diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json index 0124dac..e7c0d8e 100644 --- a/dev/.documenter-siteinfo.json +++ b/dev/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.10.3","generation_timestamp":"2024-05-03T20:21:52","documenter_version":"1.4.1"}} \ No newline at end of file +{"documenter":{"julia_version":"1.10.3","generation_timestamp":"2024-05-04T01:39:23","documenter_version":"1.4.1"}} \ No newline at end of file diff --git a/dev/index.html b/dev/index.html index a7febe7..7045512 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 eac96fa..d6d0473 100644 --- a/dev/man/examples/index.html +++ b/dev/man/examples/index.html @@ -1,6 +1,18 @@ -Some Examples · KEGGAPI.jl

Some Examples

Basics

Examples analogous to KEGG Conv

using KEGGAPI
-KEGGAPI.conv("eco", "ncbi-geneid")
KEGGAPI.KeggTupleList("https://rest.kegg.jp/conv/eco/ncbi-geneid", ["Target ID", "Source ID"], Any[["ncbi-geneid:944742", "ncbi-geneid:945803", "ncbi-geneid:947498", "ncbi-geneid:945198", "ncbi-geneid:944747", "ncbi-geneid:944749", "ncbi-geneid:944745", "ncbi-geneid:944748", "ncbi-geneid:944760", "ncbi-geneid:944792"  …  "ncbi-geneid:63925657", "ncbi-geneid:63925658", "ncbi-geneid:63925659", "ncbi-geneid:63925661", "ncbi-geneid:63925662", "ncbi-geneid:63925663", "ncbi-geneid:63925665", "ncbi-geneid:63925666", "ncbi-geneid:63925667", "ncbi-geneid:63925627"], ["eco:b0001", "eco:b0002", "eco:b0003", "eco:b0004", "eco:b0005", "eco:b0006", "eco:b0007", "eco:b0008", "eco:b0009", "eco:b0010"  …  "eco:b4794", "eco:b4795", "eco:b4796", "eco:b4797", "eco:b4798", "eco:b4799", "eco:b4800", "eco:b4801", "eco:b4802", "eco:b4803"]])
using KEGGAPI
-KEGGAPI.conv("ncbi-geneid", "eco")
KEGGAPI.KeggTupleList("https://rest.kegg.jp/conv/ncbi-geneid/eco", ["Target ID", "Source ID"], Any[["eco:b0001", "eco:b0002", "eco:b0003", "eco:b0004", "eco:b0005", "eco:b0006", "eco:b0007", "eco:b0008", "eco:b0009", "eco:b0010"  …  "eco:b4794", "eco:b4795", "eco:b4796", "eco:b4797", "eco:b4798", "eco:b4799", "eco:b4800", "eco:b4801", "eco:b4802", "eco:b4803"], ["ncbi-geneid:944742", "ncbi-geneid:945803", "ncbi-geneid:947498", "ncbi-geneid:945198", "ncbi-geneid:944747", "ncbi-geneid:944749", "ncbi-geneid:944745", "ncbi-geneid:944748", "ncbi-geneid:944760", "ncbi-geneid:944792"  …  "ncbi-geneid:63925657", "ncbi-geneid:63925658", "ncbi-geneid:63925659", "ncbi-geneid:63925661", "ncbi-geneid:63925662", "ncbi-geneid:63925663", "ncbi-geneid:63925665", "ncbi-geneid:63925666", "ncbi-geneid:63925667", "ncbi-geneid:63925627"]])
using KEGGAPI
-KEGGAPI.conv("ncbi-proteinid", "hsa:10458+ece:Z5100")
KEGGAPI.KeggTupleList("https://rest.kegg.jp/conv/ncbi-proteinid/hsa:10458+ece:Z5100", ["Target ID", "Source ID"], Any[["hsa:10458", "ece:Z5100"], ["ncbi-proteinid:NP_059345", "ncbi-proteinid:AAG58814"]])
using KEGGAPI
-KEGGAPI.conv("genes", "ncbi-geneid:948364")
KEGGAPI.KeggTupleList("https://rest.kegg.jp/conv/genes/ncbi-geneid:948364", ["Target ID", "Source ID"], Any[["ncbi-geneid:948364"], ["eco:b3809"]])
+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");
+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");
+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");
+DataFrame(
+  output.data,
+  output.colnames
+)
2×2 DataFrame
RowTarget IDSource ID
StringString
1hsa:10458ncbi-proteinid:NP_059345
2ece:Z5100ncbi-proteinid:AAG58814
output = KEGGAPI.conv("genes", "ncbi-geneid:948364");
+DataFrame(
+  output.data,
+  output.colnames
+)
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 9d620cd..6f64093 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.

