How can I save BioPerl sequence nested features in genbank or embl format?

Posted by Ryan Thompson on Stack Overflow See other posts from Stack Overflow or by Ryan Thompson
Published on 2010-04-27T18:36:14Z Indexed on 2010/04/27 21:13 UTC
Read the original article Hit count: 330

Filed under:

perl

|

bioperl

|

bioinformatics

In BioPerl, a sequence object can have any number of features, and each of these can have subfeatures nested within them. For example, a feature may be a complete coding sequence of a gene, and its subfeatures might be individual exons that are concatenated to form the full coding sequence.

However, when I use BioPerl to write a sequence object to a file in genbank or embl format, only the top-level features are written to the file, not the sub-features nested within the top-level features. How can I store my subfeatures in sequence files? Should I just convert all my subfeatures into top-level features, and then reconstruct the tree structure next time I read in the sequence?

© Stack Overflow or respective owner

Related posts about perl

Munin on Centos 6 - missing perl MODULE_COMPAT_5.8.8

as seen on Server Fault - Search for 'Server Fault'
I'm trying to install Munin on a new VPS through yum install munin but I keep getting an error about a missing perl module: Requires: perl(:MODULE_COMPAT_5.8.8). This is the perl version currently installed: v5.10.1. I've searched all around and still haven't found a solution for this. Here's the… >>> More
Pain removing a perl rootkit

as seen on Server Fault - Search for 'Server Fault'
So, we host a geoservice webserver thing at the office. Someone apparently broke into this box (probably via ftp or ssh), and put some kind of irc-managed rootkit thing. Now I'm trying to clean the whole thing up, I found the process pid who tries to connect via irc, but i can't figure out who's… >>> More
How To Avoid a Perl script calling an Another Perl Script

as seen on Stack Overflow - Search for 'Stack Overflow'
Hello, i am calling a perl script client.pl from a main script to capture the output of client.pl in @output. is there anyway to avoid the use of these two files so i can use the output of client.pl in main.pl itself here is my code.... main.pl ======= my @output = readpipe("client.pl"); client… >>> More
Perl :how to sort dates in perl

as seen on Stack Overflow - Search for 'Stack Overflow'
Hi, How can I sort the dates in perl. my @dates = ( "02/11/2009" , "12/20/2001" , "11/21/2010" ) ; I have above dates in my array . How can I sort those dates... ? My date format is dd/mm/YYYY. >>> More
please suggest a perl book exclusively for perl programs

as seen on Stack Overflow - Search for 'Stack Overflow'
I want tha name of a perl book for only PERL PROGRAMS. The reason behind is I want to improve my programming skill in perl >>> More

Related posts about bioperl

How can I save BioPerl sequence nested features in genbank or embl format?

as seen on Stack Overflow - Search for 'Stack Overflow'
In BioPerl, a sequence object can have any number of features, and each of these can have subfeatures nested within them. For example, a feature may be a complete coding sequence of a gene, and its subfeatures might be individual exons that are concatenated to form the full coding sequence. However… >>> More
Bioperl, equivalent of IO::ScalarArray for array of Seq objects?

as seen on Stack Overflow - Search for 'Stack Overflow'
In perl, we have IO::ScalarArray for treating the elements of an array like the lines of a file. In BioPerl, we have Bio::SeqIO, which can produce a filehandle that reads and writes Bio::Seq objects instead of strings representing lines of text. I would like to do a combination of the two: I would… >>> More
Where do I find Nmake for Windows XP

as seen on Super User - Search for 'Super User'
Regarding BioPerl installation in Windows XP, I have installed Active Perl in Windows XP, and by using Perl Package Manager I have installed the BioPerl Repositories too. But I am not able to run the BioPerl yet. While running the BioPerl program in emacs it is showing the following error: make… >>> More
Language Niches and Niche Libraries

as seen on Programmers - Search for 'Programmers'
"Everyone Knows" ... ... that c is widely used for low level programs in large part because operating system/device apis are usually in c. ... that Java is widely used for enterprise applications in large part because of enterprise libraries and ide support. ... that ruby is widely used for webapps… >>> More