content/3.defense-systems/panchino_gp28.md

@@ -7,13 +7,21 @@ tableColumns:
       abstract: |
         Temperate phages are common, and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses that infect mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere with the infection of lytic and temperate phages that are either closely related (homotypic defence) or unrelated (heterotypic defence) to the prophage. Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defence systems include a single-subunit restriction system, a heterotypic exclusion system and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, which acts as a highly effective counter-defence system. Prophage-mediated viral defence offers an efficient mechanism for bacterial success in host-virus dynamics, and counter-defence promotes phage co-evolution.
     PFAM: PF01170, PF02384, PF13588
+contributors: 
+  - Lucas Paoli
 relevantAbstracts:
-    - doi: 10.1038/nmicrobiol.2016.251
+  - doi: 10.1038/nmicrobiol.2016.251
 ---
 
 # Panchino_gp28
 
-## To do 
+## Description
+
+The Panchino gp28 defense system was described in :ref{doi=10.1038/nmicrobiol.2016.251} and is named after the Panchino prophage (on which it is located) and the corresponding gene. It is a single gene system.
+
+## Molecular mechanisms
+
+Panchino gp28 is act as a single gene type I restriction system :ref{doi=10.1038/nmicrobiol.2016.251,10.1016/j.mib.2023.102321}.
 
 ## Example of genomic structure
 
@@ -79,4 +87,3 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-

content/3.defense-systems/pd-t7-1.md

@@ -9,11 +9,20 @@ tableColumns:
     Sensor: Unknown
     Activator: Unknown
     Effector: Unknown
+contributors:
+    - Hugo Vaysset
 relevantAbstracts:
     - doi: 10.1038/s41564-022-01219-4
 ---
 
 # PD-T7-1
+
+## Description
+PD-T7-1 is a single gene defense systems which was discovered in :ref{doi=10.1038/s41564-022-01219-4}. Its antiphage activity was assessed in *E. coli* and it was shown to be active against T7.
+
+## Molecular mechanism
+As far as we are aware, the molecular mechanism is unknown.
+
 ## Example of genomic structure
 
 The PD-T7-1 is composed of 1 protein: PD-T7-1.
@@ -25,8 +34,12 @@ Here is an example found in the RefSeq database:
 The PD-T7-1 system in *Klebsiella sp. P1927* (GCF_018204675.1, NZ_CP073377) is composed of 1 protein: PD-T7-1 (WP_004150873.1) 
 
 ## Distribution of the system among prokaryotes
+<<<<<<< content/3.defense-systems/pd-t7-1.md
+The PD-T7-1 system is present in a total of 136 different species.
+=======
 
 Among the 22,803 complete genomes of RefSeq, the PD-T7-1 is detected in 748 genomes (3.28 %).
+>>>>>>> content/3.defense-systems/pd-t7-1.md
 
 The system was detected in 146 different species.
 

content/3.defense-systems/pd-t7-5.md

@@ -9,14 +9,22 @@ tableColumns:
     Sensor: Unknown
     Activator: Unknown
     Effector: Unknown
+contributors: 
+  - Hugo Vaysset
 relevantAbstracts:
-    - doi: 10.1038/s41564-022-01219-4
+  - doi: 10.1038/s41564-022-01219-4
 ---
 
 # PD-T7-5
-## Example of genomic structure
 
-The PD-T7-5 is composed of 1 protein: PD-T7-5.
+## Description
+PD-T7-5 is a defense system composed of a single protein which was discovered in :ref{doi=10.1038/s41564-022-01219-4}. Its antiphage activity was assessed by heterologous expression in *E. coli* against T7 and to reduce the size of lysis plaques of T3 :ref{doi=10.1038/s41564-022-01219-4}. PD-T7-5 contains a PD(D/E)XK nuclease domain like [PD-T7-1](/defense-systems/pd-t7-1).
+
+## Molecular mechanism
+As far as we are aware, the molecular mechanism is unknown. However, the presence of a PD(D/E)XK domain in PD-T7-5 suggests a mechanism of action via DNA degradation :ref{doi=10.1038/s41564-022-01219-4}.
+
+## Example of genomic structure
+The PD-T7-5 system is composed of one protein: PD-T7-5.
 
