diff --git a/tools/recentrifuge/macro.xml b/tools/recentrifuge/macro.xml index 54aff714fc9..a28fb59133c 100644 --- a/tools/recentrifuge/macro.xml +++ b/tools/recentrifuge/macro.xml @@ -1,6 +1,6 @@ - 1.12.1 + 1.13.2 0 21.05 diff --git a/tools/recentrifuge/test-data/centrifuge_test/test2_csv.log b/tools/recentrifuge/test-data/centrifuge_test/test2_csv.log index 533c9d66f35..fbab79f980b 100644 --- a/tools/recentrifuge/test-data/centrifuge_test/test2_csv.log +++ b/tools/recentrifuge/test-data/centrifuge_test/test2_csv.log @@ -1,5 +1,5 @@ -=-= /home/pierre/anaconda3/envs/__recentrifuge@1.9.1/bin/rcf =-= v1.9.1 - Jun 2022 =-= by Jose Manuel Martí =-= +=-= /home/pierre/miniconda3/envs/__recentrifuge@1.13.2/bin/rcf =-= v1.13.2 - Jan 2024 =-= by Jose Manuel Martí =-= Centrifuge .out files to analyze: ['input_dir/centrifuge_out.out'] Loading NCBI nodes... OK!  @@ -21,7 +21,7 @@ Please, wait, processing files in parallel...  Warning! 210 orphan taxids (rerun with --debug for details) input_dir/centrifuge_out sample OK! -Load elapsed time: 0.0337 sec +Load elapsed time: 0.0232 sec   Building the taxonomy multiple tree... OK! diff --git a/tools/recentrifuge/test-data/centrifuge_test/test2_csv.rcf.data.csv b/tools/recentrifuge/test-data/centrifuge_test/test2_csv.rcf.data.csv index af978e4a39b..47886f55deb 100644 --- a/tools/recentrifuge/test-data/centrifuge_test/test2_csv.rcf.data.csv +++ b/tools/recentrifuge/test-data/centrifuge_test/test2_csv.rcf.data.csv @@ -1,5 +1,5 @@ Samples,input_dir/centrifuge_out,input_dir/centrifuge_out,input_dir/centrifuge_out,Details,Details -Stats,count,unassigned,score,Rank,Name +Stats,cnt,una,sco,Rank,Name Id,,,,, 1,75,0,51.07625068955332,no_rank,root 2,75,0,51.07625068955332,superkingdom,Bacteria diff --git a/tools/recentrifuge/test-data/centrifuge_test/test4_rcf.data.tsv b/tools/recentrifuge/test-data/centrifuge_test/test4_rcf.data.tsv index ee9700c7f8c..88aaf8a6928 100644 --- a/tools/recentrifuge/test-data/centrifuge_test/test4_rcf.data.tsv +++ b/tools/recentrifuge/test-data/centrifuge_test/test4_rcf.data.tsv @@ -1,5 +1,5 @@ Samples input_dir/centrifuge_1_out input_dir/centrifuge_1_out input_dir/centrifuge_1_out input_dir/centrifuge_2_out input_dir/centrifuge_2_out input_dir/centrifuge_2_out input_dir/centrifuge_out input_dir/centrifuge_out input_dir/centrifuge_out SHARED_species SHARED_species SHARED_species SHARED_genus SHARED_genus SHARED_genus SHARED_family SHARED_family SHARED_family SHARED_order SHARED_order SHARED_order SHARED_class SHARED_class SHARED_class SHARED_phylum SHARED_phylum SHARED_phylum SHARED_SUMMARY SHARED_SUMMARY SHARED_SUMMARY Details Details -Stats count unassigned score count unassigned score count unassigned score count unassigned score count unassigned score count unassigned score count unassigned score count unassigned score count unassigned score count unassigned score Rank Name +Stats cnt una sco cnt una sco cnt una sco cnt una sco cnt una sco cnt una sco cnt una sco cnt una sco cnt una sco cnt una sco Rank Name Id 1 75 0 392.58666666666664 75 0 392.58666666666664 75 0 392.58666666666664 31 0 488.35483870967744 35 0 489.0032653061224 67 0 446.6581994080768 73 0 442.0475236076006 75 0 440.72856742250906 75 0 440.72856742250906 75 0 440.72856742250906 no_rank root 2 75 0 392.58666666666664 75 0 392.58666666666664 75 0 392.58666666666664 31 0 488.35483870967744 35 0 489.0032653061224 67 0 446.6581994080768 73 0 442.0475236076006 75 0 440.72856742250906 75 0 440.72856742250906 75 0 440.72856742250906 superkingdom Bacteria diff --git a/tools/recentrifuge/test-data/centrifuge_test/test4_tsv.html b/tools/recentrifuge/test-data/centrifuge_test/test4_tsv.html index a6330fb0560..93517261de6 100644 --- a/tools/recentrifuge/test-data/centrifuge_test/test4_tsv.html +++ b/tools/recentrifuge/test-data/centrifuge_test/test4_tsv.html @@ -74,7 +74,7 @@ // //---------------------------------------------------------------------------- // -// Copyright (C) 2017-2022 Jose Manuel Martí Martínez, for the changes in +// Copyright (C) 2017-2024 Jose Manuel Martí Martínez, for the changes in // this file from the Krona Javascript 2.0 release. // // Redistribution and use in source and binary forms, with or without @@ -4999,6 +4999,7 @@ datasets = datasetNames.length; break; + case 'n': case 'node': head = loadTreeDOM ( @@ -5052,6 +5053,7 @@ fontSize = Number(pair[1]); break; + case 'n': case 'node': nodeDefault = Number(pair[1]); break; @@ -5108,6 +5110,9 @@ if (domNode.getAttribute('href')) { newNode.href = domNode.getAttribute('href'); } + else { + newNode.href = 'https://www.google.com/search?q=' + newNode.name + } if (hueName) { newNode.hues = new Array(); @@ -5115,6 +5120,7 @@ for (var i = getFirstChild(domNode); i; i = getNextSibling(i)) { switch (i.tagName.toLowerCase()) { + case 'n': case 'node': var newChild = loadTreeDOM ( @@ -6578,4 +6584,4 @@ selectedNodeLast.getDepth() < selectedNode.getDepth()); } */
countunassignedtidrankscoreinput_dir/centrifuge_1_outinput_dir/centrifuge_2_outinput_dir/centrifuge_outSHARED_speciesSHARED_genusSHARED_familySHARED_orderSHARED_classSHARED_phylumSHARED_SUMMARY 757575313567737575751no_rank392.6392.6392.6488.4489.0446.7442.0440.7440.7440.7757575313567737575752superkingdom392.6392.6392.6488.4489.0446.7442.0440.7440.7440.775757531356773757575751224phylum392.6392.6392.6488.4489.0446.7442.0440.7440.7440.77575753135677375752227521236class392.6392.6392.6488.4489.0446.7442.0440.70440.7737373313567737366673691347order390.6390.6390.6488.4489.0446.7442.000442.0676767313567673232326732543family400.3400.3400.3488.4489.0446.7000446.7353535313535444354561genus494.0494.0494.0488.4489.00000489.031313131313131313131562species488.4488.4488.4488.400000488.4
\ No newline at end of file +" style="display:none">
cntunatidrnkscoinput_dir/centrifuge_1_outinput_dir/centrifuge_2_outinput_dir/centrifuge_outSHARED_speciesSHARED_genusSHARED_familySHARED_orderSHARED_classSHARED_phylumSHARED_SUMMARY 757575313567737575751no_rank392.59392.59392.59488.35489.00446.66442.05440.73440.73440.73757575313567737575752superkingdom392.59392.59392.59488.35489.00446.66442.05440.73440.73440.7375757531356773757575751224phylum392.59392.59392.59488.35489.00446.66442.05440.73440.73440.737575753135677375752227521236class392.59392.59392.59488.35489.00446.66442.05440.730440.73737373313567737366673691347order390.56390.56390.56488.35489.00446.66442.0500442.05676767313567673232326732543family400.34400.34400.34488.35489.00446.66000446.66353535313535444354561genus494.03494.03494.03488.35489.000000489.0031313131313131313131562species488.35488.35488.35488.3500000488.35
\ No newline at end of file diff --git a/tools/recentrifuge/test-data/kraken_test/test1_csv.log b/tools/recentrifuge/test-data/kraken_test/test1_csv.log index 42b0bf10d1d..7f7eccd22e1 100644 --- a/tools/recentrifuge/test-data/kraken_test/test1_csv.log +++ b/tools/recentrifuge/test-data/kraken_test/test1_csv.log @@ -1,5 +1,5 @@ -=-= /home/pierre/anaconda3/envs/__recentrifuge@1.9.1/bin/rcf =-= v1.9.1 - Jun 2022 =-= by Jose Manuel Martí =-= +=-= /home/pierre/miniconda3/envs/__recentrifuge@1.13.2/bin/rcf =-= v1.13.2 - Jan 2024 =-= by Jose Manuel Martí =-= Kraken .krk files to analyze: ['input_dir/kraken_out.krk'] Loading NCBI nodes... OK!  @@ -22,7 +22,7 @@ Please, wait, processing files in parallel...  Warning! 