circhemy 0.1.0

Convert module

The convert module is able to convert from a range of input circRNA ID into different one or more database identifiers.

Example: Convert a list of CircAtlas2 IDs read via STDIN from file input.csv into Circpedia2 IDs, but also output CircAtlas2 IDs, while writing the output to /tmp/output.csv:

cat input.csv | circhemy convert -q STDIN -i CircAtlas2 -o Circpedia2 CircAtlas2 -O /tmp/output.csv

Query module

The query module is able to retrieve circRNA IDs from the internal database that fulfil a set of user-defined constraints.

Example: Retrieve a list of circbase and CircAtlas2 circRNA IDs that are located on chromosome 3 of the species rattus norvegicus; only print out circRNAs from the rn6 genome build.

circhemy query -o circbase CircAtlas2 -C chr3 -s rattus_norvegicus -g rn6

Convert module

The convert module is able to convert from a range of input circRNA ID into different one or more database identifiers.

Example: Convert a list of CircAtlas2 IDs into circBase and into Circpedia2 IDs, including the Genome build.

curl -X 'POST' 'https://circhemy.jakobilab.org/api/convert'
  -H 'accept: application/json'
  -H 'Content-Type: application/json'
  -d '{
      "input": "CircAtlas2",
      "output": ["Circpedia2","CircAtlas2","Genome"],
      "query": ["hsa-MYH9_0004","hsa-MYH9_0004"]
      }'

Output is returned as JSON-formatted string which can directly be used for AG Grid tables for any other postprocessing:

{
  "columnDefs": [
    {
      "headerName": "circBase",
      "field": "circBase"
    },
    {
      "headerName": "Circpedia2",
      "field": "Circpedia2"
    }
    {
      "headerName": "Genome",
      "field": "Genome"
    }
  ],
  "rowData": [
    {
      "circBase": "hsa_circ_0004470",
      "Circpedia2": "HSA_CIRCpedia_36582"
      "Genome": "hg38"
    },
    {
      "circBase": "hsa_circ_0004470",
      "Circpedia2": "HSA_CIRCpedia_36582"
      "Genome": "hg19"
    }
  ]
}

Query module

The query module is able to retrieve circRNA IDs from the internal database that fulfil a set of user-defined constraints.

Example: Retrieve all circRNAs with a CircAtlas2 ID containing nppa in the species homo sapiens, return the IDs in circBase and CircAtlas2 format:

curl -X 'POST'
  'https://circhemy.jakobilab.org/api/query'
  -H 'accept: application/json'
  -H 'Content-Type: application/json'
  -d '{
      "input": [
        {
          "query": "nppa",
          "field": "CircAtlas2",
          "operator1": "AND",
          "operator2": "LIKE"
        },
        {
          "query": "homo_sapiens",
          "field": "Species",
          "operator1": "AND",
          "operator2": "is"
        }
      ],
      "output": [
        "circBase",
        "CircAtlas2"
      ]
    }'

Output is returned as JSON-formatted string which can directly be used for AG Grid tables for any other postprocessing:

{
  "columnDefs": [
    {
      "headerName": "circBase",
      "field": "circBase"
    },
    {
      "headerName": "CircAtlas2",
      "field": "CircAtlas2"
    }
  ],
  "rowData": [
    {
      "circBase": "",
      "CircAtlas2": "hsa-NPPA_0001"
    },
    {
      "circBase": "",
      "CircAtlas2": "hsa-NPPA_0002"
    },
    {
      "circBase": "",
      "CircAtlas2": "hsa-NPPA-AS1_0001"
    },
    {
      "circBase": "hsa_circ_0009871",
      "CircAtlas2": "hsa-NPPA-AS1_0004"
    },
    {
      "circBase": "",
      "CircAtlas2": "hsa-NPPA-AS1_0002"
    },
    {
      "circBase": "",
      "CircAtlas2": "hsa-NPPA-AS1_0003"
    },
    {
      "circBase": "",
      "CircAtlas2": "hsa-NPPA_0001"
    },
    {
      "circBase": "",
      "CircAtlas2": "hsa-NPPA_0002"
    },
    {
      "circBase": "",
      "CircAtlas2": "hsa-NPPA-AS1_0001"
    },
    {
      "circBase": "hsa_circ_0009871",
      "CircAtlas2": "hsa-NPPA-AS1_0004"
    },
    {
      "circBase": "",
      "CircAtlas2": "hsa-NPPA-AS1_0002"
    },
    {
      "circBase": "",
      "CircAtlas2": "hsa-NPPA-AS1_0003"
    }
  ]
}