149 update docs to show python api (#157)

* included gruvbox theme for highlight for highlight.js

* moved blat to separate ucsc submodule

* added blat to ucsc submodule

* used new format for archs4

* using new format for docs with table for args plus added in all python interface usages where applicable

* fix capitalization typo in docs

* ignore book outputs

.gitignore

@@ -11,3 +11,6 @@ Cargo.lock
 
 **__pycache__**
 *DS_Store*
+
+# Ignore docs book
+docs/book/**

docs/src/SUMMARY.md

@@ -16,6 +16,7 @@
 - [Info](./info.md)
 - [Seq](./seq.md)
 - [UCSC](./ucsc.md)
+  - [BLAT](./ucsc/blat.md)
 - [PDB](./pdb.md)
   - [Structure](./pdb/structure.md)
   - [Info](./pdb/info.md)

docs/src/archs4/correlate.md

@@ -1,25 +1,35 @@
 # Correlate
 
-## Help
+Performs a gene-correlation analysis using [ARCHS4](https://maayanlab.cloud/archs4).
 
-```text
-Performs a gene-correlation analysis
+## Arguments
 
-Usage: ggetrs archs4 correlate [OPTIONS] <GENE_NAME>
+| Name | Short | Long | Description |
+|------|-------|------|-------------|
+| Count | `-c` | `--count` | number of values to recover [default: 100] |
+| Output | `-o` | `--output` | optional filepath to write output to [default=stdout] |
 
-Arguments:
-  <GENE_NAME>  Gene name to query for correlation
-
-Options:
-  -c, --count <COUNT>    number of values to recover [default: 100]
-  -o, --output <OUTPUT>  output filepath to write to [default=stdout]
-  -h, --help             Print help information
-  -V, --version          Print version information
-```
-
-## Usage
+## Command Line Interface
 
 ```bash
 # Perform a gene-correlation analysis with ARCHS4
+ggetrs archs4 correlate AP2S1
+
+# Perform a gene-correlation analysis with ARCHS4
+# But only return the top 10 results
 ggetrs archs4 correlate -c 10 AP2S1
 ```
+
+## Python
+
+```python
+import ggetrs
+
+# Perform a gene-correlation analysis for AP2S1
+# and return the top 10 results
+ggetrs.archs4.correlate("AP2S1", 10)
+
+# Perform a gene-correlation analysis for AP2S1
+# and return the top 100 results
+ggetrs.archs4.correlate("AP2S1", 100)
+```

docs/src/archs4/tissue.md

@@ -1,25 +1,33 @@
 # Tissue
 
-## Help
+Performs a tissue-correlation analysis using [ARCHS4](https://maayanlab.cloud/archs4).
 
-```text
-Perform a tissue-enrichment analysis
+## Arguments
 
-Usage: ggetrs archs4 tissue [OPTIONS] <GENE_NAME>
+| Name | Short | Long | Description |
+|------|-------|------|-------------|
+| Species | `-s` | `--species` | species of organism to recover [default: human] [possible values: human, mous] |
+| Output | `-o` | `--output` | optional filepath to write output to [default=stdout] |
 
-Arguments:
-  <GENE_NAME>  Gene name to query for tissue
 
-Options:
-  -s, --species <SPECIES>  number of values to recover [default: human] [possible values: human, mouse]
-  -o, --output <OUTPUT>    output filepath to write to [default=stdout]
-  -h, --help               Print help information
-  -V, --version            Print version information
-```
-
-## Usage
+## Command Line Interface
 
 ```bash
-# Find tissue-level expression using ARCHS4
+# Find tissue-level expression for AP2S1 in Humans
 ggetrs archs4 tissue AP2S1
+
+# Find tissue-level expression for AP2S1 in Mice
+ggetrs archs4 tissue -s mouse AP2S1
+```
+
+## Python
+
+```python
+import ggetrs
+
+# perform a tissue-correlation analysis for AP2S1 in Humans
+ggetrs.archs4.tissue("AP2S1", "human")
+
+# perform a tissue-correlation analysis for AP2S1 in Mice
+ggetrs.archs4.tissue("AP2S1", "mouse")
 ```

docs/src/autocomplete.md

@@ -2,20 +2,13 @@
 
 This is used to generate autocomplete information for your terminal shell.
 
-## Help
+## Arguments
 
-```text
-Set up autocomplete for various shells
+| Name | Short | Long | Description |
+|------|-------|------|-------------|
+| Shell | `-s` | `--shell` | Shell to generate autocompletions for [possible values: bash, elvish, fish, powershell, zsh]|
 