 Here is an example found in the RefSeq database:
 
@@ -76,4 +84,3 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-

content/3.defense-systems/rm.md

@@ -3,16 +3,36 @@ title: RM
 layout: article
 tableColumns:
     article:
-      doi: 10.1093/nar/gku734
+      doi: 10.1016/j.mib.2005.06.003
       abstract: |
-        The roles of restriction-modification (R-M) systems in providing immunity against horizontal gene transfer (HGT) and in stabilizing mobile genetic elements (MGEs) have been much debated. However, few studies have precisely addressed the distribution of these systems in light of HGT, its mechanisms and its vectors. We analyzed the distribution of R-M systems in 2261 prokaryote genomes and found their frequency to be strongly dependent on the presence of MGEs, CRISPR-Cas systems, integrons and natural transformation. Yet R-M systems are rare in plasmids, in prophages and nearly absent from other phages. Their abundance depends on genome size for small genomes where it relates with HGT but saturates at two occurrences per genome. Chromosomal R-M systems might evolve under cycles of purifying and relaxed selection, where sequence conservation depends on the biochemical activity and complexity of the system and total gene loss is frequent. Surprisingly, analysis of 43 pan-genomes suggests that solitary R-M genes rarely arise from the degradation of R-M systems. Solitary genes are transferred by large MGEs, whereas complete systems are more frequently transferred autonomously or in small MGEs. Our results suggest means of testing the roles for R-M systems and their associations with MGEs.
+        The phenomena of prokaryotic restriction and modification, as well as anti-restriction, were first discovered five decades ago but have yielded only gradually to rigorous analysis. Work presented at the 5th New England Biolabs Meeting on Restriction-Modification (available on REBASE) and several recently published genetic, biochemical and biophysical analyses indicate that these fields continue to contribute significantly to basic science. Recently, there have been several studies that have shed light on the still developing field of restriction-modification and on the newly re-emerging field of anti-restriction.
     Sensor: Detecting invading nucleic acid
     Activator: Direct
     Effector: Nucleic acid degrading
     PFAM: PF00270, PF02384, PF04313, PF04851, PF12008, PF12161, PF18766
+contributors: 
+  - Aude Bernheim
+  - Florian Tesson
+relevantAbstracts:
+  - doi: 10.1016/j.mib.2005.06.003
+  - doi: 10.1093/nar/gku734
 ---
 
 # RM
+
+## Description
+Restriction modification systems are the most abundant antiphage systems. They already have their own [Wikipedia page](https://en.wikipedia.org/wiki/Restriction_modification_system)
+
+## Molecular Mechanisms
+Several reviews detail the molecular mechanisms of restriction modification systems. For example in :ref{doi=10.1016/j.mib.2005.06.003}:
+
+"Bacterial restriction-modification (R-M) systems function as prokaryotic immune systems that attack foreign DNA entering the cell :ref{doi=10.1128/jb.65.2.113-121.1953}. Typically, R-M systems have enzymes responsible for two opposing activities: a restriction endonuclease (REase) that recognizes a specific DNA sequence for cleavage and a cognate methyltransferase (MTase) that confers protection from cleavage by methylation of adenine or cytosine bases within the same recognition sequence. REases recognize ‘non-self’ DNA (Figure 1), such as that of phage and plasmids, by its lack of characteristic modification within specific recognition sites :ref{doi=10.1093/nar/29.18.3705}. Foreign DNA is then inactivated by endonucleolytic cleavage. Generally, methylation of a specific cytosine or adenine within the recognition sequence confers protection from restriction. Host DNA is normally methylated by the MTase following replication, whereas invading non-self DNA is not."
+
+![Figure_1](/rm/Figure_1_Tock_Dryden_2005.png){max-width=750px}
+
+Figure 1. The function of R-M systems, as illustrated by Type I R-M enzymes. From :ref{doi=10.1016/j.mib.2005.06.003}.
+
+
 ## Example of genomic structure
 
 A total of 5 subsystems have been described for the RM system.
@@ -52,103 +72,23 @@ Proportion of genome encoding the RM system for the 14 phyla with more than 50 g
 
