From 4faaebd7f261af4cf7f74352888cc449a0f8fcad Mon Sep 17 00:00:00 2001
From: Laura Luebbert <56094636+lauraluebbert@users.noreply.github.com>
Date: Fri, 26 Apr 2024 16:41:34 -0400
Subject: [PATCH 1/7] Update search.md
---
docs/src/en/search.md | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/docs/src/en/search.md b/docs/src/en/search.md
index b6943d61..ec357240 100644
--- a/docs/src/en/search.md
+++ b/docs/src/en/search.md
@@ -13,10 +13,12 @@ One or more free form search words, e.g. gaba nmda. (Note: Search is not case-se
Species or database to be searched.
A species can be passed in the format 'genus_species', e.g. 'homo_sapiens' or 'arabidopsis_thaliana'.
To pass a specific database, pass the name of the CORE database, e.g. 'mus_musculus_dba2j_core_105_1'.
+
All available core databases can be found here:
Vertebrates: [http://ftp.ensembl.org/pub/current/mysql/](http://ftp.ensembl.org/pub/current/mysql/)
Invertebrates: [http://ftp.ensemblgenomes.org/pub/current/](http://ftp.ensemblgenomes.org/pub/current/) + select kingdom + go to mysql/
-Supported shortcuts: 'human', 'mouse'.
+
+Supported shortcuts: 'human', 'mouse'
**Optional arguments**
`-r` `--release`
From a1654f54235b5a758c4ff9f94ce0c75cc859f946 Mon Sep 17 00:00:00 2001
From: Laura Luebbert <56094636+lauraluebbert@users.noreply.github.com>
Date: Fri, 26 Apr 2024 16:42:03 -0400
Subject: [PATCH 2/7] Update search.md
---
docs/src/es/search.md | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/docs/src/es/search.md b/docs/src/es/search.md
index f5eae290..fdc5cbef 100644
--- a/docs/src/es/search.md
+++ b/docs/src/es/search.md
@@ -13,10 +13,12 @@ Una o más palabras de búsqueda de forma libre, p. ej. gaba nmda. (Nota: la bú
Especies o base de datos a buscar.
Una especie se puede pasar en el formato 'género_especie', p. ej. 'homo_sapiens' o 'arabidopsis_thaliana'.
Para pasar una base de datos específica, pase el nombre de la base de datos CORE, p. ej. 'mus_musculus_dba2j_core_105_1'.
+
Todas las bases de datos disponibles para cada versión de Ensembl se pueden encontrar aquí:
Vertebrados: [http://ftp.ensembl.org/pub/current/mysql/](http://ftp.ensembl.org/pub/current/mysql/)
Invertebrados: [http://ftp.ensemblgenomes.org/pub/current/](http://ftp.ensemblgenomes.org/pub/current/) + selecciona reino animal + selecciona mysql/
-Accesos directos: 'human', 'mouse'.
+
+Accesos directos: 'human', 'mouse'
**Parámetros optionales**
`-r` `--release`
From 118dc40c5078094e97873707c5723bec3931fd26 Mon Sep 17 00:00:00 2001
From: Laura Luebbert <56094636+lauraluebbert@users.noreply.github.com>
Date: Fri, 26 Apr 2024 16:49:54 -0400
Subject: [PATCH 3/7] Update updates.md
---
docs/src/en/updates.md | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/docs/src/en/updates.md b/docs/src/en/updates.md
index 5ce7aaea..9ddc9753 100644
--- a/docs/src/en/updates.md
+++ b/docs/src/en/updates.md
@@ -13,7 +13,7 @@
- The regex string for regular expression matches was encapsulated as follows: "(?=(regex))" (instead of directly passing the regex string "regex") to enable capturing all occurrences of a motif when the motif length is variable and there are repeats in the sequence ([https://regex101.com/r/HUWLlZ/1](https://regex101.com/r/HUWLlZ/1)).
