Re^2: Trying to get intergenic sequences using BioPerl


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Re^2: Trying to get intergenic sequences using BioPerl

by Sosi (Sexton)

on Jul 27, 2015 at 16:43 UTC ( [id://1136494]=note: print w/replies, xml )

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in reply to Re: Trying to get intergenic sequences using BioPerl
in thread Trying to get intergenic sequences using BioPerl

Thank you very much! Yes, I read somewhere that many people criticize gbff for this sort of thing, so I started playing around with the .gff. However, the next question that raises is: in the case of organisms with multiple chromosomes/plasmids, how do you then get the subseqs out of the gbff (once you have the coordinates from the gff) by pointing for a specific chromosome? I will now look into your code and see how it goes, I hope I can convert it to regular script! Thank you very much!

<quote>Have you printed out the value of $pt to verify that it is either "CDS" , "rRNA" or "tRNA" ?</quote>

Yes, it was retrieving "CDS", "rRNA" and "tRNA". Which is strange because then I can find some "Source" within "@two"

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Re^3: Trying to get intergenic sequences using BioPerl
by biohisham (Priest) on Jul 28, 2015 at 02:59 UTC

I am not sure I can answer your question without context except through an educated guess. What species are your working with ? The subseq coordinates in the gff file should ideally have been assigned as an offset from the start of the sequence file to where they are regardless of their chromosomal position. Another possibility is that the gff files for each chromosome have been generated individually. In the first case using the coordinates can get you the region corresponding to the chromosome without needing to worry about chromosomal location. In the second scenario extracting the subsequence will be as simple as accessing the right chromosomal gff file.

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