diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json index e7c0d8e..90c3d1b 100644 --- a/dev/.documenter-siteinfo.json +++ b/dev/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.10.3","generation_timestamp":"2024-05-04T01:39:23","documenter_version":"1.4.1"}} \ No newline at end of file +{"documenter":{"julia_version":"1.10.3","generation_timestamp":"2024-05-04T02:04:55","documenter_version":"1.4.1"}} \ No newline at end of file diff --git a/dev/assets/logo.jpeg b/dev/assets/logo.jpeg new file mode 100644 index 0000000..7b0ec9f Binary files /dev/null and b/dev/assets/logo.jpeg differ diff --git a/dev/index.html b/dev/index.html index 7045512..51db0e0 100644 --- a/dev/index.html +++ b/dev/index.html @@ -1,2 +1,2 @@ -Home · KEGGAPI.jl
+Home · KEGGAPI.jl
diff --git a/dev/man/examples/index.html b/dev/man/examples/index.html index d6d0473..e943a91 100644 --- a/dev/man/examples/index.html +++ b/dev/man/examples/index.html @@ -1,13 +1,13 @@ -Some Examples · KEGGAPI.jl

Some Examples

Basics

Examples analogous to KEGG Conv

Querying the API for a simple conversion returns a list with:

  1. The API call
  2. The column headers of the call ( if the result is tabular )
  3. The data

This allows to easily convert to a data frame:

output = KEGGAPI.conv("eco", "ncbi-geneid");
+Some Examples · KEGGAPI.jl
Some Examples
KEGGAPI.conv
Examples analogous to KEGG Conv
Querying the API for a simple conversion returns a list with:
  1. The API call
  2. The column headers of the call ( if the result is tabular )
  3. The data
This allows to easily convert to a data frame:
output = KEGGAPI.conv("eco", "ncbi-geneid");
 first(DataFrame(
   output.data,
   output.colnames
-), 20)
20×2 DataFrame
RowTarget IDSource ID
StringString
1ncbi-geneid:944742eco:b0001
2ncbi-geneid:945803eco:b0002
3ncbi-geneid:947498eco:b0003
4ncbi-geneid:945198eco:b0004
5ncbi-geneid:944747eco:b0005
6ncbi-geneid:944749eco:b0006
7ncbi-geneid:944745eco:b0007
8ncbi-geneid:944748eco:b0008
9ncbi-geneid:944760eco:b0009
10ncbi-geneid:944792eco:b0010
11ncbi-geneid:944771eco:b0011
12ncbi-geneid:948295eco:b0012
13ncbi-geneid:944751eco:b0013
14ncbi-geneid:944750eco:b0014
15ncbi-geneid:944753eco:b0015
16ncbi-geneid:944754eco:b0016
17ncbi-geneid:944756eco:b0018
18ncbi-geneid:944758eco:b0019
19ncbi-geneid:944757eco:b0020
20ncbi-geneid:944743eco:b0021
output = KEGGAPI.conv("ncbi-geneid", "eco");
+), 5)
5×2 DataFrame
RowTarget IDSource ID
StringString
1ncbi-geneid:944742eco:b0001
2ncbi-geneid:945803eco:b0002
3ncbi-geneid:947498eco:b0003
4ncbi-geneid:945198eco:b0004
5ncbi-geneid:944747eco:b0005
output = KEGGAPI.conv("ncbi-geneid", "eco");
 first(DataFrame(
   output.data,
   output.colnames
-), 20)
20×2 DataFrame
RowTarget IDSource ID
StringString
1eco:b0001ncbi-geneid:944742
2eco:b0002ncbi-geneid:945803
3eco:b0003ncbi-geneid:947498
4eco:b0004ncbi-geneid:945198
5eco:b0005ncbi-geneid:944747
6eco:b0006ncbi-geneid:944749
7eco:b0007ncbi-geneid:944745
8eco:b0008ncbi-geneid:944748
9eco:b0009ncbi-geneid:944760
10eco:b0010ncbi-geneid:944792
11eco:b0011ncbi-geneid:944771
12eco:b0012ncbi-geneid:948295
13eco:b0013ncbi-geneid:944751
14eco:b0014ncbi-geneid:944750
15eco:b0015ncbi-geneid:944753
16eco:b0016ncbi-geneid:944754
17eco:b0018ncbi-geneid:944756
18eco:b0019ncbi-geneid:944758
19eco:b0020ncbi-geneid:944757
20eco:b0021ncbi-geneid:944743
output = KEGGAPI.conv("ncbi-proteinid", "hsa:10458+ece:Z5100");
+), 5)
5×2 DataFrame
RowTarget IDSource ID
StringString
1eco:b0001ncbi-geneid:944742
2eco:b0002ncbi-geneid:945803
3eco:b0003ncbi-geneid:947498
4eco:b0004ncbi-geneid:945198
5eco:b0005ncbi-geneid:944747
output = KEGGAPI.conv("ncbi-proteinid", "hsa:10458+ece:Z5100");
 DataFrame(
   output.data,
   output.colnames
@@ -15,4 +15,4 @@
 DataFrame(
   output.data,
   output.colnames
-)
1×2 DataFrame
RowTarget IDSource ID
StringString
1ncbi-geneid:948364eco:b3809

