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https://github.com/cumbof/pyrnacentral

Python tool to interact with the public RNAcentral APIs and automatically retrieve data

https://github.com/cumbof/pyrnacentral

Science Score: 26.0%

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Keywords

galaxy python rnacentral
Last synced: 7 months ago · JSON representation

Repository

Python tool to interact with the public RNAcentral APIs and automatically retrieve data

Basic Info
  • Host: GitHub
  • Owner: cumbof
  • License: bsd-2-clause
  • Language: Python
  • Default Branch: master
  • Size: 443 KB
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  • Stars: 0
  • Watchers: 1
  • Forks: 1
  • Open Issues: 0
  • Releases: 1
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galaxy python rnacentral
Created over 7 years ago · Last pushed about 6 years ago
Metadata Files
Readme License

README.md

RNAcentral-data-retrieval-tool

Python tool to interact with the public RNAcentral APIs and automatically retrieve data.

It exploits the rna endpoint of the RNAcentral public APIs v1 to automatically retrieve sequences (converted to the FASTA format) and the related metadata, starting with one or a list of RNAcentral IDs.

Usage Examples

How to download the sequence and the related metadata of a single RNAcentral ID: python rnacentral.py --id URS00005F3006

To simultaneously download a data from a list of RNAcentral IDs, switch the --id parameter with --file like below: python rnacentral.py --fasta human_AND_rna_typelncRNA.list The file specified under the --file parameter must contain one RNAcentral ID per line.

It is also possible to specify the path in which the generated FASTA and metadata files will be stored respectively with the parameters --fastadir and --metadir.

Owner

  • Name: Fabio Cumbo
  • Login: cumbof
  • Kind: user
  • Location: Cleveland, OH, USA
  • Company: Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic

Ph.D. in Computer Science and Automation Engineering, Postdoctoral Research Fellow @BlankenbergLab, GMI, LRI, Cleveland Clinic, USA

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