-Usage: ggetrs autocomplete --shell <SHELL>
-
-Options:
-  -s, --shell <SHELL>  Shell to generate autocompletions for [possible values: bash, elvish, fish, powershell, zsh]
-  -h, --help           Print help information
-  -V, --version        Print version information
-```
-
-## Usage
+## Command Line Interface
 
 ```bash
 # generate autocompletions for the fish shell

docs/src/blast.md

@@ -10,27 +10,19 @@ You may override these though by using their argument flags.
 Keep in mind that there is no logic built into validating your inputs.
 All non-default arguments will be passed to the BLAST API as is.
 
-```text
-Performs a BLAST query for a given sequence
-
-Usage: ggetrs blast [OPTIONS] <QUERY>
-
-Arguments:
-  <QUERY>  query sequence to BLAST
-
-Options:
-  -p, --program <PROGRAM>    blast program to use [possible values: blastn, blastp, blastx, tblastn, tblastx]
-  -d, --database <DATABASE>  blast database to use [possible values: nt, nr, refseq-rna, refseq-protein, swissprot, pdbaa, pdbnt]
-  -l, --limit <LIMIT>        Number of hits to return [default: 50]
-  -e, --expect <EXPECT>      Minimum expected value to consider [default: 10.0]
-  -f, --low-comp-filter      Whether to use a complexity filter (default = false)
-  -m, --megablast            Whether to use MEGABLAST (default = true)
-  -o, --output <OUTPUT>      optional filepath to write output to [default=stdout]
-  -h, --help                 Print help information
-  -V, --version              Print version information
-```
+## Arguments
+
+| Name | Short | Long | Description |
+|------|-------|------|-------------|
+| Program | `-p` | `--program` | blast program to use [possible values: blastn, blastp, blastx, tblastn, tblastx] |
+| Database | `-d` | `--database` | blast database to use [possible values: nt, nr, refseq-rna, refseq-protein, swissprot, pdbaa, pdbnt] |
+| Limit | `-l` | `--limit` | Number of hits to return [default: 50] |
+| Expect | `-e` | `--expect` | Minimum expected value to consider [default: 10.0] |
+| Low Complexity Filter | `-f` | `--low-comp-filter` | Include flag to use a complexity filter [default = false] |
+| MEGABLAST | `-m` | `--megablast` | Whether to use MEGABLAST (default = false) |
+| Output | `-o` | `--output` | optional filepath to write output to [default=stdout] |
 
-## Usage
+## Command Line Interface
 
 ```bash
 # Perform BLAST with a nucleotide sequence
@@ -42,3 +34,33 @@ ggetrs blast MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYRRYAGLYF
 # Perform BLAST with an amino acid sequence using the PDBAA database
 ggetrs blast -d pdbaa MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYRRYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEIRETSQTKVLKQLLMLQSLE
 ```
+
+## Python
+
+```python
+import ggetrs
+
+# Perform BLAST with a nucleotide sequence
+ggetrs.blast(
+  "ATACTCAGTCACACAAGCCATAGCAGGAAACAGCGAGCTTGCAGCCTCACCGACGAGTCTCAACTAAAAGGGACTCCCGGAGCTAGGGGTGGGGACTCGGCCTCACACAGTGAGTGCCGG"
+)
+
+# Perform BLAST with an amino acid sequence
+ggetrs.blast(
+  "MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYRRYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEIRETSQTKVLKQLLMLQSLE"
+)
+
+# Perform BLAST with an amino acid sequence using the PDBAA database
+ggetrs.blast(
+  "MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYRRYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEIRETSQTKVLKQLLMLQSLE",
+  database = "pdbaa"
+)
+
+# Perform BLAST with an amino acid sequence using the PDBAA database with a low complexity filter and a limit
+ggetrs.blast(
+  "MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIIYRRYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLAGEIRETSQTKVLKQLLMLQSLE",
+  database = "pdbaa",
+  limit = 10,
+  low_comp_filter=True,
+)
+```

docs/src/chembl/activity.md

@@ -1,25 +1,20 @@
 # Activity
 
-## Help
+Queries chemical bioactivity for a provided protein target and return all small molecules.
 
-```text
-Queries chemical activity for a provided item
+## Arguments
 
-Usage: ggetrs chembl activity [OPTIONS] <QUERY>
-
-Arguments:
-  <QUERY>  Query to retrieve bioactivity
-
-Options:
-  -l, --limit <LIMIT>    Number of results to return [default: 500]
-  -o, --output <OUTPUT>  Optional filepath to write output to [default=stdout]
-  -h, --help             Print help information
-  -V, --version          Print version information
-```
+| Name | Short | Long | Description |
+|------|-------|------|-------------|
+| Limit | `-l` | `--limit` | Number of results to return [default: 500] |
+| Output | `-o` | `--output` | optional filepath to write output to [default=stdout] |
 
 ## Usage
 
