Question: str handling in python
gravatar for pascalandres182
4 weeks 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 • 184 views
ADD COMMENTlink modified 4 weeks ago by zx87548.4k • written 4 weeks 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 4 weeks ago by karl.stamm3.5k

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 4 weeks ago by WouterDeCoster42k

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 4 weeks ago • written 4 weeks ago by firatuyulur290

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 4 weeks ago by Joe15k
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