 ## Structure
 
-### DISARM_1
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rm/DISARM_1,DISARM_1__drmD,0,DF-plddts_85.45851.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rm/DISARM_1,DISARM_1__drmMI,0,DF-plddts_86.22485.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rm/DISARM_1,DISARM__drmA,0,DF-plddts_88.08452.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rm/DISARM_1,DISARM__drmB,0,DF-plddts_88.41231.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rm/DISARM_1,DISARM__drmC,0,DF-plddts_93.3381.pdb
----
-::
-
-### DISARM_2
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rm/DISARM_2,DISARM_2__drmE,0,V-plddts_88.46395.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rm/DISARM_2,DISARM_2__drmMII,0,V-plddts_92.6996.pdb
----
-::
+### Experimentaly determined structure
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rm/DISARM_2,DISARM__drmA,0,V-plddts_87.64454.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rm/DISARM_2,DISARM__drmB,0,V-plddts_89.69894.pdb
----
-::
-
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rm/DISARM_2,DISARM__drmC,0,V-plddts_87.93933.pdb
----
-::
+Many structure for the different types of restriction-modification system are available on the [Protein Data Bank](https://www.rcsb.org).
 
 ### RM
+#### Restriction modification Type I Prr
 
 ::molstar-pdbe-plugin
 ---
 height: 700
-dataUrl: /rm/RM__Type_I_REases-plddts_86.33796.pdb
+dataUrls:
+  - /rm/RM__Type_I_REases-plddts_86.33796.pdb
+  - /rm/RM__Type_I_S-plddts_91.98582.pdb
+  - /prrc/PrrC__EcoprrI-plddts_91.30003.pdb
 ---
 ::
 
-::molstar-pdbe-plugin
----
-height: 700
-dataUrl: /rm/RM__Type_I_S-plddts_91.98582.pdb
----
-::
-
-## Relevant abstracts
-
-::relevant-abstracts
----
-items:
-    - doi: 10.1093/nar/gku734
-
----
-::
+## Experimental validation
+Many RM systems defend against many phages, as such we cannot map this correctly.
 

content/3.defense-systems/rnlab.md

@@ -10,11 +10,22 @@ tableColumns:
     Activator: Direct
     Effector: Nucleic acid degrading
     PFAM: PF15933, PF15935, PF18869, PF19034
+contributors: 
+  - Lucas Paoli
 relevantAbstracts:
-    - doi: 10.1534/genetics.110.121798
+  - doi: 10.1534/genetics.110.121798
 ---
 
 # RnlAB
+
+## Description
+
+RnlAB is a type II toxin-antitoxin system, in which RnlA is the toxin and RnlB the antitoxin :ref{doi=10.1534/genetics.110.121798}.
+
+## Molecular mechanisms
+
+The RnlA toxin has a RNase activity. RnlB (formerly yfjO) is the antitoxin and suppresses the RNase LS activity :ref{doi=10.1534/genetics.110.121798}.
+
 ## Example of genomic structure
 
 The RnlAB is composed of 2 proteins: RnlA and RnlB.
@@ -75,4 +86,3 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-

content/3.defense-systems/rst_duf4238.md

@@ -10,11 +10,22 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF14022
-relevantAbstracts:
-    - doi: 10.1016/j.chom.2022.02.018
+contributors:
+    - Ernest Mordret
+relevant abstracts:
+    - 10.1016/j.chom.2022.02.018
 ---
 
 # Rst_DUF4238
+
+## Description
+
+Rst_DUF4238 is a single gene system found in a screen of phage and phage-satellites antiviral hotspots :ref{doi=10.1016/j.chom.2022.02.018}. It was shown to provide E.coli with a strong resistance against phage T7.
+
+## Molecular mechanism
+
+As far as we are aware, the molecular mechanism is unknown.
+
 ## Example of genomic structure
 
 The Rst_DUF4238 is composed of 1 protein: DUF4238.
@@ -75,4 +86,3 @@ end
     style Title3 fill:none,stroke:none,stroke-width:none
     style Title4 fill:none,stroke:none,stroke-width:none
 </mermaid>
-

content/3.defense-systems/rst_rt-nitrilase-tm.md

@@ -10,11 +10,25 @@ tableColumns:
     Activator: Unknown
     Effector: Unknown
     PFAM: PF00078
+contributors:
+    - Hugo Vaysset
 relevantAbstracts:
     - doi: 10.1016/j.chom.2022.02.018
+    - doi: 10.1093/nar/gkac467
 ---
 
