Call to fasta2table in RNAseqQC seperates segments with `;`

[IanSudbery]

In 286b8d179a00343847f79d8256de522d92a587a4, the the , seperating the na, dn and length as outputs from fasta2table in characteriseTranscripts were changed to ;.

https://github.com/cgat-developers/cgat-flow/blob/bc423e431cee5b76f2e8cdc6b8d8a44935b85a75/cgatpipelines/tools/pipeline_rnaseqqc.py#L1222-L1234

This isn't valid bash and leads to a dn: command not found. @jscaber do you know why this change was made? Can I revert it?

[jscaber]

Yes please do revert it. I don’t know why I changed that, probably during some troubleshooting. Jakub

On 27 Aug 2021, at 15:40, Ian Sudbery @.**@.>> wrote:

In 286b8d1https://github.com/cgat-developers/cgat-flow/commit/286b8d179a00343847f79d8256de522d92a587a4, the the , seperating the na, dn and length as outputs from fasta2table in characteriseTranscripts were changed to ;.

https://github.com/cgat-developers/cgat-flow/blob/bc423e431cee5b76f2e8cdc6b8d8a44935b85a75/cgatpipelines/tools/pipeline_rnaseqqc.py#L1222-L1234

This isn't valid bash and leads to a dn: command not found. @jscaberhttps://github.com/jscaber do you know why this change was made? Can I revert it?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/cgat-developers/cgat-flow/issues/144, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AC4Y5MX5JVLZJO2XJ2ZLMWDT66PWZANCNFSM5C5WA6YQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

[IanSudbery]

Actaully, turns out , doesn't work with Argparse either. I think it'll work with (space), just going to try.

[jscaber]

That rings a bell, I think this was an attempt to fix this when we moved to the new parser. At the time when I pushed the changes it did run, I haven’t tried running/updating this for a while.

On 27 Aug 2021, at 15:57, Ian Sudbery @.**@.>> wrote:

Actaully, turns out , doesn't work with Argparse either. I think it'll work with (space), just going to try.

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