BP [A191002-ambient-DL--6] 1902.42212 4.422119 0.488362 0.086679 0.861538 112 0.797759 6e056b61-4da9-46e3-970b-680a22e4afd0 dd3ea070-54a6-4ea7-b99b-a6e975fdd204 1c3ad0aa-ee78-4542-93b3-aa9fdf07add1 +3 Idose (1MEOX) (5TMS) BP Idose (1MEOX) (5TMS) BP [A191005-ambient-na-1] 1897.25439 0.745605469 0.491138 0.085939 0.864662 115 0.800359 d00de57d-6fab-49d0-9aee-25e259da9180 ab025068-f464-4bc6-9c92-994c29387db2 6f4e926f-d7ef-47b6-a52c-91ff88ca567a +3 Allantoin (5TMS) Allantoin (5TMS) [A188009-ambient-na-5] 1896.99829 1.001709 0.491888 0.093722 0.866071 97 0.817843 817f2a03-9df5-46e3-973c-b2a9675109cf a999f0d6-0285-41d9-a6ba-b705987b663c 65bb54d2-6bf7-4a53-aa22-8abf71240005 +3 Glucose, U-13C- (1MEOX) (5TMS) BP Glucose, U-13C- (1MEOX) (5TMS) BP [A191001-13C-na-2] 1901.63 3.63 0.498281 0.090753 0.859504 104 0.801549 27d4dcdd-d351-4976-8ef9-76a0cc53f631 441faccb-2631-4e7d-b6ca-99437265ccb8 96441b61-2891-4e81-93dc-d0fc0ad175d4 4 no results |
| b |
| diff -r 4dc76dcbd1e7 -r 11779b6402bc test-data/output02.html --- a/test-data/output02.html Mon Dec 05 08:41:00 2016 -0500 +++ b/test-data/output02.html Wed Feb 22 07:37:36 2017 -0500 |
| [ |
| b'@@ -6,6 +6,6 @@\n $(\'.buttons-copy\').each(function(){$(this).attr("id","mytooltip2");})\n $(\'.buttons-collection\').each(function(){$(this).attr("id","mytooltip3");})\n for(var i=0;i<12;i++){$($($("table.display.stripe.dataTable")[2]).find("th")[i]).css(\'width\',$($($("table.display.stripe.dataTable")[0]).find("th")[i]).css(\'width\'));}});$(document).on(\'click\',\'.ripple\',function(e){var $rippleElement=$(\'<span class="ripple-effect" />\'),$buttonElement=$(this),btnOffset=$buttonElement.offset(),xPos=e.pageX-btnOffset.left,yPos=e.pageY-btnOffset.top,size=parseInt(Math.min($buttonElement.height(),$buttonElement.width())*0.5),animateSize=parseInt(Math.max($buttonElement.width(),$buttonElement.height())*Math.PI);$rippleElement.css({top:yPos,left:xPos,width:size,height:size,backgroundColor:$buttonElement.data("ripple-color")}).appendTo($buttonElement).animate({width:animateSize,height:animateSize,opacity:0},700,function(){$(this).remove();});});\n-</script><title>Golm Search Results</title></head><body><div class=\'mdl-layout mdl-js-layout mdl-layout--fixed-header\'> <header class=\'mdl-layout__header\'><div class=\'mdl-layout__header-row\'> <span class=\'mdl-layout-title\'><h3><b>Visualization of Golm Database Results</b></h3></span></div><div class=\'mdl-layout__tab-bar mdl-js-ripple-effect\'> <a href=\'#fixed-tab-1\' class=\'mdl-layout__tab is-active\'><b>Table</b></a> <a href=\'#fixed-tab-2\' class=\'mdl-layout__tab\'><b>Help</b></a></div> </header> <main class=\'mdl-layout__content\'> <section class=\'mdl-layout__tab-panel is-active\' id=\'fixed-tab-1\'><div class=\'page-content\'><table id=\'table_id\' class=\'display stripe\' cellspacing=\'0\' width=\'100%\' ><thead><tr><th colspan=\'1\'></th><th colspan=\'2\' style=\'text-align:center\'>NAMES</th><th colspan=\'2\' style=\'text-align:center\'>RETENTION INFOS</th><th colspan=\'5\' style=\'text-align:center\'>DISTANCE SCORES</th><th colspan=\'3\' style=\'text-align:center\'>IDs</th></tr><tr><th style=\'text-align:center;border-left: 1px solid #A7A7A7;\'>N\xc2\xb0 Spectres</th><th style=\'text-align:center;border-left: 1px solid #A7A7A7;\'>Spectrum</th><th style=\'text-align:center;border-right: 1px solid #A7A7A7;\'>Analyte</th><th style=\'text-align:center\'>Retention Index</th><th style=\'text-align:center;border-right: 1px solid #A7A7A7;\'>RI Discrepancy</th><th style=\'text-align:center\'>Dot product</th><th style=\'text-align:center\'>Euclidean</th><th style=\'text-align:center\'>Jaccard</th><th style=\'text-align:center\'>Hamming</th><th style=\'text-align:center;border-right: 1px solid #A7A7A7;\'>s12 Gower-Legendre</th><th style=\'text-align:center\'>Spectrum id</th><th style=\'text-align:center\'>Metabolite id</th><th style=\'text-align:center;border-right: 1px solid #A7A7A7;\'>Analyte id</th></tr></thead><tfoot><tr><th style=\'text-align:center\'>N\xc2\xb0 Spectre</th><th style=\'text-align:center\'>Spectrum</th><th style=\'text-align:center\'>Analyte</th><th style=\'text-align:center\'>Retention Index</th><th style=\'text-align:center\'>RI Discrepancy</th><th style=\'text-align:center\'>Dot product</th><th style=\'text-align:center\'>Euclidean</th><th style=\'text-align:center\'>Jaccard</th><th style=\'text-align:center\'>Hamming</th><th style=\'text-align:center\'>s12 Gower-Legendre</th><th style=\'text-align:center\'>Spectrum id</th><th style=\'text-align:center\'>Metabolite id</th><th style=\'text-align:center\'>Analyte id</th></tr></tfoot><tbody> <tr><td>1</td><td><a href=\'http://gmd.mpimp-golm.mpg.de/Spectrums/dd5bb721-ce4f-4cec-99ff-de2cb818304d.aspx\' target=\'_blank\'>Glucose (1MEOX) (5TMS) BP [A191001-ambient-na-23]</a></td><td><a href=\'http://gmd.mpimp-golm.mpg.de/Analytes/0a2b3536-2245-4c0e-bdbc-495766eeec67.aspx\' target=\'_blank\'>Glucose (1MEOX) (5TMS) BP</a></td><td>1899.05493</td><td>1.054953</td><td>0.00376573764</td><td>0.00648652157</td><td>0.2849162</td><td>51</td><td>0.404159725</td><td>dd5bb721-ce4f-4cec-99ff-de2cb818304d</td><td><a href=\'http://gmd.mpimp-golm.mpg.de/Metabolites/68513255-fc44-4041-bc4b-4fd2fae7541d.aspx\' target=\'_blank\'>68513255-fc44-4041-bc4b-4fd2fae7541d<'..b'ard__title\'><h1 class=\'mdl-card__title-text\'>What can the table do ?