-# Rst_RT-nitrilase-Tm
+# RT-nitrilase-Tm
+
+## Description
+RT-nitrilase-Tm (also named UG5-large) is a two genes defense system. It was discovered from P4-like satellites in *E. coli* genomes :ref{doi=10.1016/j.chom.2022.02.01} :ref{doi=10.1093/nar/gkac467}. Its antiphage activity was shown in *E. coli* against phage AL505_P2 (Myoviridae). 
+
+The first protein is a reverse transcriptase (RT) fussed with C-N hydrolase domain (nitrilase) ; the second protein is transmembrane protein :ref{doi=10.1093/nar/gkac467}.
+
+The presence of a RT protein allows to draw a parallel between this system and the [DRT defense system](/defense-systems/drt).
+
+## Molecular mechanism
+As far as we are aware, the molecular mechanism is unknown. 
+
 ## Example of genomic structure
 
 The Rst_RT-nitrilase-Tm is composed of 2 proteins: RT and RT-Tm.

content/3.defense-systems/thoeris.md

@@ -7,15 +7,34 @@ tableColumns:
       abstract: |
         The arms race between bacteria and phages led to the development of sophisticated antiphage defense systems, including CRISPR-Cas and restriction-modification systems. Evidence suggests that known and unknown defense systems are located in "defense islands" in microbial genomes. Here, we comprehensively characterized the bacterial defensive arsenal by examining gene families that are clustered next to known defense genes in prokaryotic genomes. Candidate defense systems were systematically engineered and validated in model bacteria for their antiphage activities. We report nine previously unknown antiphage systems and one antiplasmid system that are widespread in microbes and strongly protect against foreign invaders. These include systems that adopted components of the bacterial flagella and condensin complexes. Our data also suggest a common, ancient ancestry of innate immunity components shared between animals, plants, and bacteria.
     Sensor: Unknown
-    Activator: Signaling
+    Activator: Signaling system
     Effector: Nucleotide modifying
     PFAM: PF08937, PF13289, PF18185
+contributors: 
+  - Marie Guillaume
+  - Helena Shomar
+  - Florian Tesson
 relevantAbstracts:
-    - doi: 10.1038/s41586-021-04098-7
-    - doi: 10.1126/science.aar4120
+  - doi: 10.1038/s41586-021-04098-7
+  - doi: 10.1126/science.aar4120
+  - doi: 10.1038/s41467-020-16703-w
 ---
 
 # Thoeris
+
+## Description
+Thoeris is a two-gene defense system identified in more than 2000 bacterial genomes. It consists of the genes ThsA and thsB. Its anti-phage function was experimentally validated in *Bacillus subtilis* :ref{doi=10.1126/science.aar4120}. In response to phage infection, it produces an isomer of cyclic ADP-ribose, which leads to  depletion of NAD+ and results in abortive infection.
+
+ThsA contains the sirtuin-like domain which binds to nicotinamide adenine dinucleotide (NAD) metabolites. The N112A point mutation neutralizes the Thoeris defense system and abolishes the NAD+ hydrolase activity of thsA :ref{doi=10.1126/science.aar4120}. It lacks a N-terminal transmembrane domain, and is predicted to be cytoplasmic. 
+
+ThsB contains a TIR domain :ref{doi=10.1126/science.aar4120} is proposed to participate in the recognition of phage infection, as various thsB proteins sense different phage components.ThsB is found in more than 50% of Thoeris systems in multiple diverse copies :ref{doi=10.1126/science.aar4120}.
+
+## Molecular mechanism
+
+The Thoeris system functions by degrading NAD+ (a cofactor of central metabolism) to stop the growth of phage-infected cells and prevent the transmission of the phage to neighboring bacteria :ref{doi=10.1038/s41467-020-16703-w}.
+
+The protein ThsB, featuring the TIR domain, plays a cruial role in identifying phage invasion. Upon detecting the infection, the TIR domain becomes enzymatically active, initiating the synthesis of a cADPR isomer molecule :ref{doi=10.1038/s41586-021-04098-7}. This molecule acts as a signal, binding to the ThsA effector, likely through its C-terminal SLOG domain, thereby activating its NADase activity :ref{doi=10.1038/s41586-021-04098-7}. Consequently, the NADase effector reduces NAD+ cellular levels, creating an environment unsuitable for phage replication :ref{doi=10.1038/s41586-021-04098-7,10.1038/s41467-020-16703-w}.
+
 ## Example of genomic structure
 