- [`gget setup`](./setup.md): Use the `out` argument to specify a directory the ELM database will be downloaded into. Completes [this feature request](https://github.com/pachterlab/gget/issues/119).
- [`gget diamond`](./diamond.md): The DIAMOND command is now run with `--ignore-warnings` flag, allowing niche sequences such as amino acid sequences that only contain nucleotide characters and repeated sequences. This is also true for DIAMOND alignments performed within [`gget elm`](./elm.md).
-- [`gget ref`](./ref.md) and [`gget search`](./search.md) back-end change: the current Ensembl release is fetched from the new [release file](https://ftp.ensembl.org/pub/VERSION) on the Ensembl FTP site to avoid errors during uploads of new releases.
+- **[`gget ref`](./ref.md) and [`gget search`](./search.md) back-end change: the current Ensembl release is fetched from the new [release file](https://ftp.ensembl.org/pub/VERSION) on the Ensembl FTP site to avoid errors during uploads of new releases.**
- [`gget search`](./search.md):
- FTP link results (`--ftp`) are saved in txt file format instead of json.
- Fix URL links to Ensembl gene summary for species with a subspecies name and invertebrates.
From b8a1291e920c2e87393d2b3b4fd98874d39743b6 Mon Sep 17 00:00:00 2001
From: Laura Luebbert <56094636+lauraluebbert@users.noreply.github.com>
Date: Fri, 26 Apr 2024 16:50:25 -0400
Subject: [PATCH 4/7] Update updates.md
---
docs/src/es/updates.md | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/docs/src/es/updates.md b/docs/src/es/updates.md
index 1fd0cfcb..e0966495 100644
--- a/docs/src/es/updates.md
+++ b/docs/src/es/updates.md
@@ -13,7 +13,7 @@
- La cadena de expresiones regulares para coincidencias de expresiones regulares se encapsuló de la siguiente manera: "(?=(regex))" (en lugar de pasar directamente la cadena de expresiones regulares "regex") para permitir capturar todas las apariciones de un motivo cuando la longitud del motivo es variable y hay son repeticiones en la secuencia ([https://regex101.com/r/HUWLlZ/1](https://regex101.com/r/HUWLlZ/1)).
- [`gget setup`](./setup.md): utilice el argumento `out` para especificar un directorio en el que se descargará la base de datos ELM. Completa [esta solicitud de función](https://github.com/pachterlab/gget/issues/119).
- [`gget Diamond`](./diamond.md): El comando DIAMOND ahora se ejecuta con el indicador `--ignore-warnings`, lo que permite secuencias de nicho, como secuencias de aminoácidos que solo contienen caracteres de nucleótidos y secuencias repetidas. Esto también es válido para las alineaciones DIAMOND realizadas dentro de [`gget elm`](./elm.md).
-- Cambio de back-end de [`gget ref`](./ref.md) y [`gget search`](./search.md): la versión actual de Ensembl se obtiene del nuevo [archivo de versión](https://ftp.ensembl.org/pub/VERSION) en el sitio FTP de Ensembl para evitar errores durante la carga de nuevos lanzamientos.
+- **Cambio de back-end de [`gget ref`](./ref.md) y [`gget search`](./search.md): la versión actual de Ensembl se obtiene del nuevo [archivo de versión](https://ftp.ensembl.org/pub/VERSION) en el sitio FTP de Ensembl para evitar errores durante la carga de nuevos lanzamientos.**
- [`gget search`](./search.md):
- Los resultados del enlace FTP (`--ftp`) se guardan en formato de archivo txt en lugar de json.
- Se corrigieron enlaces URL al resumen de genes de Ensembl para especies con un nombre de subespecie e invertebrados.
