Non-standard amino acids (e.g. U for selenocysteine) result in failure in mhcflurry-predict-scan even when --no-throw passed

[Hilly20211122]

Hi are there any suggestions on how to use the mhcflurry-predict-scan to read FASTA sequences containing selenoproteins that use selenium (Se) in place of sulfur (S)? Thanks.

[timodonnell]

Good question. My intention was that passing --no-throw would cause these peptides to be skipped but that doesn't seem to be the case. So we can consider this issue a bug. I think a fix shouldn't be too difficult.

[Hilly20211122]

Hi Tim, Thanks for your response. Am really enjoying using McFlurry it’s an awesome prediction tool. Lex Get Outlook for iOS<https://aka.ms/o0ukef>

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________________________________ From: timodonnell ***@***.***> Sent: Wednesday, December 1, 2021 10:43:52 AM To: openvax/mhcflurry ***@***.***> Cc: Alexandra Elizabeth Hill ***@***.***>; Author ***@***.***> Subject: Re: [openvax/mhcflurry] Non-standard amino acids (e.g. U for selenocysteine) result in failure in mhcflurry-predict-scan even when --no-throw passed (Issue #199) Closed #199<#199> via #200<#200>. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#199 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AWTKLQDYJXUMY243IWZ7KGLUOVOTRANCNFSM5IPUDBOA>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.