 The Thoeris is composed of 2 proteins: ThsA and ThsB.
@@ -39,6 +58,21 @@ Proportion of genome encoding the Thoeris system for the 14 phyla with more than
 
 
 ## Structure
+
+### Experimentaly determined structure
+
+From :ref{doi=10.1038/s41467-020-16703-w} in *Bacillus cereus* MSX-D12:
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrls: 
+    - /thoeris/6lhx_BcThsA_4mer.pdb
+    - /thoeris/6lhy_BcThsB_1mer.pdb
+    - /thoeris/7uxs_BcThsA_2mer_cdpr.pdb
+---
+::
+
 ### Thoeris_I
 ##### Example 1
 

content/3.defense-systems/tiamat.md

@@ -11,7 +11,8 @@ tableColumns:
     Effector: Unknown
     PFAM: PF00656, PF13020
 contributors: 
-  - Helena Shomar, Marie Guillaume
+  - Helena Shomar
+  - Marie Guillaume
 relevantAbstracts:
   - doi: 10.1016/j.chom.2022.09.017
 

content/4.refseq.md

 ---
 title: RefSeq DB
 layout: db
-navigation: 
-  icon: "mdi-database"
+navigation.icon: 'i-tabler:database'
 ---
 
 # RefSeq DB

content/5.structure.md

@@ -2,7 +2,7 @@
 title: Structures DB
 layout: db
 navigation: 
-  icon: "mdi-database"
+  icon: 'i-tabler:database'
 ---
 
 # Structure's prediction DB

data/list-systems.json

@@ -892,7 +892,8 @@
   {
     "title": "Tiamat",
     "contributors": [
-      "Helena Shomar, Marie Guillaume"
+      "Helena Shomar",
+      "Marie Guillaume"
     ],
     "relevantAbstracts": [
       {
@@ -2412,7 +2413,7 @@
   {
     "title": "NixI",
     "contributors": [
-      "Marian Dominguez Mirazo"
+      "Marian Dominguez-Mirazo"
     ],
     "relevantAbstracts": [
       {

docker-compose.yml

@@ -8,6 +8,7 @@ services:
         BASE_URL: /wiki/
         MEILI_HOST: http://localhost:7700
         MEILI_API_KEY: f9cc073016cbb392365aae86517878cb3f3408bb85c1fafd06e27f73ccb35e3d
+        HOST_URL: http://localhost:8082
     container_name: nuxt
     environment:
       HOST: 0.0.0.0

layouts/db.vue

@@ -4,7 +4,7 @@ const { page } = useContent();
 
 </script>
 <template>
-    <LayoutWrapper :title="page.title" :fluid="true" :toc="false" :edit="false" :nav-drawer="false">
+    <LayoutWrapper :title="page?.title" :fluid="true" :toc="false" :edit="false" :nav-drawer="false">
         <slot />
     </LayoutWrapper>
 </template>

layouts/foldseek.vue

+<template>
+    <LayoutWrapper title="Foldseek results" :density="'compact'" :fluid="true" :toc="false" :edit="false"
+        :nav-drawer="false">
+        <slot />
+    </LayoutWrapper>
+</template>

nuxt.config.ts

@@ -2,12 +2,13 @@ import { md3 } from 'vuetify/blueprints'
 // https://v3.nuxtjs.org/api/configuration/nuxt.config
 export default defineNuxtConfig({
   modules: [
+    '@unocss/nuxt',
     '@nuxt/content',
     'vuetify-nuxt-module',
     '@vueuse/nuxt',
     '@pinia/nuxt',
     'nuxt-meilisearch',
-    // '@unocss/nuxt',
+
   ],
   content: {
     documentDriven: {
@@ -24,8 +25,15 @@ export default defineNuxtConfig({
     vuetifyOptions: {
       labComponents: true,
       icons: {
-        defaultSet: 'mdi',
+        defaultSet: 'unocss-mdi',
         sets: ['mdi', 'fa', 'md'],
+        unocssIcons: {
+          // default is i-mdi:close-circle
+          // database: 'i-tabler:database',
+          // even from another collection, default is i-mdi:chevron-up
+          // generalconcept: 'i-mdi:book-education-outline',
+          // help: 'i-tabler:help'
+        }
       },
       blueprint: md3
 
