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Perform Enrichment Analysis Programmatically
One can send an HTTP POST request to the backend server of ChIP-Atlas to run Enrichment Analysis programmatically. Once the server accepts the request, an enrichment analysis job is queued, and then generate the result file with the request ID.
List of POST parameters (all values must be a string):
-
format
- fixed value:
'text'
- fixed value:
-
result
- fixed value:
'www'
- fixed value:
-
genome
-
hg38
hg19
-
mm10
mm9
rn6
-
dm6
dm3
-
ce11
ce10
sacCer3
-
-
antigenClass
- See the 2nd column of
antigenList.tab
for available antigens (direct link to the file)
- See the 2nd column of
-
cellClass
- See the 2nd column of
celltypeList.tab
for available cell types (direct link to the file)
- See the 2nd column of
-
threshold
50
100
200
500
-
typeA
-
bed
- user input bed file
-
gene
- user input gene list
-
-
bedAFile
- content of user data, bed file or gene list
- all whitespaces must be converted to
_
-
typeB
-
rnd
- random permutation
-
bed
- user input bed file
-
refseq
- Refseq coding genes excluding user data
-
userlist
- user input gene list
-
-
bedBFile
- content of compared data, bed file or gene list
- put
"empty"
if the type B isrnd
- all whitespaces must be converted to
_
-
permTime
- random permutation time, speciify
1
if the type B isbed
orgene
- options
1
10
100
- random permutation time, speciify
-
title
- string
- title of the analysis
-
descriptionA
- string
- description for the user data
-
descriptionB
- string
- description for the compared data
-
distanceUp
- string
- default:
"0"
- upper limit of distance from the TSS, default: 50
-
distanceDown
- string
- default:
"0"
- lower limit of distance from the TSS, default: 50
Here is an example command-line execution of the Enrichment Analysis using curl
command. You can create a bed file by copy-and-paste the bed format data generated by the 'Try with example' button at the Enrichment Analysis web interface.
$ ls
dataA.bed
$ curl -X POST \
-d "format=text" \
-d "result=www" \
-d "genome=hg19" \
-d "antigenClass=TFs and others" \
-d "cellClass=Pluripotent stem cell" \
-d "threshold=50" \
-d "typeA=bed" \
--data-urlencode "bedAFile@dataA.bed" \
-d "typeB=rnd" \
-d "bedBFile=empty" \
-d "permTime=10" \
-d "title=10 times random permutation of my data" \
-d "descriptionA=my data" \
-d "descriptionB=random permutation 10 times" \
-d "distanceUp=0" \
-d "distanceDown=0" \
https://ddbj.nig.ac.jp/wabi/chipatlas/
Then you will get a response including requestId
to access the result looks like:
requestId: wabi_chipatlas_2020-0820-1357-35-297-993677
parameters: null
current-time: 2020-08-20 13:57:35
start-time:
current-state:
The job status can be retrieved from http://ddbj.nig.ac.jp/wabi/chipatlas/<requestId>
(it takes < a minute when the job scheduler is busy).
Once the submitted job finished, the output will be accessible from https://ddbj.nig.ac.jp/wabi/chipatlas/<requestId>?info=result&format=html
in HTML or https://ddbj.nig.ac.jp/wabi/chipatlas/<requestId>?info=result&format=tsv
in TSV.