Question: Fetching corresponding sequences from a fasta file using coordinates
0
gravatar for sharadlko1
2.6 years ago by
sharadlko10
sharadlko10 wrote:

Hi everyone, I am new to python/biopython therefore I need this help. I want to use python/biopython to fetch the corresponding sequences from a fasta file having multiple sequences using coordinates such as unique identifier, start position, end position, strand information stored in a csv file. Please let me know the script. Thanks a lot.

biopython python fasta • 1.3k views
ADD COMMENTlink modified 2.6 years ago by Biostar ♦♦ 20 • written 2.6 years ago by sharadlko10
1

Have you tried to search for past threads on this topic here?

ADD REPLYlink written 2.6 years ago by genomax75k
1

Please let me know the script.

That's not how it works. You need to show some effort from your side as well.
Also, why does it have to be python?

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by WouterDeCoster42k

No need to use Python. Here is a procedure and ready-made script for you to use with your BED file and reference genome of choice. Good luck!

ADD REPLYlink written 2.6 years ago by Alex Reynolds29k

You cannot ask for a script here. But you can ask for help resolving any issue with your script/pseudo code or discussing the basic idea what you are going to implement.

ADD REPLYlink written 2.6 years ago by lakhujanivijay4.6k
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