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Extract Multiple Genes From Multiple Fasta Files

Hi every one,

I was wondering if somebody could tell me how to extract a number of genes from a number of fastafiles (all having the same set of genes) and CONCATENATE them altogether for each fasta file?

Having said that, I've got an excel sheet (or a text file) having the entities (the Start / End nucleotide positions) for every single gene.

I would like to do it using awk and grep in Unix.

Any help is appreciated.

Cheers,
Hossein

fasta
• 3,774 views • link
updated by Ram Ram • written by hosseinv • hosseinv

If I understand it correctly, think generating a bed file from your text file and after that bedtools getfasta associate with for loop may be a shot.

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written by AndreiR AndreiR

1 answer

Hi Hossein, I think that your best shot will be using Galaxy, you can do all sorts of fasta files manipulations without programming or scripting. Good luck

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written by Asaf Asaf

Thanks Asaf for your reply. The thing is I am currently working on a small dataset and I want to do this as an example for my next bigger dataset. So I don't really want to go through uploading big data files to Galaxy.

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written by hosseinv • hosseinv

so perl or python can give you the solution. In my opinion, if you don't master awk it's easier to learn perl or python and implement these small scripts than doing it in awk

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written by Asaf Asaf

Glad to hear that. I'll have start learning Perl or Python. So would you recommend me a webpage or textbook for learning Perl please? I appreciate your help. Regards. Hossein

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written by hosseinv • hosseinv

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