OrthoXML & SeqXML
SeqXML BioPerl support
Converting between SeqXML and other sequence formats
Try it! Here are two programs, one for converting (almost) any sequence format to SeqXML:
any2seqxml (download)
and one for converting SeqXML to (almost) any sequence format:
seqxml2any (download)
Both require a recent version of BioPerl, which is available here. (installation instructions)
You can also look at the code we used to convert ref proteome fasta to seqxml.
Don’t want to install BioPerl?
There’s a quickie, “zero-install” way to get BioPerl on your system.
1) Okay, click here to download bioperl as a zip file:
https://github.com/bioperl/bioperl-live/zipball/master
when it's done downloading, unzip it if your computer hasn’t done it automatically. On the
command line, you would do:
unzip bioperl-live-bioperl-release-1-5-1-rc4-4318-g342e587.zip
or whatever the file is called. You should then have a folder with some ugly name like
bioperl-bioperl-live-558467a
3) rename that to
bioperl-live
4) move that folder to wherever you want to keep it. I keep mine in a directory called src in my
home directory.
So on my computer if I go to the command line and cd to that folder and type pwd I get:
/Users/dave/src/bioperl-live
5) in the terminal, cd to your home directory.
6) see if you have a file named .bash_profile by typing
ls -l ~/.bash_profile
7) if so, open that file in your favorite editor. if the file doesn't exist, just create the file.
8) put this line in your .bash_profile
export PERL5LIB=/Users/dave/src/bioperl-live
(obviously replacing my path info with wherever you chose to put bioperl)
9) save and close your .bash_profile
10) open a new terminal window so that the change will take effect.
11) on the command line of the new terminal, type
perl -e "use Bio::SeqIO;"
If that works, then you have "installed" bioperl. Yay!
