diff --git a/_data/programs.yml b/_data/programs.yml index 9207828f..f8db64cc 100644 --- a/_data/programs.yml +++ b/_data/programs.yml @@ -193,18 +193,9 @@ - author: watsonar programs: - name: anvi-display-contigs-stats -- author: qclayssen - programs: - - name: anvi-estimate-scg-taxonomy - - name: anvi-run-scg-taxonomy - - name: anvi-setup-scg-taxonomy -- author: shaiberalon - programs: - - name: anvi-export-locus - - name: anvi-gen-variability-profile - - name: anvi-run-workflow - author: semiller10 programs: + - name: anvi-draw-kegg-pathways - name: anvi-get-codon-frequencies - name: anvi-get-codon-usage-bias - name: anvi-get-metabolic-model-file @@ -218,6 +209,16 @@ - name: anvi-setup-kegg-data - name: anvi-setup-modelseed-database - name: anvi-trnaseq +- author: qclayssen + programs: + - name: anvi-estimate-scg-taxonomy + - name: anvi-run-scg-taxonomy + - name: anvi-setup-scg-taxonomy +- author: shaiberalon + programs: + - name: anvi-export-locus + - name: anvi-gen-variability-profile + - name: anvi-run-workflow - author: matthewlawrenceklein programs: - name: anvi-interactive diff --git a/help/main/artifacts/bam-file/index.md b/help/main/artifacts/bam-file/index.md index 99a80df8..5d3e4041 100644 --- a/help/main/artifacts/bam-file/index.md +++ b/help/main/artifacts/bam-file/index.md @@ -29,7 +29,7 @@ A BAM-type anvi'o artifact. This artifact is typically provided **by the user** ## Required or used by -

[anvi-get-short-reads-from-bam](../../programs/anvi-get-short-reads-from-bam) [anvi-get-short-reads-mapping-to-a-gene](../../programs/anvi-get-short-reads-mapping-to-a-gene) [anvi-get-tlen-dist-from-bam](../../programs/anvi-get-tlen-dist-from-bam) [anvi-profile](../../programs/anvi-profile) [anvi-profile-blitz](../../programs/anvi-profile-blitz) [anvi-report-linkmers](../../programs/anvi-report-linkmers) [anvi-script-find-misassemblies](../../programs/anvi-script-find-misassemblies) [anvi-script-get-coverage-from-bam](../../programs/anvi-script-get-coverage-from-bam) [anvi-script-reformat-bam](../../programs/anvi-script-reformat-bam)

+

[anvi-get-short-reads-from-bam](../../programs/anvi-get-short-reads-from-bam) [anvi-get-short-reads-mapping-to-a-gene](../../programs/anvi-get-short-reads-mapping-to-a-gene) [anvi-get-tlen-dist-from-bam](../../programs/anvi-get-tlen-dist-from-bam) [anvi-profile-blitz](../../programs/anvi-profile-blitz) [anvi-report-linkmers](../../programs/anvi-report-linkmers) [anvi-script-find-misassemblies](../../programs/anvi-script-find-misassemblies) [anvi-script-get-coverage-from-bam](../../programs/anvi-script-get-coverage-from-bam) [anvi-script-reformat-bam](../../programs/anvi-script-reformat-bam)

## Description diff --git a/help/main/artifacts/contigs-db/index.md b/help/main/artifacts/contigs-db/index.md index 28dcbda7..e56b12f2 100644 --- a/help/main/artifacts/contigs-db/index.md +++ b/help/main/artifacts/contigs-db/index.md @@ -29,7 +29,7 @@ A DB-type anvi'o artifact. This artifact is typically generated, used, and/or ex ## Required or used by -