+)
1×2 DataFrame
RowTarget IDSource ID
StringString
1ncbi-geneid:948364eco:b3809
diff --git a/dev/man/functions/index.html b/dev/man/functions/index.html index 6f64093..abea04b 100644 --- a/dev/man/functions/index.html +++ b/dev/man/functions/index.html @@ -1,10 +1,10 @@ -KEGGAPI.jl Functions · KEGGAPI.jl

KEGGAPI.jl Functions

KEGGAPI.conv — Method

KEGGAPI.conv(<targetdb>, <sourcedb>)

Convert KEGG identifiers to/from outside identifiers.

Example:

using KEGGAPI
+KEGGAPI.jl Functions · KEGGAPI.jl
KEGGAPI.jl Functions
KEGGAPI.conv — Method
KEGGAPI.conv(<targetdb>, <sourcedb>)
Convert KEGG identifiers to/from outside identifiers.
Example:
using KEGGAPI
 KEGGAPI.conv("eco", "ncbi-geneid")
 KEGGAPI.conv("ncbi-geneid", "eco")
 KEGGAPI.conv("ncbi-proteinid", "hsa:10458+ece:Z5100")
-KEGGAPI.conv("genes", "ncbi-geneid:948364")
source
KEGGAPI.find — Function
KEGGAPI.find(database, query) -> KeggTupleList
Find entries in a specific database from the KEGG API.
using KEGGAPI
-KEGGAPI.find("compound","glucose")
source
KEGGAPI.get_image — Method
KEGGAPI.get_image(pathway) -> Image
Get an image of a specific pathway from the KEGG API.
Example:
KEGGAPI.get_image("hsa00010")
source
KEGGAPI.info — Method
KEGGAPI.info(database) -> String
Get information about a specific database from the KEGG API.
Example:
KEGGAPI.info("kegg")
source
KEGGAPI.kegg_get — Function
KEGGAPI.get(query, option) -> Vector
Get entries from across the KEGG database. The get function takes a vector of strings and returns a vector containing the urls used and the data returned.
The get function will split the vector into groups of 10 and make a request for each chunk.
Examples
using KEGGAPI
+KEGGAPI.conv("genes", "ncbi-geneid:948364")
source
KEGGAPI.find — Function
KEGGAPI.find(database, query) -> KeggTupleList
Find entries in a specific database from the KEGG API.
using KEGGAPI
+KEGGAPI.find("compound","glucose")
source
KEGGAPI.get_image — Method
KEGGAPI.get_image(pathway) -> Image
Get an image of a specific pathway from the KEGG API.
Example:
KEGGAPI.get_image("hsa00010")
source
KEGGAPI.info — Method
KEGGAPI.info(database) -> String
Get information about a specific database from the KEGG API.
Example:
KEGGAPI.info("kegg")
source
KEGGAPI.kegg_get — Function
KEGGAPI.get(query, option) -> Vector
Get entries from across the KEGG database. The get function takes a vector of strings and returns a vector containing the urls used and the data returned.
The get function will split the vector into groups of 10 and make a request for each chunk.
Examples
using KEGGAPI
 kegg_get_genes = 
     KEGGAPI.kegg_get(
         ["hsa:10458", "hsa:10458", "hsa:10458", "hsa:10458"], 
@@ -15,5 +15,5 @@
 KEGGAPI.kegg_get(
     ["C01290","G00092"]
     );
-first(kegg_get_compounds)
source
KEGGAPI.link — Method
KEGGAPI.conv(<targetdb>, <sourcedb>)
Find related entries by using database cross-references
Example:
KEGGAPI.link("pathway", "hsa")
source
KEGGAPI.list — Function
KEGGAPI.list(database)
Get a list of entries from a specific database from the KEGG API.
Example:
KEGGAPI.list("pathway")
source
KEGGAPI.request — Method
request(url)
Make a request to the specified URL and return the response body as a string. If an error occurs, a RequestError is thrown. This function is not intended for direct use. Instead, use the info, list, and find, etc. functions.
Examples
request("https://rest.kegg.jp/info/kegg")
source
KEGGAPI.request_other — Method
request_other(url)
Make a request to the specified URL and return the response body as a vector. If an error occurs, a RequestError is thrown. This function is not intended for direct use.
Examples
request_other("https://rest.kegg.jp/image/hsa00010")
source
KEGGAPI.save_image — Method
KEGGAPI.save_image(image, filename) -> filename
Save an image to a file.
Examples
image = KEGGAPI.get_image("hsa00010")
-KEGGAPI.save_image(image, "glycolysis.png")
source