@@ -44,12 +52,13 @@ export default defineNuxtConfig({
 
     public: {
       defenseFinderWebservice: '/',
+      hostUrl: "http://localhost:8082",
       meilisearchClient: {
         hostUrl: 'http://localhost:7700',
         searchApiKey: 'api_key',
       },
-      meiliHost: 'http://localhost:7700',
-      meiliApiKey: 'api_key'
+      // meiliHost: 'http://localhost:7700',
+      // meiliApiKey: 'api_key'
     }
   },
 

package.json

 {
   "private": true,
+  "name": "defense-finder-wiki",
+  "author": "Rémi Planel <rplanel@pasteur.fr>",
   "scripts": {
     "build": "nuxt build",
     "dev": "nuxt dev",
@@ -7,13 +9,22 @@
     "preview": "nuxt preview"
   },
   "devDependencies": {
-    "@nuxt/content": "^2.9.0",
-    "@types/node": "^20.10.4",
-    "@vueuse/core": "^10.6.1",
-    "@vueuse/nuxt": "^10.6.1",
-    "nuxt": "^3.9.0",
+    "@iconify-json/game-icons": "^1.1.7",
+    "@iconify-json/gravity-ui": "^1.1.1",
+    "@iconify-json/material-symbols": "^1.1.69",
+    "@iconify-json/mdi": "^1.1.64",
+    "@iconify-json/ph": "^1.1.10",
+    "@iconify-json/tabler": "^1.1.103",
+    "@iconify-json/vscode-icons": "^1.1.32",
+    "@nuxt/content": "^2.10.0",
+    "@types/node": "^20.11.0",
+    "@unocss/nuxt": "^0.58.3",
+    "@unocss/preset-icons": "^0.58.3",
+    "@vueuse/core": "^10.7.1",
+    "@vueuse/nuxt": "^10.7.1",
+    "nuxt": "^3.9.1",
     "nuxt-meilisearch": "^1.1.0",
-    "vuetify-nuxt-module": "^0.7.3"
+    "vuetify-nuxt-module": "^0.9.0"
   },
   "overrides": {
     "vue": "latest"

packages/df-wiki-cli/df_wiki_cli/content/main.py

@@ -13,6 +13,7 @@ from pydantic import BaseModel, ValidationError
 import frontmatter
 from enum import Enum
 from rich.console import Console
+import re
 
 console = Console()
 app = typer.Typer()
@@ -216,9 +217,9 @@ def systems(
                             if "article" in table_data:
                                 sanitizedMetadata["doi"] = table_data["article"]["doi"]
                                 if "abstract" in table_data["article"]:
-                                    sanitizedMetadata["abstract"] = table_data["article"][
-                                        "abstract"
-                                    ]
+                                    sanitizedMetadata["abstract"] = table_data[
+                                        "article"
+                                    ]["abstract"]
                                 del table_data["article"]
                             if "PFAM" in table_data:
                                 del table_data["PFAM"]
@@ -241,3 +242,35 @@ def pae2png(tsv_file, png_file):
     plt.tight_layout()
     plt.savefig(png_file, dpi=150, facecolor=None, transparent=True)
     plt.close()
+
+
+@app.command()
+def refseq(
+    input: Annotated[
+        Path,
+        typer.Option(
+            exists=False,
+            file_okay=True,
+            writable=True,
+        ),
+    ],
+    output: Annotated[
+        Path,
+        typer.Option(
+            file_okay=True,
+            dir_okay=False,
+            writable=True,
+            resolve_path=True,
+        ),
+    ],
+):
+    with open(output, "w") as out, open(input, "r") as refseq_f:
+        reader = csv.DictReader(refseq_f)
+        fieldnames = reader.fieldnames
+        writer = csv.DictWriter(out, fieldnames=fieldnames)
+        writer.writeheader()
+        for row in reader:
+            result = re.sub(r"^(\w+)\.\d+(_.*)$", r"\1\2", row["sys_id"])
+            console.print(f"[green]{row['sys_id']} ->  {result}")
+            row["sys_id"] = result
+            writer.writerow(row)