Examples

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("hsa:10458+ece:Z5100", "ncbi-proteinid")
-KEGGAPI.conv("ncbi-geneid:948364", "genes")
source
KEGGAPI.find — Function
KEGGAPI.find(database, query) -> KeggTupleList
Find entries in a specific database from the KEGG API.
Examples
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.
Examples
KEGGAPI.get_image("hsa00010")
source
KEGGAPI.info — Method
KEGGAPI.info(database) -> String
Get information about a specific database from the KEGG API.
Examples
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("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
 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
Examples
KEGGAPI.link("pathway", "hsa")
source
KEGGAPI.list — Function
KEGGAPI.list(database)
Get a list of entries from a specific database from the KEGG API.
Examples
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/search_index.js b/dev/search_index.js index ab7231f..c8dac01 100644 --- a/dev/search_index.js +++ b/dev/search_index.js @@ -1,3 +1,3 @@ var documenterSearchIndex = {"docs": -[{"location":"man/examples/#Some-Examples","page":"Some Examples","title":"Some Examples","text":"","category":"section"},{"location":"man/examples/#Basics","page":"Some Examples","title":"Basics","text":"","category":"section"},{"location":"man/examples/","page":"Some Examples","title":"Some Examples","text":"Examples analogous to KEGG Conv","category":"page"},{"location":"man/examples/","page":"Some Examples","title":"Some Examples","text":"using KEGGAPI\nKEGGAPI.conv(\"eco\", \"ncbi-geneid\")","category":"page"},{"location":"man/examples/","page":"Some Examples","title":"Some Examples","text":"using KEGGAPI\nKEGGAPI.conv(\"ncbi-geneid\", \"eco\")","category":"page"},{"location":"man/examples/","page":"Some Examples","title":"Some Examples","text":"using KEGGAPI\nKEGGAPI.conv(\"ncbi-proteinid\", \"hsa:10458+ece:Z5100\")","category":"page"},{"location":"man/examples/","page":"Some Examples","title":"Some Examples","text":"using KEGGAPI\nKEGGAPI.conv(\"genes\", \"ncbi-geneid:948364\")","category":"page"},{"location":"","page":"Home","title":"Home","text":"CurrentModule = KEGGAPI","category":"page"},{"location":"#KEGGAPI","page":"Home","title":"KEGGAPI","text":"","category":"section"},{"location":"","page":"Home","title":"Home","text":"Documentation for KEGGAPI.","category":"page"},{"location":"","page":"Home","title":"Home","text":"KEGG","category":"page"},{"location":"","page":"Home","title":"Home","text":"Pages = [\n \"man/functions.md\",\n \"man/examples.md\",\n]\nDepth = 2","category":"page"},{"location":"","page":"Home","title":"Home","text":"","category":"page"},{"location":"man/functions/#KEGGAPI.jl-Functions","page":"KEGGAPI.jl Functions","title":"KEGGAPI.jl Functions","text":"","category":"section"},{"location":"man/functions/","page":"KEGGAPI.jl Functions","title":"KEGGAPI.jl Functions","text":"Modules = [KEGGAPI]","category":"page"},{"location":"man/functions/#KEGGAPI.conv-Tuple{String, String}","page":"KEGGAPI.jl Functions","title":"KEGGAPI.conv","text":"KEGGAPI.conv(, )\n\nConvert KEGG identifiers to/from outside identifiers.