+first(kegg_get_compounds)
source
KEGGAPI.link — Method

KEGGAPI.conv(<targetdb>, <sourcedb>)

Find related entries by using database cross-references

Example:

KEGGAPI.link("pathway", "hsa")
source
KEGGAPI.list — Function

KEGGAPI.list(database)

Get a list of entries from a specific database from the KEGG API.

Example:

KEGGAPI.list("pathway")
source
KEGGAPI.request — Method

request(url)

Make a request to the specified URL and return the response body as a string. If an error occurs, a RequestError is thrown. This function is not intended for direct use. Instead, use the info, list, and find, etc. functions.

Examples

request("https://rest.kegg.jp/info/kegg")
source
KEGGAPI.request_other — Method

request_other(url)

Make a request to the specified URL and return the response body as a vector. If an error occurs, a RequestError is thrown. This function is not intended for direct use.

Examples

request_other("https://rest.kegg.jp/image/hsa00010")
source
KEGGAPI.save_image — Method

KEGGAPI.save_image(image, filename) -> filename

Save an image to a file.

Examples

image = KEGGAPI.get_image("hsa00010")
+KEGGAPI.save_image(image, "glycolysis.png")
source
diff --git a/dev/man/guide/index.html b/dev/man/guide/index.html new file mode 100644 index 0000000..1ed775b --- /dev/null +++ b/dev/man/guide/index.html @@ -0,0 +1,2 @@ + +Guide · KEGGAPI.jl

Package Guide

Installation

KEGGAPI can be installed using the Julia package manager. From the Julia REPL, type ] to enter the Pkg REPL mode and run

pkg> add https://github.com/bwbioinfo/KEGGAPI.jl
diff --git a/dev/man/workflow/index.html b/dev/man/workflow/index.html new file mode 100644 index 0000000..7dfcb55 --- /dev/null +++ b/dev/man/workflow/index.html @@ -0,0 +1,2 @@ + +A More Realistic Workflow · KEGGAPI.jl
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