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huangzixia / ExUTR

ExUTR is a practical and powerful tool that enables rapid genome-wide 3'-UTR prediction from massive RNA-Seq data
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3UTR_orfs.pl does not catch library type argument issue #2

Closed pandrey-fr closed 5 years ago

pandrey-fr commented 6 years ago

When running 3UTR_orfs_*.pl without specifying the -l option (which is a user mistake), the program runs, then fails but does not say so - in fact it prints out the final success messages. It is quite obvious from the emptiness of the produced files that something went wrong, but it would be better if the script caught the issue and raised an error message informing the user about the error instead of letting them try to understand what it is that went wrong...

Since I am not a Perl programmer I do not know how to fix this issue myself, although it is probably rather simple.

pandrey-fr commented 6 years ago

Fixed by commit e5f9854 on my fork. (I learnt Perl 101 for this). If you don't like the other changes I suggest (which is fine), please integrate this fix manually.

huangzixia commented 6 years ago

Dear Paul,

Thank you for using ExUTR. I very much appreciated that you reported the errors and the suggested solutions. I am currently at the fieldwork and have limited internet access. I will update ExUTR as soon as I am able to.

Kind regards, Zixia

On 13 Jul 2018, at 14:50, Paul Andrey notifications@github.com wrote:

Fixed by commit e5f9854 https://github.com/huangzixia/ExUTR/commit/e5f985427183d4a88dd16ac2b6e30fb027770b9d on my fork. (I learnt Perl 101 for this). If you don't like the other changes I suggest (which is fine), please integrate this fix manually.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/huangzixia/ExUTR/issues/2#issuecomment-404839300, or mute the thread https://github.com/notifications/unsubscribe-auth/APJ8M94nVpu4NuD0KpcLTPd6ARDZVxuDks5uGKWXgaJpZM4VLMoI.

Zixia Huang Laboratory of Molecular Evolution and Mammalian Phylogenetics University College Dublin Ireland http://batlab.ucd.ie/ http://batlab.ucd.ie/

pandrey-fr commented 6 years ago

Dear Zixia,

Thank you for your answer. Apart from the handling of the issue I referenced, the modifications I pushed are only meant as suggestions, but if you ever would like to talk them through please feel free to write me - my github posts are a bit scarce, and I they ever seem harsh I apologize.

To be completely transparent, I started working on a re-implementation in Python, as a pet project and mainly to help myself understand precisely the way how ExUTR works. If I actually complete it (which I hope), I will test whether it changes anything as to performance (in terms of execution time) and outputs (due to the small differences in potential ORFs identification), and come back to you to see whether it seems sensible or not to publish it on Github - and if so, we'll discuss how we manage licensing and authorship referencing, since remains your tool at any rate.

Best regards, Paul

De : huangzixia notifications@github.com Envoyé : mercredi 18 juillet 2018 11:49 À : huangzixia/ExUTR Cc : Paul Andrey; Author Objet : Re: [huangzixia/ExUTR] 3UTR_orfs.pl does not catch library type argument issue (#2)

Dear Paul,

Thank you for using ExUTR. I very much appreciated that you reported the errors and the suggested solutions. I am currently at the fieldwork and have limited internet access. I will update ExUTR as soon as I am able to.

Kind regards, Zixia

On 13 Jul 2018, at 14:50, Paul Andrey notifications@github.com wrote:

Fixed by commit e5f9854 https://github.com/huangzixia/ExUTR/commit/e5f985427183d4a88dd16ac2b6e30fb027770b9d on my fork. (I learnt Perl 101 for this). If you don't like the other changes I suggest (which is fine), please integrate this fix manually.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/huangzixia/ExUTR/issues/2#issuecomment-404839300, or mute the thread https://github.com/notifications/unsubscribe-auth/APJ8M94nVpu4NuD0KpcLTPd6ARDZVxuDks5uGKWXgaJpZM4VLMoI.

Zixia Huang Laboratory of Molecular Evolution and Mammalian Phylogenetics University College Dublin Ireland http://batlab.ucd.ie/ http://batlab.ucd.ie/

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/huangzixia/ExUTR/issues/2#issuecomment-405875776, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ATuSAg4vt_dnZaWVPzVJrVLnXyPrjGsZks5uHwSbgaJpZM4VLMoI.