[anvi-cluster-contigs](../../programs/anvi-cluster-contigs) [anvi-compute-completeness](../../programs/anvi-compute-completeness) [anvi-db-info](../../programs/anvi-db-info) [anvi-delete-functions](../../programs/anvi-delete-functions) [anvi-delete-hmms](../../programs/anvi-delete-hmms) [anvi-display-contigs-stats](../../programs/anvi-display-contigs-stats) [anvi-display-metabolism](../../programs/anvi-display-metabolism) [anvi-display-structure](../../programs/anvi-display-structure) [anvi-draw-kegg-pathways](../../programs/anvi-draw-kegg-pathways) [anvi-estimate-genome-completeness](../../programs/anvi-estimate-genome-completeness) [anvi-estimate-metabolism](../../programs/anvi-estimate-metabolism) [anvi-estimate-scg-taxonomy](../../programs/anvi-estimate-scg-taxonomy) [anvi-estimate-trna-taxonomy](../../programs/anvi-estimate-trna-taxonomy) [anvi-export-contigs](../../programs/anvi-export-contigs) [anvi-export-functions](../../programs/anvi-export-functions) [anvi-export-gene-calls](../../programs/anvi-export-gene-calls) [anvi-export-gene-coverage-and-detection](../../programs/anvi-export-gene-coverage-and-detection) [anvi-export-locus](../../programs/anvi-export-locus) [anvi-export-misc-data](../../programs/anvi-export-misc-data) [anvi-export-splits-and-coverages](../../programs/anvi-export-splits-and-coverages) [anvi-export-splits-taxonomy](../../programs/anvi-export-splits-taxonomy) [anvi-gen-fixation-index-matrix](../../programs/anvi-gen-fixation-index-matrix) [anvi-gen-gene-consensus-sequences](../../programs/anvi-gen-gene-consensus-sequences) [anvi-gen-gene-level-stats-databases](../../programs/anvi-gen-gene-level-stats-databases) [anvi-gen-structure-database](../../programs/anvi-gen-structure-database) [anvi-gen-variability-profile](../../programs/anvi-gen-variability-profile) [anvi-get-aa-counts](../../programs/anvi-get-aa-counts) [anvi-get-codon-frequencies](../../programs/anvi-get-codon-frequencies) [anvi-get-codon-usage-bias](../../programs/anvi-get-codon-usage-bias) [anvi-get-metabolic-model-file](../../programs/anvi-get-metabolic-model-file) [anvi-get-pn-ps-ratio](../../programs/anvi-get-pn-ps-ratio) [anvi-get-sequences-for-gene-calls](../../programs/anvi-get-sequences-for-gene-calls) [anvi-get-sequences-for-hmm-hits](../../programs/anvi-get-sequences-for-hmm-hits) [anvi-get-short-reads-from-bam](../../programs/anvi-get-short-reads-from-bam) [anvi-get-short-reads-mapping-to-a-gene](../../programs/anvi-get-short-reads-mapping-to-a-gene) [anvi-get-split-coverages](../../programs/anvi-get-split-coverages) [anvi-import-collection](../../programs/anvi-import-collection) [anvi-import-functions](../../programs/anvi-import-functions) [anvi-import-misc-data](../../programs/anvi-import-misc-data) [anvi-import-taxonomy-for-genes](../../programs/anvi-import-taxonomy-for-genes) [anvi-inspect](../../programs/anvi-inspect) [anvi-interactive](../../programs/anvi-interactive) [anvi-merge](../../programs/anvi-merge) [anvi-migrate](../../programs/anvi-migrate) [anvi-profile](../../programs/anvi-profile) [anvi-profile-blitz](../../programs/anvi-profile-blitz) [anvi-reaction-network](../../programs/anvi-reaction-network) [anvi-refine](../../programs/anvi-refine) [anvi-rename-bins](../../programs/anvi-rename-bins) [anvi-run-cazymes](../../programs/anvi-run-cazymes) [anvi-run-hmms](../../programs/anvi-run-hmms) [anvi-run-interacdome](../../programs/anvi-run-interacdome) [anvi-run-kegg-kofams](../../programs/anvi-run-kegg-kofams) [anvi-run-ncbi-cogs](../../programs/anvi-run-ncbi-cogs) [anvi-run-pfams](../../programs/anvi-run-pfams) [anvi-run-scg-taxonomy](../../programs/anvi-run-scg-taxonomy) [anvi-run-trna-taxonomy](../../programs/anvi-run-trna-taxonomy) [anvi-scan-trnas](../../programs/anvi-scan-trnas) [anvi-search-functions](../../programs/anvi-search-functions) [anvi-search-palindromes](../../programs/anvi-search-palindromes) [anvi-search-sequence-motifs](../../programs/anvi-search-sequence-motifs) [anvi-show-misc-data](../../programs/anvi-show-misc-data) [anvi-split](../../programs/anvi-split) [anvi-summarize](../../programs/anvi-summarize) [anvi-summarize-blitz](../../programs/anvi-summarize-blitz) [anvi-update-db-description](../../programs/anvi-update-db-description) [anvi-update-structure-database](../../programs/anvi-update-structure-database) [anvi-script-add-default-collection](../../programs/anvi-script-add-default-collection) [anvi-script-estimate-metabolic-independence](../../programs/anvi-script-estimate-metabolic-independence) [anvi-script-filter-hmm-hits-table](../../programs/anvi-script-filter-hmm-hits-table) [anvi-script-gen-distribution-of-genes-in-a-bin](../../programs/anvi-script-gen-distribution-of-genes-in-a-bin) [anvi-script-gen-genomes-file](../../programs/anvi-script-gen-genomes-file) [anvi-script-get-hmm-hits-per-gene-call](../../programs/anvi-script-get-hmm-hits-per-gene-call) [anvi-script-merge-collections](../../programs/anvi-script-merge-collections) [anvi-script-permute-trnaseq-seeds](../../programs/anvi-script-permute-trnaseq-seeds)

