the size of the protein sequences

[xjhzjucas]

Hi developer, thank you for this nice tool! I wonder does it limit the size of faa file for input? when I enter a long sequence, it turned out error like:OSError: [Errno 36] File name too long: How can i solve this? Thank you!

[rochoa85]

Thank you for using PepFun. Indeed the error is because the sequence is very long and this is used to create the report file. It can be easily fixed in the code, but I would recommend you to use the last version of the package called pepfunn. You can install it with:

pip install git+https://github.com/novonordisk-research/pepfunn.git

Then you can import the module and then run the line replacing PEPTIDE with your sequence: from pepfunn.sequence import Sequence pep = Sequence('PEPTIDE', report_liabilities=True)

You will get a file called rules_report.txt with more details of the liabilities.

I hope it can be helpful. For more information about pepfunn you can find notebooks in the github repo.

All the best

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From: xjhzjucas @.> Sent: Friday, October 4, 2024 9:23:07 AM To: rochoa85/PepFun @.> Cc: Subscribed @.***> Subject: [rochoa85/PepFun] the size of the protein sequences (Issue #3)

Hi developer, thank you for this nice tool! I wonder does it limit the size of faa file for input? when I enter a long sequence, it turned out error like:OSError: [Errno 36] File name too long: How can i solve this? Thank you!

— Reply to this email directly, view it on GitHubhttps://github.com/rochoa85/PepFun/issues/3, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAVOA3B5HG657HXXSKSS4A3ZZY65RAVCNFSM6AAAAABPLJFSQKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGU3DKNRUHEYDKMA. You are receiving this because you are subscribed to this thread.Message ID: @.***>

[xjhzjucas]

Thank you for using PepFun. Indeed the error is because the sequence is very long and this is used to create the report file. It can be easily fixed in the code, but I would recommend you to use the last version of the package called pepfunn. You can install it with: pip install git+https://github.com/novonordisk-research/pepfunn.git Then you can import the module and then run the line replacing PEPTIDE with your sequence: from pepfunn.sequence import Sequence pep = Sequence('PEPTIDE', report_liabilities=True) You will get a file called rules_report.txt with more details of the liabilities. I hope it can be helpful. For more information about pepfunn you can find notebooks in the github repo. All the best Get Outlook for Androidhttps://aka.ms/AAb9ysg … ____ From: xjhzjucas @.> Sent: Friday, October 4, 2024 9:23:07 AM To: rochoa85/PepFun @.> Cc: Subscribed @.> Subject: [rochoa85/PepFun] the size of the protein sequences (Issue #3) Hi developer, thank you for this nice tool! I wonder does it limit the size of faa file for input? when I enter a long sequence, it turned out error like:OSError: [Errno 36] File name too long: How can i solve this? Thank you! — Reply to this email directly, view it on GitHub<#3>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAVOA3B5HG657HXXSKSS4A3ZZY65RAVCNFSM6AAAAABPLJFSQKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGU3DKNRUHEYDKMA. You are receiving this because you are subscribed to this thread.Message ID: @.>

Thank you for your help, let me try it! All the best

[xjhzjucas]

Hi developer, I want to ask another basic question. I don't know the strict definition of peptide, does peptide have length limited? If I have some protein/peptide seqs, I don't know which part of them are belonged to peptide, and whether they're legal to put into Pepfun or pepfunn. Thank you so much!

[rochoa85]

For peptides ideally should be below 50 or 60 residues

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From: JHXu @.> Sent: Thursday, October 17, 2024 2:48:07 PM To: rochoa85/PepFun @.> Cc: Rodrigo Ochoa @.>; Comment @.> Subject: Re: [rochoa85/PepFun] the size of the protein sequences (Issue #3)

Hi developer, I want to ask another basic question. I don't know the strict definition of peptide, does peptide have length limited? If I have some protein/peptide seqs, I don't know which part of them are belonged to peptide, and whether they're legal to put into Pepfun or pepfunn. Thank you so much!

— Reply to this email directly, view it on GitHubhttps://github.com/rochoa85/PepFun/issues/3#issuecomment-2419454466, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAVOA3FPPX7DHRE2DVZILTTZ36WYPAVCNFSM6AAAAABPLJFSQKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMJZGQ2TINBWGY. You are receiving this because you commented.Message ID: @.***>