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lazear / sage

Proteomics search & quantification so fast that it feels like magic
https://sage-docs.vercel.app
MIT License
201 stars 38 forks source link

Closes #92 New semi-enzymatic function with new notation. #94

Closed FriedLabJHU closed 8 months ago

FriedLabJHU commented 8 months ago

This update adds a semi-enzymatic function with new notation. "?KR" would produce all non-specific digests between all tryptic peptides. This update can also account for missed cleavages.

Updated the broken code in my previously PR

lazear commented 8 months ago

Got through some initial testing and everything looks good! Will do a couple more tests when I get some more time and then merge.

How do you feel about specifying semi-enzymatic searching by a parameter instead of modifying the enzyme string? I think this is more in line with how other tools are configured e.g.:

"enzyme": {
        "missed_cleavages": 2,
        "min_len": 7,
        "max_len": 50,
        "cleave_at": "KR",
        "restrict": "P",
        "semi_enzymatic": true  // <-- new param
    },