+

[anvi-cluster-contigs](../../programs/anvi-cluster-contigs) [anvi-compute-completeness](../../programs/anvi-compute-completeness) [anvi-db-info](../../programs/anvi-db-info) [anvi-delete-functions](../../programs/anvi-delete-functions) [anvi-delete-hmms](../../programs/anvi-delete-hmms) [anvi-display-contigs-stats](../../programs/anvi-display-contigs-stats) [anvi-display-metabolism](../../programs/anvi-display-metabolism) [anvi-display-structure](../../programs/anvi-display-structure) [anvi-draw-kegg-pathways](../../programs/anvi-draw-kegg-pathways) [anvi-estimate-genome-completeness](../../programs/anvi-estimate-genome-completeness) [anvi-estimate-metabolism](../../programs/anvi-estimate-metabolism) [anvi-estimate-scg-taxonomy](../../programs/anvi-estimate-scg-taxonomy) [anvi-estimate-trna-taxonomy](../../programs/anvi-estimate-trna-taxonomy) [anvi-export-contigs](../../programs/anvi-export-contigs) [anvi-export-functions](../../programs/anvi-export-functions) [anvi-export-gene-calls](../../programs/anvi-export-gene-calls) [anvi-export-gene-coverage-and-detection](../../programs/anvi-export-gene-coverage-and-detection) [anvi-export-locus](../../programs/anvi-export-locus) [anvi-export-misc-data](../../programs/anvi-export-misc-data) [anvi-export-splits-and-coverages](../../programs/anvi-export-splits-and-coverages) [anvi-export-splits-taxonomy](../../programs/anvi-export-splits-taxonomy) [anvi-gen-fixation-index-matrix](../../programs/anvi-gen-fixation-index-matrix) [anvi-gen-gene-consensus-sequences](../../programs/anvi-gen-gene-consensus-sequences) [anvi-gen-gene-level-stats-databases](../../programs/anvi-gen-gene-level-stats-databases) [anvi-gen-structure-database](../../programs/anvi-gen-structure-database) [anvi-gen-variability-profile](../../programs/anvi-gen-variability-profile) [anvi-get-aa-counts](../../programs/anvi-get-aa-counts) [anvi-get-codon-frequencies](../../programs/anvi-get-codon-frequencies) [anvi-get-codon-usage-bias](../../programs/anvi-get-codon-usage-bias) [anvi-get-metabolic-model-file](../../programs/anvi-get-metabolic-model-file) [anvi-get-pn-ps-ratio](../../programs/anvi-get-pn-ps-ratio) [anvi-get-sequences-for-gene-calls](../../programs/anvi-get-sequences-for-gene-calls) [anvi-get-sequences-for-hmm-hits](../../programs/anvi-get-sequences-for-hmm-hits) [anvi-get-short-reads-from-bam](../../programs/anvi-get-short-reads-from-bam) [anvi-get-short-reads-mapping-to-a-gene](../../programs/anvi-get-short-reads-mapping-to-a-gene) [anvi-get-split-coverages](../../programs/anvi-get-split-coverages) [anvi-import-collection](../../programs/anvi-import-collection) [anvi-import-functions](../../programs/anvi-import-functions) [anvi-import-misc-data](../../programs/anvi-import-misc-data) [anvi-import-taxonomy-for-genes](../../programs/anvi-import-taxonomy-for-genes) [anvi-inspect](../../programs/anvi-inspect) [anvi-interactive](../../programs/anvi-interactive) [anvi-merge](../../programs/anvi-merge) [anvi-migrate](../../programs/anvi-migrate) [anvi-profile-blitz](../../programs/anvi-profile-blitz) [anvi-reaction-network](../../programs/anvi-reaction-network) [anvi-refine](../../programs/anvi-refine) [anvi-rename-bins](../../programs/anvi-rename-bins) [anvi-run-cazymes](../../programs/anvi-run-cazymes) [anvi-run-hmms](../../programs/anvi-run-hmms) [anvi-run-interacdome](../../programs/anvi-run-interacdome) [anvi-run-kegg-kofams](../../programs/anvi-run-kegg-kofams) [anvi-run-ncbi-cogs](../../programs/anvi-run-ncbi-cogs) [anvi-run-pfams](../../programs/anvi-run-pfams) [anvi-run-scg-taxonomy](../../programs/anvi-run-scg-taxonomy) [anvi-run-trna-taxonomy](../../programs/anvi-run-trna-taxonomy) [anvi-scan-trnas](../../programs/anvi-scan-trnas) [anvi-search-functions](../../programs/anvi-search-functions) [anvi-search-palindromes](../../programs/anvi-search-palindromes) [anvi-search-sequence-motifs](../../programs/anvi-search-sequence-motifs) [anvi-show-misc-data](../../programs/anvi-show-misc-data) [anvi-split](../../programs/anvi-split) [anvi-summarize](../../programs/anvi-summarize) [anvi-summarize-blitz](../../programs/anvi-summarize-blitz) [anvi-update-db-description](../../programs/anvi-update-db-description) [anvi-update-structure-database](../../programs/anvi-update-structure-database) [anvi-script-add-default-collection](../../programs/anvi-script-add-default-collection) [anvi-script-estimate-metabolic-independence](../../programs/anvi-script-estimate-metabolic-independence) [anvi-script-filter-hmm-hits-table](../../programs/anvi-script-filter-hmm-hits-table) [anvi-script-gen-distribution-of-genes-in-a-bin](../../programs/anvi-script-gen-distribution-of-genes-in-a-bin) [anvi-script-gen-genomes-file](../../programs/anvi-script-gen-genomes-file) [anvi-script-get-hmm-hits-per-gene-call](../../programs/anvi-script-get-hmm-hits-per-gene-call) [anvi-script-merge-collections](../../programs/anvi-script-merge-collections) [anvi-script-permute-trnaseq-seeds](../../programs/anvi-script-permute-trnaseq-seeds)

