Generate the events from the GTF file argument -f

[Ekomshiro]

The command line to generate local AS events will be of the form:

python3.4 suppa.py generateEvents -i <input-file.gtf> -o -f ioe -e
The command to generate the transcript "events" would be of the form:

python3.4 suppa.py generateEvents -i <input-file.gtf> -o -f ioi

It seems the -f argument is no longer supported or needed in the current release.
Running the local AS events command failed with msg:
suppa.py: error: unrecognized arguments: -f ioe
And in the tutorial this argument is not used.

[EduEyras]

Thanks for the message. We'll update this shortly E.

…

On Tue, Apr 10, 2018 at 4:34 PM, Ekomshiro ***@***.***> wrote: The command line to generate local AS events will be of the form: python3.4 suppa.py generateEvents -i <input-file.gtf> -o -f ioe -e The command to generate the transcript "events" would be of the form: python3.4 suppa.py generateEvents -i <input-file.gtf> -o -f ioi It seems the -f argument is no longer supported or needed in the current release. Running the local AS events command failed with msg: suppa.py: error: unrecognized arguments: -f ioe And in the tutorial this argument is not used. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#24>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AMWVBynO-iWzZEISAAuUX7zrB5iGG6sJks5tnMLogaJpZM4TOYjp> .

-- Dr E Eyras ICREA Research Professor Universitat Pompeu Fabra PRBB, Dr Aiguader 88 Tel: +34 93 316 0502 E08003 Barcelona, Spain Fax: +34 93 316 0550 http://scholar.google.com/citations?user=LiojlGoAAAAJ http://www.researcherid.com/rid/L-1053-2014 http://regulatorygenomics.upf.edu/

[linglingtingfei]

Hi,
Is this question solved? I downloaded the software yesterday, I met the same question, no argument -f.

[EduEyras]

Hi,

This command works:
python3.4 suppa.py generateEvents -i <input-file.gtf> -o -f ioi

Please let us know if it does not work for you

Thanks
E.

[linglingtingfei]

@EduEyras
I tried it, but it didn't work. see below screenshot. However, i tried another python3.4 /export/software/ISO/anaconda3/envs/anaCogent3.4/lib/python3.4/site-packages/SUPPA/suppa.py generateEvents -i all.collapsed.gff -o 2_B01.events -e SE SS MX RI FL , i could run successfully. It seems that the "ioe" was setted by default.

[renzhonglu]

@EduEyras Yes, I also use the SUPPA version 2.2.1 downloaded from pip, but it doesn't work. I used python version 3.5, suppa told me "unrecognized arguments: --format ioi". Is this option abandoned? Thank you!

[EduEyras]

It should work fine. Could you provide us with an example of the command line? Thanks E.

…

On Mon, 25 Mar 2019 at 18:46, renzhonglu ***@***.***> wrote: @EduEyras <https://github.com/EduEyras> Yes, I also use the SUPPA version 2.2.1 downloaded from pip, but it doesn't work. I used python version 3.5, suppa told me "unrecognized arguments: --format ioi". Is this option abandoned? Thank you! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#24 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AMWVB2s2lhx9lpi0U9gdUXPt0MLLzyvrks5vaH7AgaJpZM4TOYjp> .

-- Prof. E Eyras EMBL Group Leader The John Curtin School of Medical Research Australian National University 131 Garran Road, Acton ACT 2601, Canberra, Australia https://github.com/comprna http://scholar.google.com/citations?user=LiojlGoAAAAJ http://www.researcherid.com/rid/L-1053-2014

[renzhonglu]

@EduEyras , Thanks!
Yestoday, I tried to download the latest version of SUPPA v2.3 tar.gz file from Github. After unzipped this file, I directly run suppa.py again, it works!

[EduEyras]

Great! thanks for letting us know E.

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On Tue, 26 Mar 2019 at 13:50, renzhonglu ***@***.***> wrote: @EduEyras <https://github.com/EduEyras> , Thanks! Yestoday, I tried to download the latest version of SUPPA v2.3 tar.gz file from Github. After unzipped this file, I directly run suppa.py again, it works! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#24 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AMWVB6TskVhwVoQ_KoB3GOWuLQbTgwafks5vaYrtgaJpZM4TOYjp> .

-- Prof. E Eyras EMBL Group Leader The John Curtin School of Medical Research Australian National University 131 Garran Road, Acton ACT 2601, Canberra, Australia https://github.com/comprna http://scholar.google.com/citations?user=LiojlGoAAAAJ http://www.researcherid.com/rid/L-1053-2014