[Biopython-dev] Tutorial documentation for Bio.SeqIO

Peter biopython-dev at maubp.freeserve.co.uk
Wed Mar 14 22:42:01 UTC 2007

Thanks for the feedback Michiel and Ed.

When I get back from my holiday (by which time I hope that Biopython 
1.43 will have been released without any big issues), I plan to update 
Section 4.4 "Dealing with alignments".  I've made a few changes to the 
Tutorial in CVS today, but I think I've finished now.

Michiel Jan Laurens de Hoon wrote:
> If it's easier for you, you can also submit Turorial.tex to CVS, then 
> I'll get it from there, run hevea on it and put it up for a proof read 
> (since hevea will be used for the final version).

That would be easier for me.

You might notice that I tweaked the all URLs (and updated the addresses 
of a few that had changed).  This got rid of the recursive anchor tag 
warnings I was getting from hevea, and hasn't had any side effects as 
far as I can tell.

I have just checked the updated Tutorial.tex works on Linux with both 
pdflatex (for Tutorial.pdf) and hevea (for the HTML version).

I have not installed hevea on Windows, but after adding the hevea.sty 
file to my windows latex installation (I use MikTex) I was able to build 
Tutorial.pdf on Windows too.

>Ed Schofield wrote:
>> - The links to ls_orchid.fasta and ls_orchid.gbk are also dead.
> I've added these files on the server.

Great.  I've updated the URLs in the tutorial to point at those files. 
It might be nice to upload the rest of the files used Bio/Doc/examples/ 
as well...

I had previously made some of the other examples point to ViewCVS to 
download the relevant file - this works but is a bit clumsy.

Certainly when I was first reading the Tutorial, my immediate reaction 
was to think where can I get these examples sequence files - and having 
a URL right there in the HTMl and PDF editions is very nice.


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