## Description diff --git a/help/main/index.md b/help/main/index.md index 53a14425..1c5da873 100644 --- a/help/main/index.md +++ b/help/main/index.md @@ -17,7 +17,7 @@ If you need an introduction to the terminology used in 'omics research or in anv {:.notice} -The help contents were last updated on **03 Sep 24 07:09:30** for anvi'o version **8-dev (marie)**. +The help contents were last updated on **03 Sep 24 14:24:09** for anvi'o version **8-dev (marie)**. {% include _project-anvio-version.html %} @@ -132,7 +132,7 @@ Listed below **a total of 137 artifacts**. Anvi'o programs perform atomic tasks that can be weaved together to implement complete 'omics workflows. Please note that there may be programs that are not listed on this page. You can type 'anvi-' in your terminal, and press the TAB key twice to see the full list of programs available to you on your system, and type `anvi-program-name --help` to read the full list of command line options. -Listed below **a total of 154 programs**. +Listed below **a total of 155 programs**.
@@ -2609,7 +2609,7 @@ Listed below **a total of 154 programs**. 🧀 - [bam-file](artifacts/bam-file) [contigs-db](artifacts/contigs-db) + n/a @@ -3243,6 +3243,40 @@ Listed below **a total of 154 programs**.
+
+ + + + + + + + + + + + + + + +
+ 🔥 **[anvi-self-test](programs/anvi-self-test)**. A program for anvi'o to test itself. +
+ 🧀 + n/a +
+ 🍕 + n/a +
+ 🧠
+
+
+
+
+ +
+
+
diff --git a/help/main/programs/anvi-draw-kegg-pathways/index.md b/help/main/programs/anvi-draw-kegg-pathways/index.md index 17c681c1..4d54f751 100644 --- a/help/main/programs/anvi-draw-kegg-pathways/index.md +++ b/help/main/programs/anvi-draw-kegg-pathways/index.md @@ -103,7 +103,7 @@ anvi-draw-kegg-pathways --contigs-dbs [bam-file](../../artifacts/bam-file) [contigs-db](../../artifacts/contigs-db)