From eb4738118929d87763450da01d07adc13882311c Mon Sep 17 00:00:00 2001
From: Laura Luebbert <56094636+lauraluebbert@users.noreply.github.com>
Date: Fri, 26 Apr 2024 16:55:34 -0400
Subject: [PATCH 5/7] Update introduction.md
---
docs/src/en/introduction.md | 2 ++
1 file changed, 2 insertions(+)
diff --git a/docs/src/en/introduction.md b/docs/src/en/introduction.md
index 325f79a0..96d32645 100644
--- a/docs/src/en/introduction.md
+++ b/docs/src/en/introduction.md
@@ -15,6 +15,8 @@
`gget` consists of a collection of separate but interoperable modules, each designed to facilitate one type of database querying in a single line of code.
+The databases queried by `gget` are continuously being updated which sometimes changes their structure. `gget` modules are tested automatically on a biweekly basis and updated to match new database structures when necessary. If you encounter a problem, please upgrade to the latest `gget` version using `pip install --upgrade gget`. If the problem persists, please [report the issue](https://github.com/pachterlab/gget/issues/new/choose).
+
[
Request a new feature
](https://github.com/pachterlab/gget/issues/new/choose)
From cc97d24d978e9272dd5c750f086fd67ae68d9a2f Mon Sep 17 00:00:00 2001
From: Laura Luebbert <56094636+lauraluebbert@users.noreply.github.com>
Date: Fri, 26 Apr 2024 16:57:05 -0400
Subject: [PATCH 6/7] Update introduction.md
---
docs/src/es/introduction.md | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/docs/src/es/introduction.md b/docs/src/es/introduction.md
index e67578a6..06fb2aca 100644
--- a/docs/src/es/introduction.md
+++ b/docs/src/es/introduction.md
@@ -13,9 +13,10 @@
`gget` es un programa gratuito de código fuente abierta de Terminal y Python que permite la consulta eficiente de bases de datos genómicas.
-`gget` consiste en un conjunto de módulos separados pero interoperables, cada uno diseñado para facilitar un tipo de consulta de base de datos en una sola línea de código.
+`gget` consiste en un conjunto de módulos separados pero interoperables, cada uno diseñado para facilitar un tipo de consulta de base de datos en una sola línea de código.
+
+Las bases de datos consultadas por `gget` se actualizan continuamente, lo que a veces cambia su estructura. Los módulos `gget` se prueban automáticamente cada dos semanas y se actualizan para que coincidan con las nuevas estructuras de la base de datos cuando es necesario. Si encuentra algún problema, actualice a la última versión de `gget` usando `pip install --upgrade gget`. Si el problema persiste, [informa el problema](https://github.com/pachterlab/gget/issues/new/choose).
-
[
Solicitar una nueva función
](https://github.com/pachterlab/gget/issues/new/choose)
From a2b0358e2acdcddb68372bb79aca56f5ffcb365d Mon Sep 17 00:00:00 2001
From: Laura Luebbert <56094636+lauraluebbert@users.noreply.github.com>
Date: Fri, 26 Apr 2024 16:58:00 -0400
Subject: [PATCH 7/7] Update introduction.md
---
docs/src/en/introduction.md | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/docs/src/en/introduction.md b/docs/src/en/introduction.md
index 96d32645..03b85f23 100644
--- a/docs/src/en/introduction.md
+++ b/docs/src/en/introduction.md
@@ -15,9 +15,8 @@
`gget` consists of a collection of separate but interoperable modules, each designed to facilitate one type of database querying in a single line of code.
-The databases queried by `gget` are continuously being updated which sometimes changes their structure. `gget` modules are tested automatically on a biweekly basis and updated to match new database structures when necessary. If you encounter a problem, please upgrade to the latest `gget` version using `pip install --upgrade gget`. If the problem persists, please [report the issue](https://github.com/pachterlab/gget/issues/new/choose).
+The databases queried by `gget` are continuously being updated which sometimes changes their structure. `gget` modules are tested automatically on a biweekly basis and updated to match new database structures when necessary. If you encounter a problem, please upgrade to the latest `gget` version using `pip install --upgrade gget`. If the problem persists, please [report the issue](https://github.com/pachterlab/gget/issues/new/choose).
-
[
Request a new feature
](https://github.com/pachterlab/gget/issues/new/choose)