</h1></div><div class=\'mdl-card__supporting-text\'><ul class=\'list-icon mdl-list\'><li class=\'mdl-list__item\'> <span class=\'mdl-list__item-primary-content\'> <i class=\'material-icons mdl-list__item-icon\'>filter_list</i> By default, the spectra numbers (N\xc2\xb0 Spectra) are ordered by ascending values. You can manage your data ordering as you wish. You can even order data according to multiple columns: SHIFT + LEFT CLICK on column headers. This will order by the first column clicked, then the second, etc. You can sort data specifically by clicking on any entry in boxes under each columns. </span></li><li class=\'mdl-list__item\'> <span class=\'mdl-list__item-primary-content\'> <i class=\'material-icons mdl-list__item-icon\'>delete_sweep</i> You can delete multiple entries that are selected: Select wanted entries and click on the button DELETE SELECTED ROWS. </span></li><li class=\'mdl-list__item\'> <span class=\'mdl-list__item-primary-content\'> <i class=\'material-icons mdl-list__item-icon\'>remove_red_eye</i> You have the possibility to toggle columns by clicking on SHOW MORE. </span></li><li class=\'mdl-list__item\'> <span class=\'mdl-list__item-primary-content\'> <i class=\'material-icons mdl-list__item-icon\'>save</i> You can print, copy, or export to excel and csv the table on its actual state, with the three buttons right above the table. </span></li></ul></div></div> </br><div id="large_card" class=\'card-wide mdl-card mdl-shadow--3dp\'> <figure class=\'mdl-card__media\' style=\'background-color: white\'> <img src=\'http://image005.flaticon.com/1/svg/125/125279.svg\' style=\'height: 60px; width: 60px;\'> </figure><div class=\'mdl-card__title\'><h1 class=\'mdl-card__title-text\'>Distances scores</h1></div><div class=\'mdl-card__supporting-text\'><table id="dist_table" style="color: rgba(0,0,0,.87);"><tr><td style="padding-right:10px;><b style="white-space: nowrap;"><b>S12Gower-Legendre Distance</b></td><td> The distance measure S12GowLeg = sqrt(1 - s12) is derived from the S12 coefficient of Gower & Legendre defined as s12 = a / sqrt((a + b)(a + c)), with "a" representing the number of positions at which both spectra are in "on-state" and "b" respectively "c" representing the number of positions at which only the query spectrum or the hit spectrum are in "on-state".</td></tr><tr><td style="padding-right:10px;"><b style="white-space: nowrap;">Hamming Distance</b></td><td> In information theory, the Hamming distance between two strings of equal length is the number of positions for which the corresponding symbols are different. Put another way, it measures the minimum number of substitutions required to change one into the other, or the number of errors that transformed one string into the other.</td></tr><tr><td style="padding-right:10px;"><b style="white-space: nowrap;">Jaccard Distance</b></td><td>Number of matches (a mass with appropriate intensity in both spectra) divided by the sum of matches and mismatches (a mass where only one of both spectra has a intensity). The jaccard distance is a binary distance.</td></tr><tr><td style="padding-right:10px;"><b style="white-space: nowrap;padding-right:60px;">Dotproduct Distance</b></td><td>The Dotproduct distance is summing the multiplied intensities over all matching peaks within both spectra. Here, to satisfy the conditions of a metric I) non-negativity, II) identity of indiscernibles, III) symmetry and IV) subadditivity / triangle inequality, we use 1-Dotproduct. Both spectra are normalised prior to the spectral vector norm in that way, that the absolute value of the squared intensities is equal to 1.</td></tr><tr><td style="padding-right:10px;"><b style="white-space: nowrap;padding-right:60px;">Euclidean Distance</b></td><td>The Euclid is the square root of the sum of the squared differences over all matching peaks.</td></tr></table></div></div></div> </br></br></center> </section> </main></div></body></html>\n \t\t\n \t\n\\ No newline at end of file\n' |
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| diff -r 4dc76dcbd1e7 -r 11779b6402bc test-data/output02.tabular --- a/test-data/output02.tabular Mon Dec 05 08:41:00 2016 -0500 +++ b/test-data/output02.tabular Wed Feb 22 07:37:36 2017 -0500 |
| [ |
| @@ -1,9 +1,9 @@ "Num Spectre" "Analyte Name" "Spectrum Name" "Retention Index" "RI Discrepancy" "DotproductDistance" "EuclideanDistance" "JaccardDistance" "HammingDistance" "s12GowerLegendreDistance" "Spectrum ID" "Metabolite ID" "Analyte ID" -"1" "Glucose (1MEOX) (5TMS) BP" "Glucose (1MEOX) (5TMS) BP [A191001-ambient-na-23]" "1899.05493" "1.054953" "0.00376573764" "0.00648652157" "0.2849162" "51" "0.404159725" "dd5bb721-ce4f-4cec-99ff-de2cb818304d" "68513255-fc44-4041-bc4b-4fd2fae7541d" "0a2b3536-2245-4c0e-bdbc-495766eeec67" -"1" "Idose (1MEOX) (5TMS) BP" "Idose (1MEOX) (5TMS) BP [A191005-ambient-na-1]" "1897.25439" "0.745605469" "0.0041610254" "0.007327365" "0.238709673" "37" "0.367506444" "d00de57d-6fab-49d0-9aee-25e259da9180" "ab025068-f464-4bc6-9c92-994c29387db2" "6f4e926f-d7ef-47b6-a52c-91ff88ca567a" -"1" "Galactose (1MEOX) (5TMS) BP" "Galactose (1MEOX) (5TMS) BP [A191002-ambient-DL--9]" "1902.42212" "4.422119" "0.004838638" "0.007118009" "0.31937173" "61" "0.428936034" "c1226b8e-944e-4d32-ae01-8a9d12465d34" "dd3ea070-54a6-4ea7-b99b-a6e975fdd204" "1c3ad0aa-ee78-4542-93b3-aa9fdf07add1" -"1" "Glucuronic acid-3,6-lactone (1MEOX) (3TMS) MP" "Glucuronic acid-3,6-lactone (1MEOX) (3TMS) MP [A189014-ambient-na-1]" "1893.44385" "4.55619574" "0.048192542" "0.02056068" "0.4473684" "102" "0.5224351" "2b364030-9fa7-4066-b685-52d7946110a6" "00ce759f-d1f9-492e-89f7-b7400a34c72d" "da9d76f5-a2af-4fd1-89e1-c8426ad16980" -"1" "Glucose, U-13C- (1MEOX) (5TMS) BP" "Glucose, U-13C- (1MEOX) (5TMS) BP [A191001-13C-na-2]" "1901.63" "3.63" "0.0682447553" "0.027927408" "0.514285743" "90" "0.586345" "27d4dcdd-d351-4976-8ef9-76a0cc53f631" "441faccb-2631-4e7d-b6ca-99437265ccb8" "96441b61-2891-4e81-93dc-d0fc0ad175d4" -"1" "Allantoin (5TMS)" "Allantoin (5TMS) [A188009-ambient-na-6]" "1896.99829" "1.001709" "0.07800486" "0.02792935" "0.615" "123" "0.6662978" "063fa226-ed62-4d9f-9d5c-ee52c0974e55" "a999f0d6-0285-41d9-a6ba-b705987b663c" "65bb54d2-6bf7-4a53-aa22-8abf71240005" -"1" "Erythrose-4-phosphate (1MEOX) (4TMS) MP" "Erythrose-4-phosphate (1MEOX) (4TMS) MP [A191009-ambient-na-1]" "1895.98438" "2.01558065" "0.0896345749" "0.0207340773" "0.6666667" "278" "0.6522111" "85927200-53a4-492a-ad57-0a7b1d8a6e85" "d4f07f67-d45b-43b6-bd4c-d08708d1a7ad" "2665f816-5c52-45ed-901e-4481cf048257" -"1" "Pyruvic acid, 4-hydroxyphenyl- (1MEOX) (2TMS) MP" "Pyruvic acid, 4-hydroxyphenyl- (1MEOX) (2TMS) MP [A190013-ambient-no-9]" "1902.77417" "4.77417" "0.111977287" "0.0264962576" "0.6551724" "209" "0.673893869" "8bbd7202-8794-4486-8b16-61d8dff4c5bd" "87e988c4-f26c-4e03-9a40-1b0c0b36ca67" "163bf790-e995-46a9-8059-446172ddca0f" +"1" "Glucose (1MEOX) (5TMS) BP" "Glucose (1MEOX) (5TMS) BP [A191001-ambient-na-23]" "1899.05493" "1.054953" "0.003766" "0.006487" "0.284916" "51" "0.404160" "dd5bb721-ce4f-4cec-99ff-de2cb818304d" "68513255-fc44-4041-bc4b-4fd2fae7541d" "0a2b3536-2245-4c0e-bdbc-495766eeec67" +"1" "Idose (1MEOX) (5TMS) BP" "Idose (1MEOX) (5TMS) BP [A191005-ambient-na-1]" "1897.25439" "0.745605469" "0.004161" "0.007327" "0.238710" "37" "0.367506" "d00de57d-6fab-49d0-9aee-25e259da9180" "ab025068-f464-4bc6-9c92-994c29387db2" "6f4e926f-d7ef-47b6-a52c-91ff88ca567a" +"1" "Galactose (1MEOX) (5TMS) BP" "Galactose (1MEOX) (5TMS) BP [A191002-ambient-DL--9]" "1902.42212" "4.422119" "0.004839" "0.007118" "0.319372" "61" "0.428936" "c1226b8e-944e-4d32-ae01-8a9d12465d34" "dd3ea070-54a6-4ea7-b99b-a6e975fdd204" "1c3ad0aa-ee78-4542-93b3-aa9fdf07add1" +"1" "Glucuronic acid-3,6-lactone (1MEOX) (3TMS) MP" "Glucuronic acid-3,6-lactone (1MEOX) (3TMS) MP [A189014-ambient-na-1]" "1893.44385" "4.55619574" "0.048193" "0.020561" "0.447368" "102" "0.522435" "2b364030-9fa7-4066-b685-52d7946110a6" "00ce759f-d1f9-492e-89f7-b7400a34c72d" "da9d76f5-a2af-4fd1-89e1-c8426ad16980" +"1" "Glucose, U-13C- (1MEOX) (5TMS) BP" "Glucose, U-13C- (1MEOX) (5TMS) BP [A191001-13C-na-2]" "1901.63" "3.63" "0.068245" "0.027927" "0.514286" "90" "0.586345" "27d4dcdd-d351-4976-8ef9-76a0cc53f631" "441faccb-2631-4e7d-b6ca-99437265ccb8" "96441b61-2891-4e81-93dc-d0fc0ad175d4" +"1" "Allantoin (5TMS)" "Allantoin (5TMS) [A188009-ambient-na-6]" "1896.99829" "1.001709" "0.078005" "0.027929" "0.615000" "123" "0.666298" "063fa226-ed62-4d9f-9d5c-ee52c0974e55" "a999f0d6-0285-41d9-a6ba-b705987b663c" "65bb54d2-6bf7-4a53-aa22-8abf71240005" +"1" "Erythrose-4-phosphate (1MEOX) (4TMS) MP" "Erythrose-4-phosphate (1MEOX) (4TMS) MP [A191009-ambient-na-1]" "1895.98438" "2.01558065" "0.089635" "0.020734" "0.666667" "278" "0.652211" "85927200-53a4-492a-ad57-0a7b1d8a6e85" "d4f07f67-d45b-43b6-bd4c-d08708d1a7ad" "2665f816-5c52-45ed-901e-4481cf048257" +"1" "Pyruvic acid, 4-hydroxyphenyl- (1MEOX) (2TMS) MP" "Pyruvic acid, 4-hydroxyphenyl- (1MEOX) (2TMS) MP [A190013-ambient-no-9]" "1902.77417" "4.77417" "0.111977" "0.026496" "0.655172" "209" "0.673894" "8bbd7202-8794-4486-8b16-61d8dff4c5bd" "87e988c4-f26c-4e03-9a40-1b0c0b36ca67" "163bf790-e995-46a9-8059-446172ddca0f" |
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| diff -r 4dc76dcbd1e7 -r 11779b6402bc test-data/output02.txt --- a/test-data/output02.txt Mon Dec 05 08:41:00 2016 -0500 +++ b/test-data/output02.txt Wed Feb 22 07:37:36 2017 -0500 |
| [ |
| @@ -1,9 +1,9 @@ Num Spectre Analyte Name Spectrum Name Retention Index RI Discrepancy DotproductDistance EuclideanDistance JaccardDistance HammingDistance s12GowerLegendreDistance Spectrum ID Metabolite ID Analyte ID -1 Glucose (1MEOX) (5TMS) BP Glucose (1MEOX) (5TMS) BP [A191001-ambient-na-23] 1899.05493 1.054953 0.00376573764 0.00648652157 0.2849162 51 0.404159725 dd5bb721-ce4f-4cec-99ff-de2cb818304d 68513255-fc44-4041-bc4b-4fd2fae7541d 0a2b3536-2245-4c0e-bdbc-495766eeec67 -1 Idose (1MEOX) (5TMS) BP Idose (1MEOX) (5TMS) BP [A191005-ambient-na-1] 1897.25439 0.745605469 0.0041610254 0.007327365 0.238709673 37 0.367506444 d00de57d-6fab-49d0-9aee-25e259da9180 ab025068-f464-4bc6-9c92-994c29387db2 6f4e926f-d7ef-47b6-a52c-91ff88ca567a -1 Galactose (1MEOX) (5TMS) BP Galactose (1MEOX) (5TMS) BP [A191002-ambient-DL--9] 1902.42212 4.422119 0.004838638 0.007118009 0.31937173 61 0.428936034 c1226b8e-944e-4d32-ae01-8a9d12465d34 dd3ea070-54a6-4ea7-b99b-a6e975fdd204 1c3ad0aa-ee78-4542-93b3-aa9fdf07add1 -1 Glucuronic acid-3,6-lactone (1MEOX) (3TMS) MP Glucuronic acid-3,6-lactone (1MEOX) (3TMS) MP [A189014-ambient-na-1] 1893.44385 4.55619574 0.048192542 0.02056068 0.4473684 102 0.5224351 2b364030-9fa7-4066-b685-52d7946110a6 00ce759f-d1f9-492e-89f7-b7400a34c72d da9d76f5-a2af-4fd1-89e1-c8426ad16980 -1 Glucose, U-13C- (1MEOX) (5TMS) BP Glucose, U-13C- (1MEOX) (5TMS) BP [A191001-13C-na-2] 1901.63 3.63 0.0682447553 0.027927408 0.514285743 90 0.586345 27d4dcdd-d351-4976-8ef9-76a0cc53f631 441faccb-2631-4e7d-b6ca-99437265ccb8 96441b61-2891-4e81-93dc-d0fc0ad175d4 -1 Allantoin (5TMS) Allantoin (5TMS) [A188009-ambient-na-6] 1896.99829 1.001709 0.07800486 0.02792935 0.615 123 0.6662978 063fa226-ed62-4d9f-9d5c-ee52c0974e55 a999f0d6-0285-41d9-a6ba-b705987b663c 65bb54d2-6bf7-4a53-aa22-8abf71240005 -1 Erythrose-4-phosphate (1MEOX) (4TMS) MP Erythrose-4-phosphate (1MEOX) (4TMS) MP [A191009-ambient-na-1] 1895.98438 2.01558065 0.0896345749 0.0207340773 0.6666667 278 0.6522111 85927200-53a4-492a-ad57-0a7b1d8a6e85 d4f07f67-d45b-43b6-bd4c-d08708d1a7ad 2665f816-5c52-45ed-901e-4481cf048257 -1 Pyruvic acid, 4-hydroxyphenyl- (1MEOX) (2TMS) MP