\n\nExamples\n\nusing KEGGAPI\nKEGGAPI.conv(\"eco\", \"ncbi-geneid\")\nKEGGAPI.conv(\"ncbi-geneid\", \"eco\")\nKEGGAPI.conv(\"hsa:10458+ece:Z5100\", \"ncbi-proteinid\")\nKEGGAPI.conv(\"ncbi-geneid:948364\", \"genes\")\n\n\n\n\n\n","category":"method"},{"location":"man/functions/#KEGGAPI.find","page":"KEGGAPI.jl Functions","title":"KEGGAPI.find","text":"KEGGAPI.find(database, query) -> KeggTupleList\n\nFind entries in a specific database from the KEGG API.\n\nExamples\n\nusing KEGGAPI\nKEGGAPI.find(\"compound\",\"glucose\")\n\n\n\n\n\n","category":"function"},{"location":"man/functions/#KEGGAPI.get_image-Tuple{String}","page":"KEGGAPI.jl Functions","title":"KEGGAPI.get_image","text":"KEGGAPI.get_image(pathway) -> Image\n\nGet an image of a specific pathway from the KEGG API.\n\nExamples\n\nKEGGAPI.get_image(\"hsa00010\")\n\n\n\n\n\n","category":"method"},{"location":"man/functions/#KEGGAPI.info-Tuple{String}","page":"KEGGAPI.jl Functions","title":"KEGGAPI.info","text":"KEGGAPI.info(database) -> String\n\nGet information about a specific database from the KEGG API.\n\nExamples\n\nKEGGAPI.info(\"kegg\")\n\n\n\n\n\n","category":"method"},{"location":"man/functions/#KEGGAPI.kegg_get","page":"KEGGAPI.jl Functions","title":"KEGGAPI.kegg_get","text":"KEGGAPI.get(query, option) -> Vector\n\nGet entries from across the KEGG database. 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The get function takes a vector of strings and returns a vector containing the urls used and the data returned.\n\nThe get function will split the vector into groups of 10 and make a request for each chunk.\n\nExamples\n\nusing KEGGAPI\nkegg_get_genes = \n KEGGAPI.kegg_get(\n [\"hsa:10458\", \"hsa:10458\", \"hsa:10458\", \"hsa:10458\"], \n \"ntseq\"\n );\nfirst(kegg_get_genes)\nkegg_get_compounds = \nKEGGAPI.kegg_get(\n [\"C01290\",\"G00092\"]\n );\nfirst(kegg_get_compounds)\n\n\n\n\n\n","category":"function"},{"location":"man/functions/#KEGGAPI.link-Tuple{String, String}","page":"KEGGAPI.jl Functions","title":"KEGGAPI.link","text":"KEGGAPI.conv(, )\n\nFind related entries by using database cross-references\n\nExample:\n\nKEGGAPI.link(\"pathway\", \"hsa\")\n\n\n\n\n\n","category":"method"},{"location":"man/functions/#KEGGAPI.list","page":"KEGGAPI.jl Functions","title":"KEGGAPI.list","text":"KEGGAPI.list(database)\n\nGet a list of entries from a specific database from the KEGG API.\n\nExample:\n\nKEGGAPI.list(\"pathway\")\n\n\n\n\n\n","category":"function"},{"location":"man/functions/#KEGGAPI.request-Tuple{String}","page":"KEGGAPI.jl Functions","title":"KEGGAPI.request","text":"request(url)\n\nMake 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.\n\nExamples\n\nrequest(\"https://rest.kegg.jp/info/kegg\")\n\n\n\n\n\n","category":"method"},{"location":"man/functions/#KEGGAPI.request_other-Tuple{String}","page":"KEGGAPI.jl Functions","title":"KEGGAPI.request_other","text":"request_other(url)\n\nMake 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.\n\nExamples\n\nrequest_other(\"https://rest.kegg.jp/image/hsa00010\")\n\n\n\n\n\n","category":"method"},{"location":"man/functions/#KEGGAPI.save_image-Tuple{Vector, String}","page":"KEGGAPI.jl Functions","title":"KEGGAPI.save_image","text":"KEGGAPI.save_image(image, filename) -> filename\n\nSave an image to a file.\n\nExamples\n\nimage = KEGGAPI.get_image(\"hsa00010\")\nKEGGAPI.save_image(image, \"glycolysis.png\")\n\n\n\n\n\n","category":"method"}] }