+This program seems to know what its doing. It needs no input material from its user. Good program. ## Can provide diff --git a/help/main/programs/anvi-profile/network.json b/help/main/programs/anvi-profile/network.json index 4b92fb59..00c6ecfc 100644 --- a/help/main/programs/anvi-profile/network.json +++ b/help/main/programs/anvi-profile/network.json @@ -29,25 +29,7 @@ "type": "CONCEPT" }, { - "size": 1, - "score": 1, - "color": "#AA0000", - "id": "bam-file", - "name": "bam-file", - "provided_by_anvio": false, - "type": "BAM" - }, - { - "size": 1, - "score": 0.5, - "color": "#00AA00", - "id": "contigs-db", - "name": "contigs-db", - "provided_by_anvio": true, - "type": "DB" - }, - { - "size": 5, + "size": 3, "score": 0.1, "color": "#AAAA00", "id": "anvi-profile", @@ -57,24 +39,16 @@ ], "links": [ { - "source": 5, + "source": 3, "target": 0 }, { - "source": 5, + "source": 3, "target": 1 }, { - "source": 5, + "source": 3, "target": 2 - }, - { - "target": 5, - "source": 3 - }, - { - "target": 5, - "source": 4 } ], "directed": false, diff --git a/help/main/programs/anvi-self-test/index.md b/help/main/programs/anvi-self-test/index.md new file mode 100644 index 00000000..52fb60b3 --- /dev/null +++ b/help/main/programs/anvi-self-test/index.md @@ -0,0 +1,66 @@ +--- +layout: program +title: anvi-self-test +excerpt: An anvi'o program. A program for anvi'o to test itself. +categories: [anvio] +comments: false +redirect_from: /m/anvi-self-test +image: + featurerelative: ../../../images/header.png + display: true +--- + +A program for anvi'o to test itself. + +🔙 **[To the main page](../../)** of anvi'o programs and artifacts. + + +{% include _toc.html %} +
+{% capture network_path %}{{ "network.json" }}{% endcapture %} +{% capture network_height %}{{ 300 }}{% endcapture %} +{% include _project-anvio-graph.html %} + + +## Authors + +
A. Murat Eren (Meren)
WebEmailTwitterGithub
+ +
Samuel Miller
WebEmailTwitterGithub
+ +
Evan Kiefl
WebEmailTwitterGithub
+ +
Iva Veseli
EmailTwitterGithub
+ +
Matthew Schechter
EmailTwitterGithub
+ + + +## Can consume + + +This program seems to know what its doing. It needs no input material from its user. Good program. + + +## Can provide + + +This program does not seem to provide any artifacts. Such programs usually print out some information for you to see or alter some anvi'o artifacts without producing any immediate outputs. + + +## Usage + + +This program enables an anvi'o user to run component tests on various anvi'o functionality to ensure they are working on their system. + + +{:.notice} +Edit [this file](https://github.com/merenlab/anvio/tree/master/anvio/docs/programs/anvi-self-test.md) to update this information. + + +## Additional Resources + + + +{:.notice} +Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit [this file](https://github.com/merenlab/anvio/tree/master/bin/anvi-self-test) on GitHub. If you are not sure how to do that, find the `__resources__` tag in [this file](https://github.com/merenlab/anvio/blob/master/bin/anvi-interactive) to see an example. diff --git a/help/main/programs/anvi-self-test/network.json b/help/main/programs/anvi-self-test/network.json new file mode 100644 index 00000000..ee8aecc3 --- /dev/null +++ b/help/main/programs/anvi-self-test/network.json @@ -0,0 +1,7 @@ +{ + "graph": [], + "nodes": [], + "links": [], + "directed": false, + "multigraph": false +} \ No newline at end of file diff --git a/images/icons/FASTQ.png b/images/icons/FASTQ.png new file mode 100644 index 00000000..2f12bfa6 Binary files /dev/null and b/images/icons/FASTQ.png differ diff --git a/network/network.json b/network/network.json index 4452277e..97276219 100644 --- a/network/network.json +++ b/network/network.json @@ -65,7 +65,7 @@ "type": "DB" }, { - "size": 76, + "size": 75, "score": 0.5, "color": "#00AA00", "id": "contigs-db", @@ -695,7 +695,7 @@ "type": "FASTA" }, { - "size": 11, + "size": 10, "score": 1, "color": "#AA0000", "id": "bam-file", @@ -1838,7 +1838,7 @@ "type": "PROGRAM" }, { - "size": 7, + "size": 4, "score": 0.1, "color": "#AAAA00", "id": "anvi-profile", @@ -3271,10 +3271,6 @@ "target": 209, "source": 7 }, - { - "target": 213, - "source": 7 - }, { "target": 214, "source": 7 @@ -4467,10 +4463,6 @@ "source": 201, "target": 77 }, - { - "target": 213, - "source": 77 - }, { "target": 214, "source": 77