Newbie: extract subsequence

[cmnailecin]

Hello,

I am new here and I was looking through previous posts on the topic which I fully intend to try. I have been using a program called fastahack (download here... https://github.com/ekg/fastahack) to extract subsequences from a fasta file (whole genome).

IT has been working very well and is fairly simple to use. However, I need to extract multiple (more than 1000) subsequences so doing this manually would be out of the question.

I would like to know if there is a way to use this program but have it extract multiple subsequences from a fasta file with different start and stop positions. I would like to use this same method on a different genome with, again, different start and stop positions so a 'generic' solution would be necessary.

Please help if you can

* perl script, incrementing loop??? edit program coding? batch files???

[maasha]

This question has been asked in this forum before IIRC. You can use Biopieces (www.biopieces.org) to solve this. Have a look at get_seq.

[Jeremy]

you can do it using the seqinr R package for R quite easily with the getFrag command, but you need to know some R basics. If you do try this way make sure you do not set as.string to TRUE otherwise R needs to convert everything back to character first and takes twice as long.

[volks]

fastaFromBed from bedtools?

[cmnailecin]

Thank you all! At this point I am going to be using get_seq from biopieces. The only downfall to this is the many prerequisites but I'm working through them. Thank you very much maasha.