Question: str handling in python
gravatar for pascalandres182
11 months ago by
pascalandres1820 wrote:

I need to use a python to order a str like:

Uncharacterized protein YiiQ OS = Escherichia coli (strain K12) GN = yiiQ PE = 3 SV = 1

and that the result of this matches PROKKA format

> SeqID EC_number ~~~ gene ~~~ product ~~~ COG
python • 295 views
ADD COMMENTlink modified 11 months ago by zx87549.6k • written 11 months ago by pascalandres1820

So don't use a language you aren't familiar with. If you have no programming skills, try the programming forums. It's not a bioinformatics issue.

ADD REPLYlink written 11 months ago by karl.stamm3.8k

help please I'm new to python

None of us was born with (python) programming skills, so it's worth spending some effort to fix your problem and show us what you tried. Also, from your question, it is not clear to me how the reformatting should be done.

ADD REPLYlink written 11 months ago by WouterDeCoster44k

I don't mind helping although I agree with whats been said. Yet, maybe its me but, I couldn't understand much from what you've typed in. Could you explain a bit better with a full example

ADD REPLYlink modified 11 months ago • written 11 months ago by firatuyulur300

Your first problem is not that you don't know the python to do this, it's that your starting string literally does not contain the information you need to create the correctly formatted prokka header; you have no EC number, you have no Sequence ID (though this is arbitrary anyway), and you don't have any COGs (but I think these may be optional in prokka - don't quote me on that).

ADD REPLYlink written 11 months ago by Joe18k
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