 ```bash
 # Query the Chembl database for small molecules with bioactivity targeting NSD1
 ggetrs chembl activity NSD1
+
+# Query the Chembl database for the top 20 bioactive molecules for NSD1
+ggetrs chembl activity -l 20 NSD1
 ```

docs/src/enrichr/enrichr.md

@@ -5,35 +5,29 @@ Perform an enrichment analysis on a list of genes using [Enrichr](https://maayan
 This requires at minimum a database name (listed [here](https://maayanlab.cloud/Enrichr/#libraries))
 and any number of gene symbols to perform enrichment analysis on.
 
-## Help
+## Library Shorthands
 
-```text
-Usage: ggetrs enrichr enrichr [OPTIONS] --library <LIBRARY> <GENE_LIST>...
+Some shorthands for the library are built into the program for convenience.
+These can be used in the command line interface or in the python interface.
 
-Arguments:
-  <GENE_LIST>...  list of gene symbols to perform enrichment analysis on
+| Alias | Library |
+|-------|---------|
+| pathway               | KEGG_2021_Human | 
+| transcription         | ChEA_2016 | 
+| ontology              | GO_Biological_Processes_2021 | 
+| diseases_drugs        | GWAS_Catalog_2019 | 
+| celltypes             | PangloaDB_Augmented_2021 | 
+| kinase_interactions   | KEA_2015 | 
 
-Options:
-  -l, --library <LIBRARY>  any database listed at: https://maayanlab.cloud/Enrichr/#libraries some shorthands include: pathway, transcription, ontology, diseases_drugs, celltypes, and kinase_interactions
-  -o, --output <OUTPUT>    optional filepath to write output to [default=stdout]
-  -h, --help               Print help information
-  -V, --version            Print version information
-```
-
-### Library Shorthands
+## Arguments
 
-Some shorthands for the library are built into the program for convenience:
+| Name | Short | Long | Description |
+|------|-------|------|-------------|
+| Library | `-l` | `--library` | a [library shorthand](#library-shorthands) or any [Enrichr library](https://maayanlab.cloud/Enrichr/#libraries) |
+| Output | `-o` | `--output` | optional filepath to write output to [default=stdout] |
 
-```text
-pathway               KEGG_2021_Human
-transcription         ChEA_2016
-ontology              GO_Biological_Processes_2021
-diseases_drugs        GWAS_Catalog_2019
-celltypes             PangloaDB_Augmented_2021
-kinase_interactions   KEA_2015
-```
 
-## Usage
+## Command Line Interface
 
 ```bash
 # Perform an enrichment analysis using Enrichr
@@ -46,3 +40,15 @@ ggetrs enrichr enrichr -l ontology AP2S1 NSD1 RFX3
 # Perform an enrichment analysis on pathway
 ggetrs enrichr enrichr -l pathway AP2S1 NSD1 RFX3
 ```
+
+## Python
+
+```python
+import ggetrs
+
+# Search using the ontology shorthand
+ggetrs.enrichr("ontology", ["AP2S1", "RFX3", "NSD1"])
+
+# Search using the kinase_interactions shorthand
+ggetrs.enrichr("kinase_interactions", ["AP2S1", "RFX3", "NSD1"])
+```

docs/src/enrichr/list.md

@@ -2,21 +2,14 @@
 
 Lists available libraries and their statistics available on [Enrichr](https://maayanlab.cloud/Enrichr).
 
-## Help
-
-```text
-List all available libraries and their descriptions
-
-Usage: ggetrs enrichr list [OPTIONS]
-
-Options:
-  -m, --minimal              Return library names in plaintext
-  -t, --list-categories      List the categorization of libraries
-  -c, --category <CATEGORY>  Filter to a category ID
-  -o, --output <OUTPUT>      optional filepath to write output to [default=stdout]
-  -h, --help                 Print help information
-  -V, --version              Print version information
-```
+## Arguments
+
+| Name | Short | Long | Description |
+|------|-------|------|-------------|
+| Minimal | `-m` | `--minimal` | Return only library names in results |
+| List Categories | `-t` | `--list-categories` | List the categorization of libraries |
+| Categories | `-c` | `--category` | Filter libraries with a specified category ID |
+| Output | `-o` | `--output` | optional filepath to write output to [default=stdout] |
 
 ## Usage
 

docs/src/ensembl/database.md

@@ -4,21 +4,14 @@ Prints all available databases on Ensembl's SQL server.
 
 This is used if you are interested in querying a specific database and can be passed into [`ggetrs search`](./search.md).
 
-## Help
+## Arguments
 
-```text
-Prints all available databases on Ensembl's SQL database
+| Name | Short | Long | Description |
+|------|-------|------|-------------|
+| Filter | `-f` | `--filter` | Provides a substring filter to only return databases which contain the substring |
+| Output | `-o` | `--output` | optional filepath to write output to [default=stdout] |
 
-Usage: ggetrs ensembl database [OPTIONS]
-
-Options:
-  -f, --filter <FILTER>  Provides a substring filter to only return databases which contain the substring
-  -o, --output <OUTPUT>  optional filepath to write output to [default=stdout]
-  -h, --help             Print help information
-  -V, --version          Print version information
-```
-
-## Usage
+## Command Line Interface
 
 ```bash
 # show all databases in the SQL server
@@ -30,3 +23,18 @@ ggetrs ensembl database -f sapiens
 # filter for databases with the `cerevisiae` substring
 ggetrs ensembl database -f cerevisiae
 ```
+
+## Python
+
+```python
+import ggetrs
+
+# show all databases in the SQL server
+ggetrs.ensembl.database()
+
+# filter for databases with the `sapiens` substring
+ggetrs.ensembl.database("sapiens")
+
+# filter for databases with the `cerevisiae` substring
+ggetrs.ensembl.database("cerevisiae")
+```