Pyruvic acid, 4-hydroxyphenyl- (1MEOX) (2TMS) MP [A190013-ambient-no-9] 1902.77417 4.77417 0.111977287 0.0264962576 0.6551724 209 0.673893869 8bbd7202-8794-4486-8b16-61d8dff4c5bd 87e988c4-f26c-4e03-9a40-1b0c0b36ca67 163bf790-e995-46a9-8059-446172ddca0f +1 Glucose (1MEOX) (5TMS) BP Glucose (1MEOX) (5TMS) BP [A191001-ambient-na-23] 1899.05493 1.054953 0.003766 0.006487 0.284916 51 0.404160 dd5bb721-ce4f-4cec-99ff-de2cb818304d 68513255-fc44-4041-bc4b-4fd2fae7541d 0a2b3536-2245-4c0e-bdbc-495766eeec67 +1 Idose (1MEOX) (5TMS) BP Idose (1MEOX) (5TMS) BP [A191005-ambient-na-1] 1897.25439 0.745605469 0.004161 0.007327 0.238710 37 0.367506 d00de57d-6fab-49d0-9aee-25e259da9180 ab025068-f464-4bc6-9c92-994c29387db2 6f4e926f-d7ef-47b6-a52c-91ff88ca567a +1 Galactose (1MEOX) (5TMS) BP Galactose (1MEOX) (5TMS) BP [A191002-ambient-DL--9] 1902.42212 4.422119 0.004839 0.007118 0.319372 61 0.428936 c1226b8e-944e-4d32-ae01-8a9d12465d34 dd3ea070-54a6-4ea7-b99b-a6e975fdd204 1c3ad0aa-ee78-4542-93b3-aa9fdf07add1 +1 Glucuronic acid-3,6-lactone (1MEOX) (3TMS) MP Glucuronic acid-3,6-lactone (1MEOX) (3TMS) MP [A189014-ambient-na-1] 1893.44385 4.55619574 0.048193 0.020561 0.447368 102 0.522435 2b364030-9fa7-4066-b685-52d7946110a6 00ce759f-d1f9-492e-89f7-b7400a34c72d da9d76f5-a2af-4fd1-89e1-c8426ad16980 +1 Glucose, U-13C- (1MEOX) (5TMS) BP Glucose, U-13C- (1MEOX) (5TMS) BP [A191001-13C-na-2] 1901.63 3.63 0.068245 0.027927 0.514286 90 0.586345 27d4dcdd-d351-4976-8ef9-76a0cc53f631 441faccb-2631-4e7d-b6ca-99437265ccb8 96441b61-2891-4e81-93dc-d0fc0ad175d4 +1 Allantoin (5TMS) Allantoin (5TMS) [A188009-ambient-na-6] 1896.99829 1.001709 0.078005 0.027929 0.615000 123 0.666298 063fa226-ed62-4d9f-9d5c-ee52c0974e55 a999f0d6-0285-41d9-a6ba-b705987b663c 65bb54d2-6bf7-4a53-aa22-8abf71240005 +1 Erythrose-4-phosphate (1MEOX) (4TMS) MP Erythrose-4-phosphate (1MEOX) (4TMS) MP [A191009-ambient-na-1] 1895.98438 2.01558065 0.089635 0.020734 0.666667 278 0.652211 85927200-53a4-492a-ad57-0a7b1d8a6e85 d4f07f67-d45b-43b6-bd4c-d08708d1a7ad 2665f816-5c52-45ed-901e-4481cf048257 +1 Pyruvic acid, 4-hydroxyphenyl- (1MEOX) (2TMS) MP Pyruvic acid, 4-hydroxyphenyl- (1MEOX) (2TMS) MP [A190013-ambient-no-9] 1902.77417 4.77417 0.111977 0.026496 0.655172 209 0.673894 8bbd7202-8794-4486-8b16-61d8dff4c5bd 87e988c4-f26c-4e03-9a40-1b0c0b36ca67 163bf790-e995-46a9-8059-446172ddca0f |
| b |
| diff -r 4dc76dcbd1e7 -r 11779b6402bc test-data/output03.html --- a/test-data/output03.html Mon Dec 05 08:41:00 2016 -0500 +++ b/test-data/output03.html Wed Feb 22 07:37:36 2017 -0500 |
| [ |
| b'@@ -6,6 +6,6 @@\n $(\'.buttons-copy\').each(function(){$(this).attr("id","mytooltip2");})\n $(\'.buttons-collection\').each(function(){$(this).attr("id","mytooltip3");})\n for(var i=0;i<12;i++){$($($("table.display.stripe.dataTable")[2]).find("th")[i]).css(\'width\',$($($("table.display.stripe.dataTable")[0]).find("th")[i]).css(\'width\'));}});$(document).on(\'click\',\'.ripple\',function(e){var $rippleElement=$(\'<span class="ripple-effect" />\'),$buttonElement=$(this),btnOffset=$buttonElement.offset(),xPos=e.pageX-btnOffset.left,yPos=e.pageY-btnOffset.top,size=parseInt(Math.min($buttonElement.height(),$buttonElement.width())*0.5),animateSize=parseInt(Math.max($buttonElement.width(),$buttonElement.height())*Math.PI);$rippleElement.css({top:yPos,left:xPos,width:size,height:size,backgroundColor:$buttonElement.data("ripple-color")}).appendTo($buttonElement).animate({width:animateSize,height:animateSize,opacity:0},700,function(){$(this).remove();});});\n-</script><title>Golm Search Results</title></head><body><div class=\'mdl-layout mdl-js-layout mdl-layout--fixed-header\'> <header class=\'mdl-layout__header\'><div class=\'mdl-layout__header-row\'> <span class=\'mdl-layout-title\'><h3><b>Visualization of Golm Database Results</b></h3></span></div><div class=\'mdl-layout__tab-bar mdl-js-ripple-effect\'> <a href=\'#fixed-tab-1\' class=\'mdl-layout__tab is-active\'><b>Table</b></a> <a href=\'#fixed-tab-2\' class=\'mdl-layout__tab\'><b>Help</b></a></div> </header> <main class=\'mdl-layout__content\'> <section class=\'mdl-layout__tab-panel is-active\' id=\'fixed-tab-1\'><div class=\'page-content\'><table id=\'table_id\' class=\'display stripe\' cellspacing=\'0\' width=\'100%\' ><thead><tr><th colspan=\'1\'></th><th colspan=\'2\' style=\'text-align:center\'>NAMES</th><th colspan=\'2\' style=\'text-align:center\'>RETENTION INFOS</th><th colspan=\'5\' style=\'text-align:center\'>DISTANCE SCORES</th><th colspan=\'3\' style=\'text-align:center\'>IDs</th></tr><tr><th style=\'text-align:center;border-left: 1px solid #A7A7A7;\'>N\xc2\xb0 Spectres</th><th style=\'text-align:center;border-left: 1px solid #A7A7A7;\'>Spectrum</th><th style=\'text-align:center;border-right: 1px solid #A7A7A7;\'>Analyte</th><th style=\'text-align:center\'>Retention Index</th><th style=\'text-align:center;border-right: 1px solid #A7A7A7;\'>RI Discrepancy</th><th style=\'text-align:center\'>Dot product</th><th style=\'text-align:center\'>Euclidean</th><th style=\'text-align:center\'>Jaccard</th><th style=\'text-align:center\'>Hamming</th><th style=\'text-align:center;border-right: 1px solid #A7A7A7;\'>s12 Gower-Legendre</th><th style=\'text-align:center\'>Spectrum id</th><th style=\'text-align:center\'>Metabolite id</th><th style=\'text-align:center;border-right: 1px solid #A7A7A7;\'>Analyte id</th></tr></thead><tfoot><tr><th style=\'text-align:center\'>N\xc2\xb0 Spectre</th><th style=\'text-align:center\'>Spectrum</th><th style=\'text-align:center\'>Analyte</th><th style=\'text-align:center\'>Retention Index</th><th style=\'text-align:center\'>RI Discrepancy</th><th