11 orphan taxids (rerun with --debug for details) input_dir/kraken_out sample OK! -Load elapsed time: 0.00392 sec +Load elapsed time: 0.00283 sec   Building the taxonomy multiple tree... OK! diff --git a/tools/recentrifuge/test-data/kraken_test/test1_csv.rcf.data.csv b/tools/recentrifuge/test-data/kraken_test/test1_csv.rcf.data.csv index 4264ad6df6d..321a85341d6 100644 --- a/tools/recentrifuge/test-data/kraken_test/test1_csv.rcf.data.csv +++ b/tools/recentrifuge/test-data/kraken_test/test1_csv.rcf.data.csv @@ -1,5 +1,5 @@ Samples,input_dir/kraken_out,input_dir/kraken_out,input_dir/kraken_out,Details,Details -Stats,count,unassigned,score,Rank,Name +Stats,cnt,una,sco,Rank,Name Id,,,,, 1,9,0,13.614815253856928,no_rank,root 2,9,0,13.614815253856928,superkingdom,Bacteria diff --git a/tools/recentrifuge/test-data/kraken_test/test1_csv.rcf.html b/tools/recentrifuge/test-data/kraken_test/test1_csv.rcf.html index 1dd2c09d645..d106f232e0e 100644 --- a/tools/recentrifuge/test-data/kraken_test/test1_csv.rcf.html +++ b/tools/recentrifuge/test-data/kraken_test/test1_csv.rcf.html @@ -74,7 +74,7 @@ // //---------------------------------------------------------------------------- // -// Copyright (C) 2017-2022 Jose Manuel Martí Martínez, for the changes in +// Copyright (C) 2017-2024 Jose Manuel Martí Martínez, for the changes in // this file from the Krona Javascript 2.0 release. // // Redistribution and use in source and binary forms, with or without @@ -4999,6 +4999,7 @@ datasets = datasetNames.length; break; + case 'n': case 'node': head = loadTreeDOM ( @@ -5052,6 +5053,7 @@ fontSize = Number(pair[1]); break; + case 'n': case 'node': nodeDefault = Number(pair[1]); break; @@ -5108,6 +5110,9 @@ if (domNode.getAttribute('href')) { newNode.href = domNode.getAttribute('href'); } + else { + newNode.href = 'https://www.google.com/search?q=' + newNode.name + } if (hueName) { newNode.hues = new Array(); @@ -5115,6 +5120,7 @@ for (var i = getFirstChild(domNode); i; i = getNextSibling(i)) { switch (i.tagName.toLowerCase()) { + case 'n': case 'node': var newChild = loadTreeDOM ( @@ -6578,4 +6584,4 @@ selectedNodeLast.getDepth() < selectedNode.getDepth()); } */
countunassignedtidrankscoreinput_dir/kraken_out 91no_rank13.692superkingdom13.691224phylum13.691236class13.6991347order13.699543family13.6
\ No newline at end of file +" style="display:none">
cntunatidrnkscoinput_dir/kraken_out 91no_rank13.6192superkingdom13.6191224phylum13.6191236class13.61991347order13.6199543family13.61
\ No newline at end of file diff --git a/tools/recentrifuge/test-data/kraken_test/test3_rcf.data.tsv b/tools/recentrifuge/test-data/kraken_test/test3_rcf.data.tsv index 66ef90c5696..4307473207b 100644 --- a/tools/recentrifuge/test-data/kraken_test/test3_rcf.data.tsv +++ b/tools/recentrifuge/test-data/kraken_test/test3_rcf.data.tsv @@ -1,5 +1,5 @@ Samples input_dir/kraken_out input_dir/kraken_out input_dir/kraken_out Details Details -Stats count unassigned score Rank Name +Stats cnt una sco Rank Name Id 1 9 0 2.7230463906265316 no_rank root 2 9 0 2.7230463906265316 superkingdom Bacteria diff --git a/tools/recentrifuge/test-data/kraken_test/test3_tsv.log b/tools/recentrifuge/test-data/kraken_test/test3_tsv.log index c16931866f8..ef4250c3758 100644 --- a/tools/recentrifuge/test-data/kraken_test/test3_tsv.log +++ b/tools/recentrifuge/test-data/kraken_test/test3_tsv.log @@ -1,5 +1,5 @@ -=-= /home/pierre/anaconda3/envs/__recentrifuge@1.9.1/bin/rcf =-= v1.9.1 - Jun 2022 =-= by Jose Manuel Martí =-= +=-= /home/pierre/miniconda3/envs/__recentrifuge@1.13.2/bin/rcf =-= v1.13.2 - Jan 2024 =-= by Jose Manuel Martí =-= CAUTION! --strain experimental mode activated! Kraken .krk files to analyze: ['input_dir/kraken_out.krk'] @@ -23,7 +23,7 @@ Please, wait, processing files in parallel...  Warning! 11 orphan taxids (rerun with --debug for details) input_dir/kraken_out sample OK! -Load elapsed time: 0.00395 sec +Load elapsed time: 0.00424 sec   Building the taxonomy multiple tree... OK!