alternative to prodres_db.nr100.sqlite3 database

[lhersemann]

Hi,
We recently setup TOPCONS2 on our HPC cluster using a singularity container but unfortunately, we cannot work with sqlite3 databases on our system. If I understood correctly, the pfam_scan_to_profile.py script would deal with cases where the sqlite3 database is not present and use an alternative one instead and we thought about trying this approach. The alternative file specified in the script is database/pfamfull/uniref100.pfam27.pfamseq.nr90 but this file doesn't exist in the database we downloaded and also seems to point to an outdated version as you already updated to Pfam32.0. I already check the data provided by Pfam but am not sure what the right equivalent would be to fit with the data you provide in your PRODRES database and would be happy if you could let me know where I can find the necessary data.

Many thanks,
Lena

[arneelof]

Where did you find pfam_scan_to_profile.py ? (I cannot find it) Yours Arne

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----------------------------------------- Arne Elofsson Science for Life Laboratory Tel:+46-(0)70 695 1045 Stockholm University http://bioinfo.se/ Box 1031, Email: ***@***.*** 17121 Solna, Sweden Twitter: https://twitter.com/arneelof Zoom: https://stockholmuniversity.zoom.us/my/arneelof/ Scholar: http://scholar.google.se/citations?user=s3OCM3AAAAAJ ORCID: 0000-0002-7115-9751 <https://orcid.org/0000-0002-7115-9751>

On Wed, Aug 3, 2022 at 4:02 PM Lena Hersemann ***@***.***> wrote: Hi, We recently setup TOPCONS2 on our HPC cluster using a singularity container but unfortunately, we cannot work with sqlite3 databases on our system. If I understood correctly, the pfam_scan_to_profile.py script would deal with cases where the sqlite3 database is not present and use an alternative one instead and we thought about trying this approach. The alternative file specified in the script is database/pfamfull/uniref100.pfam27.pfamseq.nr90 but this file doesn't exist in the database we downloaded and also seems to point to an outdated version as you already updated to Pfam32.0. I already check the data provided by Pfam but am not sure what the right equivalent would be to fit with the data you provide in your PRODRES database and would be happy if you could let me know where I can find the necessary data. Many thanks, Lena — Reply to this email directly, view it on GitHub <#14>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA3LGSMZTVOOAAEP3QB4LGLVXJ3YBANCNFSM55O7JV5A> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[lhersemann]

Hi Arne,
I found the script here: https://github.com/ElofssonLab/TOPCONS2/blob/master/topcons2_webserver/workflow/pfam_scan_to_profile.py

Best,
Lena

[arneelof]

Please find the pfamfull.zip <https://drive.google.com/file/d/1ItLkWEIwZaGDnCWQ0qxq0mYr4tFQU8pz/view?usp=drive_web> Yours Arne

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----------------------------------------- Arne Elofsson Science for Life Laboratory Tel:+46-(0)70 695 1045 Stockholm University http://bioinfo.se/ Box 1031, Email: ***@***.*** 17121 Solna, Sweden Twitter: https://twitter.com/arneelof Zoom: https://stockholmuniversity.zoom.us/my/arneelof/ Scholar: http://scholar.google.se/citations?user=s3OCM3AAAAAJ ORCID: 0000-0002-7115-9751 <https://orcid.org/0000-0002-7115-9751>

On Thu, Aug 4, 2022 at 1:04 PM Lena Hersemann ***@***.***> wrote: Hi Arne, I found the script here: https://github.com/ElofssonLab/TOPCONS2/blob/master/topcons2_webserver/workflow/pfam_scan_to_profile.py Best, Lena — Reply to this email directly, view it on GitHub <#14 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA3LGSL32PECZCIWCRYGBCLVXOPS7ANCNFSM55O7JV5A> . You are receiving this because you commented.Message ID: ***@***.***>