style=\'text-align:center\'>Dot product</th><th style=\'text-align:center\'>Euclidean</th><th style=\'text-align:center\'>Jaccard</th><th style=\'text-align:center\'>Hamming</th><th style=\'text-align:center\'>s12 Gower-Legendre</th><th style=\'text-align:center\'>Spectrum id</th><th style=\'text-align:center\'>Metabolite id</th><th style=\'text-align:center\'>Analyte id</th></tr></tfoot><tbody> <tr><td>1</td><td><a href=\'http://gmd.mpimp-golm.mpg.de/Spectrums/1b34c722-1fd3-4d61-a48b-da2614f96e23.aspx\' target=\'_blank\'>Erythrose-4-phosphate (1MEOX) (4TMS) MP [A191009-ambient-na-5]</a></td><td><a href=\'http://gmd.mpimp-golm.mpg.de/Analytes/2665f816-5c52-45ed-901e-4481cf048257.aspx\' target=\'_blank\'>Erythrose-4-phosphate (1MEOX) (4TMS) MP</a></td><td>1895.98438</td><td>2.01558065</td><td>0.417125851</td><td>0.047484044</td><td>0.6108108</td><td>226</td><td>0.628439844</td><td>1b34c722-1fd3-4d61-a48b-da2614f96e23</td><td><a href=\'http://gmd.mpimp-golm.mpg.de/Metabolites/d4f07f67-d45b-43b6-bd4c-d08708d1a7ad.aspx\' target=\'_blank\'>d4f07f67-d4'..b'ard__title\'><h1 class=\'mdl-card__title-text\'>What can the table do ?</h1></div><div class=\'mdl-card__supporting-text\'><ul class=\'list-icon mdl-list\'><li class=\'mdl-list__item\'> <span class=\'mdl-list__item-primary-content\'> <i class=\'material-icons mdl-list__item-icon\'>filter_list</i> By default, the spectra numbers (N\xc2\xb0 Spectra) are ordered by ascending values. You can manage your data ordering as you wish. You can even order data according to multiple columns: SHIFT + LEFT CLICK on column headers. This will order by the first column clicked, then the second, etc. You can sort data specifically by clicking on any entry in boxes under each columns. </span></li><li class=\'mdl-list__item\'> <span class=\'mdl-list__item-primary-content\'> <i class=\'material-icons mdl-list__item-icon\'>delete_sweep</i> You can delete multiple entries that are selected: Select wanted entries and click on the button DELETE SELECTED ROWS. </span></li><li class=\'mdl-list__item\'> <span class=\'mdl-list__item-primary-content\'> <i class=\'material-icons mdl-list__item-icon\'>remove_red_eye</i> You have the possibility to toggle columns by clicking on SHOW MORE. </span></li><li class=\'mdl-list__item\'> <span class=\'mdl-list__item-primary-content\'> <i class=\'material-icons mdl-list__item-icon\'>save</i> You can print, copy, or export to excel and csv the table on its actual state, with the three buttons right above the table. </span></li></ul></div></div> </br><div id="large_card" class=\'card-wide mdl-card mdl-shadow--3dp\'> <figure class=\'mdl-card__media\' style=\'background-color: white\'> <img src=\'http://image005.flaticon.com/1/svg/125/125279.svg\' style=\'height: 60px; width: 60px;\'> </figure><div class=\'mdl-card__title\'><h1 class=\'mdl-card__title-text\'>Distances scores</h1></div><div class=\'mdl-card__supporting-text\'><table id="dist_table" style="color: rgba(0,0,0,.87);"><tr><td style="padding-right:10px;><b style="white-space: nowrap;"><b>S12Gower-Legendre Distance</b></td><td> The distance measure S12GowLeg = sqrt(1 - s12) is derived from the S12 coefficient of Gower & Legendre defined as s12 = a / sqrt((a + b)(a + c)), with "a" representing the number of positions at which both spectra are in "on-state" and "b" respectively "c" representing the number of positions at which only the query spectrum or the hit spectrum are in "on-state".</td></tr><tr><td style="padding-right:10px;"><b style="white-space: nowrap;">Hamming Distance</b></td><td> In information theory, the Hamming distance between two strings of equal length is the number of positions for which the corresponding symbols are different. Put another way, it measures the minimum number of substitutions required to change one into the other, or the number of errors that transformed one string into the other.</td></tr><tr><td style="padding-right:10px;"><b style="white-space: nowrap;">Jaccard Distance</b></td><td>Number of matches (a mass with appropriate intensity in both spectra) divided by the sum of matches and mismatches (a mass where only one of both spectra has a intensity). The jaccard distance is a binary distance.</td></tr><tr><td style="padding-right:10px;"><b style="white-space: nowrap;padding-right:60px;">Dotproduct Distance</b></td><td>The Dotproduct distance is summing the multiplied intensities over all matching peaks within both spectra. Here, to satisfy the conditions of a metric I) non-negativity, II) identity of indiscernibles, III) symmetry and IV) subadditivity / triangle inequality, we use 1-Dotproduct. Both spectra are normalised prior to the spectral vector norm in that way, that the absolute value of the squared intensities is equal to 1.</td></tr><tr><td style="padding-right:10px;"><b style="white-space: nowrap;padding-right:60px;">Euclidean Distance</b></td><td>The Euclid is the square root of the sum of the squared differences over all matching peaks.</td></tr></table></div></div></div> </br></br></center> </section> </main></div></body></html>\n \t\t\n \t\n\\ No newline at end of file\n' |
| b |
| diff -r 4dc76dcbd1e7 -r 11779b6402bc test-data/output03.tabular --- a/test-data/output03.tabular Mon Dec 05 08:41:00 2016 -0500 +++ b/test-data/output03.tabular Wed Feb 22 07:37:36 2017 -0500 |
| [ |
