Extracting A Gene Sequence Into A Fasta File

Question

[Yasmine]

I'm writing a software tool that will extract gene sequences from the chromosome. Can anyone help me with this?

For each (non-header) line in the gene file, create an entry for the FastA file as follows. For a sequence like:

NM_00100344 chr11 + 5925152 5926098 5925152 5926098 2 5925152,5925652, 5925404,5926098,

I want an information line that looks like the following (unspliced version):

>NM_00100343|chr11(+):5925152Z5926098

or (spliced&version):

>NM_00100343|chr11(+):5925152Z5926098|5925151Z5925404,5925652Z5926098

Following the information line should be the actual sequence (extracted from the chromosome file, and reverse-complemented if necessary), using a column width of 70.

You don't have to show me exactly how to do it, I just want a way to get started.

Answer 1

[Zev.Kronenberg]

start by looking at some of these biopython examples.

Examples