Outformat support for EMBL-EBI RADAR (Rapid Automatic Detection and Alignment of Repeats in protein sequences)
I've been using RADAR on EMBL's web service through the command line with the rest API. The documentation (below) suggests I should be able to output the results as a CSV but I have no example of the acceptable syntax for this. I've tried --outformat csv/.csv/outfile name.csv.
Any help on this would be amazing! Thanks
[General]
-h, --help Show this help message and exit.
--asyncjob Forces to make an asynchronous query.
--title Title for job.
--status Get job status.
--resultTypes Get available result types for job.
--polljob Poll for the status of a job.
--pollFreq Poll frequency in seconds (default 3s).
--jobid JobId that was returned when an asynchronous job was submitted.
--outfile File name for results (default is JobId; for STDOUT).
--outformat Result format(s) to retrieve. It accepts comma-separated values.
--params List input parameters.
--paramDetail Display details for input parameter.
--verbose Increase output.
--version Prints out the version of the Client and exit.
--quiet Decrease output.
--baseUrl Base URL. Defaults to:
https://www.ebi.ac.uk/Tools/services/rest/radar
• 1,340 views
•
link
0 answers
No answers yet.
Log in to answer this question.
Did you try
--outformat csv --outfile output_file.csv?Gave it a go just now. Same story. The job appears to execute and finishes, but it does not create the output fie.
Anything printed to STDOUT/STDERR? Also, can you give us a reproducible example with the full command and sample input please?