update biopython optional package to 1.52

[5d2aaf09-c963-473a-bf79-1f742a72700f]

Updating to biopython-1.52, which was released September 22, 2009. Main improvements were to alignment and sequence file conversion, population genetics statistics, and the Bio.SeqIO.indexed_dict() for handling large numbers of sequences.

Here is an example that will not work with previous biopython packages:

sage: import urllib2 as U
sage: f = U.urlopen('http://biopython.org/DIST/docs/tutorial/examples/ls_orchid.gbk')
sage: orchidfile = file(DATA+"ls_orchid.gbk",'w')
sage: orchidfile.write(f.read())
sage: orchidfile.close()
sage: f.close()
sage: from Bio import SeqIO
sage: orchid_dict = SeqIO.index(DATA+"ls_orchid.gbk", "genbank")
sage: print 'Number of records: ' + str(len(orchid_dict))
sage: orchid_dict.keys()
sage: seq_record = orchid_dict["Z78475.1"]
sage: print 'Description: ' + seq_record.description
sage: seq_record.seq

Number of records: 94
Description: P.supardii 5.8S rRNA gene and ITS1 and ITS2 DNA.
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...GGT', IUPACAmbiguousDNA())

CC: @sagetrac-tkeller

Component: packages: optional

Keywords: biopython

Issue created by migration from https://trac.sagemath.org/ticket/7019

[cb6db86b-3b9b-456b-aef6-be35d93fcec6]

comment:3

Where is the spkg? ~ Adam

[5d2aaf09-c963-473a-bf79-1f742a72700f]

comment:4

Oops! Sorry about that. I put a copy here:

http://sage.math.washington.edu/home/mhampton/biopython-1.52.spkg

Thanks very much for taking a look!

Marshall

[cb6db86b-3b9b-456b-aef6-be35d93fcec6]

comment:5

The program itself looks nice but the package does not seem to conform to the guidelines at http://www.sagemath.org/doc/developer/producing_spkgs.html.

For example:

• no hg repository
• no src directory: there is a source directory and then a link to it.
• missing parts in the SPKG.txt (Description,License,Upstream Contact)
• this package does have it's own test suite so a spkg-check would also be nice

Do you have time or should I work on it?

Cheers, Adam

[cb6db86b-3b9b-456b-aef6-be35d93fcec6]

comment:6

Some suggestions. ;-)

SPKG.txt

== Description ==

Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.

It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.

== License ==

Biopython License

== SPKG Maintainers ==

  -- Marshall Hampton, mhampton at d.umn.edu or hamptonio at gmail.com.

== Upstream Contact ==

  -- wiki - http://biopython.org/wiki/Main_Page

spkg-check (keeping biopython as directory name)

#!/usr/bin/env bash

if [ "$SAGE_LOCAL" = "" ]; then
   echo "SAGE_LOCAL undefined ... exiting";
   echo "Maybe run 'sage -sh'?"
   exit 1
fi

cd biopython
python setup.py test

if [ $? -ne 0 ]; then
   echo "Error testing biopython"
   exit 1
fi

I hope this is useful,

Adam

[5d2aaf09-c963-473a-bf79-1f742a72700f]

comment:7

Thanks, that's very useful. The biopython optional package has existed for quite a while - William Stein added it for me in 2006 I think - and so it predates some of those good newer conventions.

I don't have a lot of time for sprucing it up, so if you want to to take the lead on that please go ahead!

The test suite is quite extensive, and I agree that it would be good to have a spkg-check for it. I have experienced some funny issues running the tests, with some path-related failures unless I copied the tests into the sage directory structure. Unfortunately I don't really understand what causes them. If those path issues are cleared up then everything in the test suite should pass.

Realistically I won't have time to improve the spkg until mid-November at least.

[cb6db86b-3b9b-456b-aef6-be35d93fcec6]

comment:8

OK,

I'll see what I can do. ~ Adam

[cb6db86b-3b9b-456b-aef6-be35d93fcec6]

comment:9

Where do I put the spkg when I have it done? Is there an in-box or something? ~ Adam

[5d2aaf09-c963-473a-bf79-1f742a72700f]

comment:10

Well, uploading it anywhere you have access to is fine. If you don't have a good place to park it, you should ask for a sage.math account and put it there. Just email William Stein, or ask on IRC. I'm not sure, maybe Minh or someone else also has the ability to make sage.math accounts.

-Marshall

[cb6db86b-3b9b-456b-aef6-be35d93fcec6]

comment:11

I put a new spkg at http://sage.math.washington.edu/home/awebb/biopython-1.52.p0.spkg.

Adam

[5d2aaf09-c963-473a-bf79-1f742a72700f]

comment:12

Looks good! Thanks! I'm a little confused on how to use the spkg-check script, but that's not your fault I think. I will write to sage-devel about that. I just haven't used such a script before.

[williamstein]

comment:13

I posted it.