| b'@@ -1,123 +1,123 @@\n "Num Spectre"\t"Analyte Name"\t"Spectrum Name"\t"Retention Index"\t"RI Discrepancy"\t"DotproductDistance"\t"EuclideanDistance"\t"JaccardDistance"\t"HammingDistance"\t"s12GowerLegendreDistance"\t"Spectrum ID"\t"Metabolite ID"\t"Analyte ID"\n-"1"\t"Erythrose-4-phosphate (1MEOX) (4TMS) MP"\t"Erythrose-4-phosphate (1MEOX) (4TMS) MP [A191009-ambient-na-5]"\t"1895.98438"\t"2.01558065"\t"0.417125851"\t"0.047484044"\t"0.6108108"\t"226"\t"0.628439844"\t"1b34c722-1fd3-4d61-a48b-da2614f96e23"\t"d4f07f67-d45b-43b6-bd4c-d08708d1a7ad"\t"2665f816-5c52-45ed-901e-4481cf048257"\n-"2"\t"Glucose (1MEOX) (5TMS) BP"\t"Glucose (1MEOX) (5TMS) BP [A191001-ambient-na-2]"\t"1899.05493"\t"1.054953"\t"0.4496568"\t"0.07338332"\t"0.7784431"\t"130"\t"0.796108663"\t"34a5b91e-e473-4ed6-9a40-067e0cd944f9"\t"68513255-fc44-4041-bc4b-4fd2fae7541d"\t"0a2b3536-2245-4c0e-bdbc-495766eeec67"\n-"2"\t"Galactose (1MEOX) (5TMS) BP"\t"Galactose (1MEOX) (5TMS) BP [A191002-ambient-DL--8]"\t"1902.42212"\t"4.422119"\t"0.4884424"\t"0.0594931729"\t"0.75"\t"207"\t"0.7356502"\t"9c570b75-fe0c-43b8-9311-7b8af17dd55b"\t"dd3ea070-54a6-4ea7-b99b-a6e975fdd204"\t"1c3ad0aa-ee78-4542-93b3-aa9fdf07add1"\n-"3"\t"Galactose (1MEOX) (5TMS) BP"\t"Galactose (1MEOX) (5TMS) BP [A191002-ambient-DL--2]"\t"1902.42212"\t"4.422119"\t"0.38635543"\t"0.0406771079"\t"0.8201285"\t"383"\t"0.7784506"\t"0bfc9541-70d5-4d50-89c4-351a87971133"\t"dd3ea070-54a6-4ea7-b99b-a6e975fdd204"\t"1c3ad0aa-ee78-4542-93b3-aa9fdf07add1"\n-"3"\t"Glucose (1MEOX) (5TMS) BP"\t"Glucose (1MEOX) (5TMS) BP [A191001-ambient-na-2]"\t"1899.05493"\t"1.054953"\t"0.397179246"\t"0.06756685"\t"0.75287354"\t"131"\t"0.776361"\t"34a5b91e-e473-4ed6-9a40-067e0cd944f9"\t"68513255-fc44-4041-bc4b-4fd2fae7541d"\t"0a2b3536-2245-4c0e-bdbc-495766eeec67"\n-"3"\t"Idose (1MEOX) (5TMS) BP"\t"Idose (1MEOX) (5TMS) BP [A191005-ambient-na-1]"\t"1897.25439"\t"0.745605469"\t"0.432195932"\t"0.07130679"\t"0.629411757"\t"107"\t"0.6740747"\t"d00de57d-6fab-49d0-9aee-25e259da9180"\t"ab025068-f464-4bc6-9c92-994c29387db2"\t"6f4e926f-d7ef-47b6-a52c-91ff88ca567a"\n-"3"\t"Glucose, U-13C- (1MEOX) (5TMS) BP"\t"Glucose, U-13C- (1MEOX) (5TMS) BP [A191001-13C-na-10]"\t"1901.63"\t"3.63"\t"0.442519277"\t"0.050286"\t"0.76"\t"266"\t"0.7361843"\t"0d5164ce-be48-454d-979b-ed8b92e32c1d"\t"441faccb-2631-4e7d-b6ca-99437265ccb8"\t"96441b61-2891-4e81-93dc-d0fc0ad175d4"\n-"3"\t"Propanoic acid, 3-amino-3-(4-hydroxyphenyl)- (3TMS)"\t"Propanoic acid, 3-amino-3-(4-hydroxyphenyl)- (3TMS) [A189024-ambient-na-2]"\t"1897.83862"\t"0.161383286"\t"0.444237381"\t"0.04988712"\t"0.717086852"\t"256"\t"0.6841814"\t"c1d0193b-0442-41fe-aab0-fc2438624170"\t"151fe4e1-8ae4-43fc-aa1f-cf6e2a62b7ff"\t"471f9ab0-1cf5-40d3-ba88-edc2458d3242"\n-"3"\t"Pyruvic acid, 4-hydroxyphenyl- (1MEOX) (2TMS) MP"\t"Pyruvic acid, 4-hydroxyphenyl- (1MEOX) (2TMS) MP [A190013-ambient-no-1]"\t"1902.77417"\t"4.77417"\t"0.4479848"\t"0.0491427779"\t"0.7304582"\t"271"\t"0.6947696"\t"7508f46a-70b0-43eb-b5b6-0421ff41c0e8"\t"87e988c4-f26c-4e03-9a40-1b0c0b36ca67"\t"163bf790-e995-46a9-8059-446172ddca0f"\n-"3"\t"Glucuronic acid-3,6-lactone (1MEOX) (3TMS) MP"\t"Glucuronic acid-3,6-lactone (1MEOX) (3TMS) MP [A189014-ambient-na-1]"\t"1893.44385"\t"4.55619574"\t"0.452163756"\t"0.06325701"\t"0.6106195"\t"138"\t"0.63247633"\t"2b364030-9fa7-4066-b685-52d7946110a6"\t"00ce759f-d1f9-492e-89f7-b7400a34c72d"\t"da9d76f5-a2af-4fd1-89e1-c8426ad16980"\n-"3"\t"Glucose, 2-amino-2-deoxy- (5TMS) MP"\t"Glucose, 2-amino-2-deoxy- (5TMS) MP [A193015-ambient-DL--3]"\t"1899.495"\t"1.49494946"\t"0.474485427"\t"0.0493914336"\t"0.7429306"\t"289"\t"0.7034532"\t"754097ce-c7df-40cb-bec1-ba8b0fad83f8"\t"2b4d44b2-d5ac-4da4-9be6-a4ae9574e4a6"\t"539fe164-0ea9-4509-bf37-fc9bc8073646"\n-"4"\t"Glucuronic acid-3,6-lactone (1MEOX) (3TMS) MP"\t"Glucuronic acid-3,6-lactone (1MEOX) (3TMS) MP [A189014-ambient-na-1]"\t"1893.44385"\t"4.55619574"\t"0.40254572"\t"0.05791846"\t"0.445833325"\t"107"\t"0.528728"\t"2b364030-9fa7-4066-b685-52d7946110a6"\t"00ce759f-d1f9-492e-89f7-b7400a34c72d"\t"da9d76f5-a2af-4fd1-89e1-c8426ad16980"\n-"4"\t"Galactose (1MEOX) (5TMS) BP"\t"Galactose (1MEOX) (5TMS) BP [A191002-ambient-DL--2]"\t"1902.42212"\t"4.422119"\t"0.40'..b'esults"\t""\t""\t""\t""\t""\t""\t""\t""\t""\t""\n-"228"\t"Glucuronic acid-3,6-lactone (1MEOX) (3TMS) MP"\t"Glucuronic acid-3,6-lactone (1MEOX) (3TMS) MP [A189014-ambient-na-2]"\t"1893.44385"\t"4.55619574"\t"0.49236843"\t"0.0423520021"\t"0.5974499"\t"328"\t"0.6059947"\t"8bf796f1-f7cf-4df5-afbc-979b0d95a383"\t"00ce759f-d1f9-492e-89f7-b7400a34c72d"\t"da9d76f5-a2af-4fd1-89e1-c8426ad16980"\n+"228"\t"Glucuronic acid-3,6-lactone (1MEOX) (3TMS) MP"\t"Glucuronic acid-3,6-lactone (1MEOX) (3TMS) MP [A189014-ambient-na-2]"\t"1893.44385"\t"4.55619574"\t"0.492368"\t"0.042352"\t"0.597450"\t"328"\t"0.605995"\t"8bf796f1-f7cf-4df5-afbc-979b0d95a383"\t"00ce759f-d1f9-492e-89f7-b7400a34c72d"\t"da9d76f5-a2af-4fd1-89e1-c8426ad16980"\n "229"\t""\t"no results"\t""\t""\t""\t""\t""\t""\t""\t""\t""\t""\n "230"\t""\t"no results"\t""\t""\t""\t""\t""\t""\t""\t""\t""\t""\n-"231"\t"Glucose (1MEOX) (5TMS) BP"\t"Glucose (1MEOX) (5TMS) BP [A191001-ambient-na-24]"\t"1899.05493"\t"1.054953"\t"0.191139191"\t"0.0709223449"\t"0.8947368"\t"68"\t"0.878837764"\t"d87f501a-9d45-4244-9461-f8dd1943930e"\t"68513255-fc44-4041-bc4b-4fd2fae7541d"\t"0a2b3536-2245-4c0e-bdbc-495766eeec67"\n-"231"\t"Glucose, U-13C- (1MEOX) (5TMS) BP"\t"Glucose, U-13C- (1MEOX) (5TMS) BP [A191001-13C-na-2]"\t"1901.63"\t"3.63"\t"0.193600208"\t"0.0558800921"\t"0.887096763"\t"110"\t"0.8399839"\t"27d4dcdd-d351-4976-8ef9-76a0cc53f631"\t"441faccb-2631-4e7d-b6ca-99437265ccb8"\t"96441b61-2891-4e81-93dc-d0fc0ad175d4"\n-"231"\t"Galactose (1MEOX) (5TMS) BP"\t"Galactose (1MEOX) (5TMS) BP [A191002-ambient-DL--10]"\t"1902.42212"\t"4.422119"\t"0.216909975"\t"0.06141944"\t"0.8869565"\t"102"\t"0.845184863"\t"314b38dc-9bfb-4a7f-aaaa-bd80ef4ec82d"\t"dd3ea070-54a6-4ea7-b99b-a6e975fdd204"\t"1c3ad0aa-ee78-4542-93b3-aa9fdf07add1"\n-"231"\t"Allantoin (5TMS)"\t"Allantoin (5TMS) [A188009-ambient-na-2]"\t"1896.99829"\t"1.001709"\t"0.242943108"\t"0.08852613"\t"0.887096763"\t"55"\t"0.8791416"\t"bb9eafcc-28ff-4a63-8786-2e5e1053b337"\t"a999f0d6-0285-41d9-a6ba-b705987b663c"\t"65bb54d2-6bf7-4a53-aa22-8abf71240005"\n+"231"\t"Glucose (1MEOX) (5TMS) BP"\t"Glucose (1MEOX) (5TMS) BP [A191001-ambient-na-24]"\t"1899.05493"\t"1.054953"\t"0.191139"\t"0.070922"\t"0.894737"\t"68"\t"0.878838"\t"d87f501a-9d45-4244-9461-f8dd1943930e"\t"68513255-fc44-4041-bc4b-4fd2fae7541d"\t"0a2b3536-2245-4c0e-bdbc-495766eeec67"\n+"231"\t"Glucose, U-13C- (1MEOX) (5TMS) BP"\t"Glucose, U-13C- (1MEOX) (5TMS) BP [A191001-13C-na-2]"\t"1901.63"\t"3.63"\t"0.193600"\t"0.055880"\t"0.887097"\t"110"\t"0.839984"\t"27d4dcdd-d351-4976-8ef9-76a0cc53f631"\t"441faccb-2631-4e7d-b6ca-99437265ccb8"\t"96441b61-2891-4e81-93dc-d0fc0ad175d4"\n+"231"\t"Galactose (1MEOX) (5TMS) BP"\t"Galactose (1MEOX) (5TMS) BP [A191002-ambient-DL--10]"\t"1902.42212"\t"4.422119"\t"0.216910"\t"0.061419"\t"0.886957"\t"102"\t"0.845185"\t"314b38dc-9bfb-4a7f-aaaa-bd80ef4ec82d"\t"dd3ea070-54a6-4ea7-b99b-a6e975fdd204"\t"1c3ad0aa-ee78-4542-93b3-aa9fdf07add1"\n+"231"\t"Allantoin (5TMS)"\t"Allantoin (5TMS) [A188009-ambient-na-2]"\t"1896.99829"\t"1.001709"\t"0.242943"\t"0.088526"\t"0.887097"\t"55"\t"0.879142"\t"bb9eafcc-28ff-4a63-8786-2e5e1053b337"\t"a999f0d6-0285-41d9-a6ba-b705987b663c"\t"65bb54d2-6bf7-4a53-aa22-8abf71240005"\n "232"\t""\t"no results"\t""\t""\t""\t""\t""\t""\t""\t""\t""\t""\n "233"\t""\t"no results"\t""\t""\t""\t""\t""\t""\t""\t""\t""\t""\n "234"\t""\t"no results"\t""\t""\t""\t""\t""\t""\t""\t""\t""\t""\n@@ -383,7 +383,7 @@\n "245"\t""\t"no results"\t""\t""\t""\t""\t""\t""\t""\t""\t""\t""\n "246"\t""\t"no results"\t""\t""\t""\t""\t""\t""\t""\t""\t""\t""\n "247"\t""\t"no results"\t""\t""\t""\t""\t""\t""\t""\t""\t""\t""\n-"248"\t"Nonadecane"\t"Nonadecane [A190001-ambient-n--1]"\t"1900"\t"2"\t"0.05944854"\t"0.04527639"\t"0.7586207"\t"44"\t"0.7132295"\t"44b956d8-a487-4269-baee-49e6ba5658c3"\t"5dff1f48-853a-4ce2-852c-81c871ef1da6"\t"5dff1f48-853a-4ce2-852c-81c871ef1da6"\n+"248"\t"Nonadecane"\t"Nonadecane [A190001-ambient-n--1]"\t"1900"\t"2"\t"0.059449"\t"0.045276"\t"0.758621"\t"44"\t"0.713229"\t"44b956d8-a487-4269-baee-49e6ba5658c3"\t"5dff1f48-853a-4ce2-852c-81c871ef1da6"\t"5dff1f48-853a-4ce2-852c-81c871ef1da6"\n "249"\t""\t"no results"\t""\t""\t""\t""\t""\t""\t""\t""\t""\t""\n "250"\t""\t"no results"\t""\t""\t""\t""\t""\t""\t""\t""\t""\t""\n "251"\t""\t"no results"\t""\t""\t""\t""\t""\t""\t""\t""\t""\t""\n' |
| b |
| diff -r 4dc76dcbd1e7 -r 11779b6402bc test-data/output03.txt --- a/test-data/output03.txt Mon Dec 05 08:41:00 2016 -0500 +++ b/test-data/output03.txt Wed Feb 22 07:37:36 2017 -0500 |
| [ |
| b'@@ -1,123 +1,123 @@\n Num Spectre\tAnalyte Name\tSpectrum Name\tRetention Index\tRI Discrepancy\tDotproductDistance\tEuclideanDistance\tJaccardDistance\tHammingDistance\ts12GowerLegendreDistance\tSpectrum ID\tMetabolite ID\tAnalyte ID\n-1\tErythrose-4-phosphate (1MEOX) (4TMS) MP\tErythrose-4-phosphate (1MEOX) (4TMS) MP [A191009-ambient-na-5]\t1895.98438\t2.01558065\t0.417125851\t0.047484044\t0.6108108\t226\t0.628439844\t1b34c722-1fd3-4d61-a48b-da2614f96e23\td4f07f67-d45b-43b6-bd4c-d08708d1a7ad\t2665f816-5c52-45ed-901e-4481cf048257\n-2\tGlucose (1MEOX) (5TMS) BP\tGlucose (1MEOX) (5TMS) BP [A191001-ambient-na-2]\t1899.05493\t1.054953\t0.4496568\t0.07338332\t0.7784431\t130\t0.796108663\t34a5b91e-e473-4ed6-9a40-067e0cd944f9\t68513255-fc44-4041-bc4b-4fd2fae7541d\t0a2b3536-2245-4c0e-bdbc-495766eeec67\n-2\tGalactose (1MEOX) (5TMS) BP\tGalactose (1MEOX) (5TMS) BP [A191002-ambient-DL--8]\t1902.42212\t4.422119\t0.4884424\t0.0594931729\t0.75\t207\t0.7356502\t9c570b75-fe0c-43b8-9311-7b8af17dd55b\tdd3ea070-54a6-4ea7-b99b-a6e975fdd204\t1c3ad0aa-ee78-4542-93b3-aa9fdf07add1\n-3\tGalactose (1MEOX) (5TMS) BP\tGalactose (1MEOX) (5TMS) BP [A191002-ambient-DL--2]\t1902.42212\t4.422119\t0.38635543\t0.0406771079\t0.8201285\t383\t0.7784506\t0bfc9541-70d5-4d50-89c4-351a87971133\tdd3ea070-54a6-4ea7-b99b-a6e975fdd204\t1c3ad0aa-ee78-4542-93b3-aa9fdf07add1\n-3\tGlucose (1MEOX) (5TMS) BP\tGlucose (1MEOX) (5TMS) BP [A191001-ambient-na-2]\t1899.05493\t1.054953\t0.397179246\t0.06756685\t0.75287354\t131\t0.776361\t34a5b91e-e473-4ed6-9a40-067e0cd944f9\t68513255-fc44-4041-bc4b-4fd2fae7541d\t0a2b3536-2245-4c0e-bdbc-495766eeec67\n-3\tIdose (1MEOX) (5TMS) BP\tIdose (1MEOX) (5TMS) BP [A191005-ambient-na-1]\t1897.25439\t0.745605469\t0.432195932\t0.07130679\t0.629411757\t107\t0.6740747\td00de57d-6fab-49d0-9aee-25e259da9180\tab025068-f464-4bc6-9c92-994c29387db2\t6f4e926f-d7ef-47b6-a52c-91ff88ca567a\n-3\tGlucose, U-13C- (1MEOX) (5TMS) BP\tGlucose, U-13C- (1MEOX) (5TMS) BP [A191001-13C-na-10]\t1901.63\t3.63\t0.442519277\t0.050286\t0.76\t266\t0.7361843\t0d5164ce-be48-454d-979b-ed8b92e32c1d\t441faccb-2631-4e7d-b6ca-99437265ccb8\t96441b61-2891-4e81-93dc-d0fc0ad175d4\n-3\tPropanoic acid, 3-amino-3-(4-hydroxyphenyl)- (3TMS)\tPropanoic acid, 3-amino-3-(4-hydroxyphenyl)- (3TMS) [A189024-ambient-na-2]\t1897.83862\t0.161383286\t0.444237381\t0.04988712\t0.717086852\t256\t0.6841814\tc1d0193b-0442-41fe-aab0-fc2438624170\t151fe4e1-8ae4-43fc-aa1f-cf6e2a62b7ff\t471f9ab0-1cf5-40d3-ba88-edc2458d3242\n-3\tPyruvic acid, 4-hydroxyphenyl- (1MEOX) (2TMS) MP\tPyruvic acid, 4-hydroxyphenyl- (1MEOX) (2TMS) MP [A190013-ambient-no-1]\t1902.77417\t4.77417\t0.4479848\t0.0491427779\t0.7304582\t271\t0.6947696\t7508f46a-70b0-43eb-b5b6-0421ff41c0e8\t87e988c4-f26c-4e03-9a40-1b0c0b36ca67\t163bf790-e995-46a9-8059-446172ddca0f\n-3\tGlucuronic acid-3,6-lactone (1MEOX) (3TMS) MP\tGlucuronic acid-3,6-lactone (1MEOX) (3TMS) MP [A189014-ambient-na-1]\t1893.44385\t4.55619574\t0.452163756\t0.06325701\t0.6106195\t138\t0.63247633\t2b364030-9fa7-4066-b685-52d7946110a6\t00ce759f-d1f9-492e-89f7-b7400a34c72d\tda9d76f5-a2af-4fd1-89e1-c8426ad16980\n-3\tGlucose, 2-amino-2-deoxy- (5TMS) MP\tGlucose, 2-amino-2-deoxy- (5TMS) MP [A193015-ambient-DL--3]\t1899.495\t1.49494946\t0.474485427\t0.0493914336\t0.7429306\t289\t0.7034532\t754097ce-c7df-40cb-bec1-ba8b0fad83f8\t2b4d44b2-d5ac-4da4-9be6-a4ae9574e4a6\t539fe164-0ea9-4509-bf37-fc9bc8073646\n-4\tGlucuronic acid-3,6-lactone (1MEOX) (3TMS) MP\tGlucuronic acid-3,6-lactone (1MEOX) (3TMS) MP [A189014-ambient-na-1]\t1893.44385\t4.55619574\t0.40254572\t0.05791846\t0.445833325\t107\t0.528728\t2b364030-9fa7-4066-b685-52d7946110a6\t00ce759f-d1f9-492e-89f7-b7400a34c72d\tda9d76f5-a2af-4fd1-89e1-c8426ad16980\n-4\tGalactose (1MEOX) (5TMS) BP\tGalactose (1MEOX) (5TMS) BP [A191002-ambient-DL--2]\t1902.42212\t4.422119\t0.403359115\t0.0413857177\t0.7048832\t332\t0.694246054\t0bfc9541-70d5-4d50-89c4-351a87971133\tdd3ea070-54a6-4ea7-b99b-a6e975fdd204\t1c3ad0aa-ee78-4542-93b3-aa9fdf07add1\n-4\tGlucose (1MEOX) (5TMS) BP\tGlucose (1MEOX) (5TMS) BP [A191001-ambient-na-12]\t1899.05493\t1.054953\t0.410697162\t0.06408566\t0.56\t112\t0.6205492\t833ab58c-a8fa-4389-8b42-95e618cafb91\t68513255-fc44'..b'4d44b2-d5ac-4da4-9be6-a4ae9574e4a6\t539fe164-0ea9-4509-bf37-fc9bc8073646\n+226\tGlucose, U-13C- (1MEOX) (5TMS) BP\tGlucose, U-13C- (1MEOX) (5TMS) BP [A191001-13C-na-7]\t1901.63\t3.63\t0.453271\t0.062110\t0.761702\t179\t0.738404\t6c360eba-d726-44d9-a666-d0695d8448cf\t441faccb-2631-4e7d-b6ca-99437265ccb8\t96441b61-2891-4e81-93dc-d0fc0ad175d4\n+226\tErythrose-4-phosphate (1MEOX) (4TMS) MP\tErythrose-4-phosphate (1MEOX) (4TMS) MP [A191009-ambient-na-5]\t1895.98438\t2.01558065\t0.483826\t0.050798\t0.461333\t173\t0.530144\t1b34c722-1fd3-4d61-a48b-da2614f96e23\td4f07f67-d45b-43b6-bd4c-d08708d1a7ad\t2665f816-5c52-45ed-901e-4481cf048257\n 227\t\tno results\t\t\t\t\t\t\t\t\t\t\n-228\tGlucuronic acid-3,6-lactone (1MEOX) (3TMS) MP\tGlucuronic acid-3,6-lactone (1MEOX) (3TMS) MP [A189014-ambient-na-2]\t1893.44385\t4.55619574\t0.49236843\t0.0423520021\t0.5974499\t328\t0.6059947\t8bf796f1-f7cf-4df5-afbc-979b0d95a383\t00ce759f-d1f9-492e-89f7-b7400a34c72d\tda9d76f5-a2af-4fd1-89e1-c8426ad16980\n+228\tGlucuronic acid-3,6-lactone (1MEOX) (3TMS) MP\tGlucuronic acid-3,6-lactone (1MEOX) (3TMS) MP [A189014-ambient-na-2]\t1893.44385\t4.55619574\t0.492368\t0.042352\t0.597450\t328\t0.605995\t8bf796f1-f7cf-4df5-afbc-979b0d95a383\t00ce759f-d1f9-492e-89f7-b7400a34c72d\tda9d76f5-a2af-4fd1-89e1-c8426ad16980\n 229\t\tno results\t\t\t\t\t\t\t\t\t\t\n 230\t\tno results\t\t\t\t\t\t\t\t\t\t\n-231\tGlucose (1MEOX) (5TMS) BP\tGlucose (1MEOX) (5TMS) BP [A191001-ambient-na-24]\t1899.05493\t1.054953\t0.191139191\t0.0709223449\t0.8947368\t68\t0.878837764\td87f501a-9d45-4244-9461-f8dd1943930e\t68513255-fc44-4041-bc4b-4fd2fae7541d\t0a2b3536-2245-4c0e-bdbc-495766eeec67\n-231\tGlucose, U-13C- (1MEOX) (5TMS) BP\tGlucose, U-13C- (1MEOX) (5TMS) BP [A191001-13C-na-2]\t1901.63\t3.63\t0.193600208\t0.0558800921\t0.887096763\t110\t0.8399839\t27d4dcdd-d351-4976-8ef9-76a0cc53f631\t441faccb-2631-4e7d-b6ca-99437265ccb8\t96441b61-2891-4e81-93dc-d0fc0ad175d4\n-231\tGalactose (1MEOX) (5TMS) BP\tGalactose (1MEOX) (5TMS) BP [A191002-ambient-DL--10]\t1902.42212\t4.422119\t0.216909975\t0.06141944\t0.8869565\t102\t0.845184863\t314b38dc-9bfb-4a7f-aaaa-bd80ef4ec82d\tdd3ea070-54a6-4ea7-b99b-a6e975fdd204\t1c3ad0aa-ee78-4542-93b3-aa9fdf07add1\n-231\tAllantoin (5TMS)\tAllantoin (5TMS) [A188009-ambient-na-2]\t1896.99829\t1.001709\t0.242943108\t0.08852613\t0.887096763\t55\t0.8791416\tbb9eafcc-28ff-4a63-8786-2e5e1053b337\ta999f0d6-0285-41d9-a6ba-b705987b663c\t65bb54d2-6bf7-4a53-aa22-8abf71240005\n+231\tGlucose (1MEOX) (5TMS) BP\tGlucose (1MEOX) (5TMS) BP [A191001-ambient-na-24]\t1899.05493\t1.054953\t0.191139\t0.070922\t0.894737\t68\t0.878838\td87f501a-9d45-4244-9461-f8dd1943930e\t68513255-fc44-4041-bc4b-4fd2fae7541d\t0a2b3536-2245-4c0e-bdbc-495766eeec67\n+231\tGlucose, U-13C- (1MEOX) (5TMS) BP\tGlucose, U-13C- (1MEOX) (5TMS) BP [A191001-13C-na-2]\t1901.63\t3.63\t0.193600\t0.055880\t0.887097\t110\t0.839984\t27d4dcdd-d351-4976-8ef9-76a0cc53f631\t441faccb-2631-4e7d-b6ca-99437265ccb8\t96441b61-2891-4e81-93dc-d0fc0ad175d4\n+231\tGalactose (1MEOX) (5TMS) BP\tGalactose (1MEOX) (5TMS) BP [A191002-ambient-DL--10]\t1902.42212\t4.422119\t0.216910\t0.061419\t0.886957\t102\t0.845185\t314b38dc-9bfb-4a7f-aaaa-bd80ef4ec82d\tdd3ea070-54a6-4ea7-b99b-a6e975fdd204\t1c3ad0aa-ee78-4542-93b3-aa9fdf07add1\n+231\tAllantoin (5TMS)\tAllantoin (5TMS) [A188009-ambient-na-2]\t1896.99829\t1.001709\t0.242943\t0.088526\t0.887097\t55\t0.879142\tbb9eafcc-28ff-4a63-8786-2e5e1053b337\ta999f0d6-0285-41d9-a6ba-b705987b663c\t65bb54d2-6bf7-4a53-aa22-8abf71240005\n 232\t\tno results\t\t\t\t\t\t\t\t\t\t\n 233\t\tno results\t\t\t\t\t\t\t\t\t\t\n 234\t\tno results\t\t\t\t\t\t\t\t\t\t\n@@ -383,7 +383,7 @@\n 245\t\tno results\t\t\t\t\t\t\t\t\t\t\n 246\t\tno results\t\t\t\t\t\t\t\t\t\t\n 247\t\tno results\t\t\t\t\t\t\t\t\t\t\n-248\tNonadecane\tNonadecane [A190001-ambient-n--1]\t1900\t2\t0.05944854\t0.04527639\t0.7586207\t44\t0.7132295\t44b956d8-a487-4269-baee-49e6ba5658c3\t5dff1f48-853a-4ce2-852c-81c871ef1da6\t5dff1f48-853a-4ce2-852c-81c871ef1da6\n+248\tNonadecane\tNonadecane [A190001-ambient-n--1]\t1900\t2\t0.059449\t0.045276\t0.758621\t44\t0.713229\t44b956d8-a487-4269-baee-49e6ba5658c3\t5dff1f48-853a-4ce2-852c-81c871ef1da6\t5dff1f48-853a-4ce2-852c-81c871ef1da6\n 249\t\tno results\t\t\t\t\t\t\t\t\t\t\n 250\t\tno results\t\t\t\t\t\t\t\t\t\t\n 251\t\tno results\t\t\t\t\t\t\t\t\t\t\n' |