Question: GFF3 to BED using Python
0
gravatar for onemore100iq
8 days ago by
onemore100iq20
onemore100iq20 wrote:

how to transform GFF3 format to BED format using Python? and how to convert a gene features column from GFF3 format to BED format using Python? I tried this line but did not work:

$GFF2BED <foo.gff3

Any help is highly appreciated

python bed gff3 • 149 views
ADD COMMENTlink modified 8 days ago • written 8 days ago by onemore100iq20

Hello,

please let me give you a Brief Reminder On How To Ask A Good Question

I tried this line but did not work:

Why do you thing "it didn't work"?

fin swimmer

ADD REPLYlink modified 8 days ago • written 8 days ago by finswimmer9.9k

of course because it did not get the expected BED format, is this not enough reason to call it "did not work"?

ADD REPLYlink written 8 days ago by onemore100iq20

It is fine to call it "did not work". But you have to provide examples of:

  • how you input looks like
  • how the output looks like
  • how the expected output should look like

Without these information we are not able to understand what "did not work" nor we can provide a solution.

fin swimmer

ADD REPLYlink written 8 days ago by finswimmer9.9k

I forgot to thank you for directing me regarding how to ask a question. But I noticed that there are many other questions are asked and have same format as my question and yet got right away help/hint/ guidance/website link i.e. non of them was treated the same way as my question where you asked me questions that investigated my question instead of helping me although that I asked one straightforward question like many other questions format where they did not provide input nor output nor expected output !!!!!!!!! Thank you anyway for your great help

ADD REPLYlink written 8 days ago by onemore100iq20

Do not take it personally. Finswimmer is asking for further information to improve the question thread. This makes it easier for us to help you.

But, perhaps more importantly, this forum isn’t just about the question when you ask it - it is a repository of knowledge for the future, so the post should ideally be clearly organised so that people who have the same issue in future can find the solution quickly.

ADD REPLYlink written 8 days ago by jrj.healey10k

never mind i got it

ADD REPLYlink written 8 days ago by onemore100iq20
2

Please share your solution.

ADD REPLYlink written 8 days ago by zx87546.5k
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