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bowmanjeffs / paprica

paprica - PAthway PRediction by phylogenetIC plAcement
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assigning enzyme names to E.C numbers #52

Closed garimaraj closed 7 years ago

garimaraj commented 7 years ago

How do I assign enzyme names to the E.C numbers, from ec_tally.csv?

bowmanjeffs commented 7 years ago

This isn't done automatically, though I can try to implement something like this in the future. The best way is to reference the EC definitions at http://www.enzyme-database.org/downloads.php. You can automate the queries if you download the sql or xml files.

garimaraj commented 7 years ago

Thank you for your reply. I have downloaded the xml file but I have no idea how to automate. I am very new to computational field and work in the wet lab. I am trying to understand my results but it takes a lot of time for me to understand all the tools and packages. I will be very grateful if you can kindly tell me how to use either xml or sql file.

Thank you,

Regards,

On Mon, Jun 19, 2017 at 7:21 PM, bowmanjeffs notifications@github.com wrote:

This isn't done automatically, though I can try to implement something like this in the future. The best way is to reference the EC definitions at http://www.enzyme-database.org/downloads.php. You can automate the queries if you download the sql or xml files.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/bowmanjeffs/paprica/issues/52#issuecomment-309445845, or mute the thread https://github.com/notifications/unsubscribe-auth/AVPUtdb1SfOY92zR09VvCX_ydVHiUTRRks5sFnzkgaJpZM4N9g9F .

-- Garima Raj Junior Research Fellow, Institute of Advanced Study in Science and Technology Vigyan Path, Paschim Boragaon Guwahati-781035, Assam India

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bowmanjeffs commented 7 years ago

Unfortunately I don't have time this month; behind on proposals with looming deadlines. I know it seems a little daunting but I encourage you to use the opportunity to learn a little scripting. You'll need it regardless so you may as well learn it now! It's how we all start. I'll try to put together a utility at some point but it will be a little while before I get to it.

garimaraj commented 7 years ago

Thank you Jeff, I think I have figured it out to some extent. I will post if I have come with a solution. Thanks a lot anyway.

Regards,

On Jun 20, 2017 20:04, "bowmanjeffs" notifications@github.com wrote:

Unfortunately I don't have time this month; behind on proposals with looming deadlines. I know it seems a little daunting but I encourage you to use the opportunity to learn a little scripting. You'll need it regardless so you may as well learn it now! It's how we all start. I'll try to put together a utility at some point but it will be a little while before I get to it.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/bowmanjeffs/paprica/issues/52#issuecomment-309776259, or mute the thread https://github.com/notifications/unsubscribe-auth/AVPUtfy3jY-HkWYxTcob28sk9iWWkTmpks5sF9iLgaJpZM4N9g9F .