headers
bugzilla-daemon | 1 Oct 2006 08:10

[Bug 1939] Doc/Makefile does not build pdf, html, txt files completely correctly

http://bugzilla.open-bio.org/show_bug.cgi?id=1939

mdehoon <at> ims.u-tokyo.ac.jp changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED

------- Comment #19 from mdehoon <at> ims.u-tokyo.ac.jp  2006-10-01 02:10 -------
I've taken bits and pieces of the patch to get the recursive behavior for make.
Getting html output from biopdb_faq is not essential, and does not warrant
adding a hack to Biopython.

--

-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.
Permalink | Reply | 2 comments |
headers
Chris Lasher | 10 Oct 2006 04:55
Picon
Gravatar

ranlib.c missing in Bio/Cluster

I just checked out the latest CVS and setup.py failed on installation
during gcc compilation of ranlib.o since Bio/Cluster/ranlib.c couldn't
be found. Any suggestions? Was this file supposed to be in the CVS?
The checkout notes indicate that it has been replaced with something
else.

Thanks,
Chris
Permalink | Reply | 1 comment |
headers
Michiel de Hoon | 10 Oct 2006 06:10
Favicon

Re: ranlib.c missing in Bio/Cluster

There was some confusion about the license status of ranlib, so I 
removed it from Bio.Cluster and replaced it with a new random number 
generator written from scratch. Apparently I forgot to update setup.py 
in CVS accordingly. I have done that now, so if you get the new setup.py 
  from CVS the compilation should work. You could also edit your local 
copy of setup.py and remove ranlib.c, linpack.c, and com.c.
Sorry for the confusion.

--Michiel.

Chris Lasher wrote:
> I just checked out the latest CVS and setup.py failed on installation
> during gcc compilation of ranlib.o since Bio/Cluster/ranlib.c couldn't
> be found. Any suggestions? Was this file supposed to be in the CVS?
> The checkout notes indicate that it has been replaced with something
> else.
> 
> Thanks,
> Chris
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython-dev
Permalink | Reply | 0 comments |
headers
Chris Lasher | 10 Oct 2006 06:46
Picon
Gravatar

Subversion Repository

Anybody know if BioPython (I suppose all Open Bio projects) will
switch over to Subversion, and if so, when? I think the merits and
advantages of Subversion over CVS speak for themselves. It's certainly
become my revision control system of preference. Anybody else's?

Curious,
Chris
Permalink | Reply | 20 comments |
headers
bugzilla-daemon | 19 Oct 2006 06:14

[Bug 2014] Bio/Blast/NCBIStandalone.py parsing of psiblast fails

http://bugzilla.open-bio.org/show_bug.cgi?id=2014

mdehoon <at> ims.u-tokyo.ac.jp changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED

------- Comment #1 from mdehoon <at> ims.u-tokyo.ac.jp  2006-10-19 00:14 -------
Fixed in CVS, thanks.

Note though that the parser for plain-text blast output is very difficult to
maintain, because the output format keeps changing with different versions of
blast. I'd encourage you to use the XML parser instead, as it is much more
stable.

--

-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.
Permalink | Reply | 0 comments |
headers
bugzilla-daemon | 19 Oct 2006 06:21

[Bug 2032] query_to and sbjct_to added in parsed NCBI-Blast XML

http://bugzilla.open-bio.org/show_bug.cgi?id=2032

mdehoon <at> ims.u-tokyo.ac.jp changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED

------- Comment #1 from mdehoon <at> ims.u-tokyo.ac.jp  2006-10-19 00:21 -------
Fixed in CVS following same bug report on the mailing list.

--

-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.
Permalink | Reply | 0 comments |
headers
bugzilla-daemon | 19 Oct 2006 06:44

[Bug 2051] XML Blast parser unusable with multiple queries and recent (2.2.13) blast - patch attached

http://bugzilla.open-bio.org/show_bug.cgi?id=2051

mdehoon <at> ims.u-tokyo.ac.jp changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
                 CC|                            |mdehoon <at> ims.u-tokyo.ac.jp

------- Comment #4 from mdehoon <at> ims.u-tokyo.ac.jp  2006-10-19 00:44 -------
A new blast version (2.2.15) came out recently, so I tried the XML parser with
the its output of a multiple query. I didn't notice a problem except that all
alignments are put into one list, which is annoying because then we have to
find out which alignment corresponds to which query.
So, which specific problem with the XML parser are you trying to solve? And do
these problems still occur with blast 2.2.15? (as far as I can tell, its XML
output is the same as for blast 2.2.14, so it's probably here to stay).

--

-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.
Permalink | Reply | 0 comments |
headers
Chris Lasher | 25 Oct 2006 04:22
Picon
Gravatar

Re: [BioPython] Martel-based parsing of Unigene flat files

Hi Sean,

FWIW this should probably have been posted to BioPython-dev, but I
don't think that would improve your chances of getting a response. I
am cross-posting it there, anyways. Unfortunately for you, I do not
have an answer for you. :-(

I, myself, would be interested in a response to this question from the
Devs, as I would like to write a parser for PTT files. Last I saw
there was a lot of chatter about the Martel parsers being incredibly
slow compared to straightforward solutions. It seems that standard
format parsers would be one of the easiest ways for BioPython newbies
to contribute to developing the BioPython project, however, there
isn't very much in the way of documentation on the BioPython way to do
so, let alone developer documentation at all. I would like to know
what can be done to get some dev docs going on the wiki.

Chris

On 10/20/06, Sean Davis <sdavis2 <at> mail.nih.gov> wrote:
> I am relatively new to python and biopython (coming from perl side of
> things).  I would like to make a parser for Unigene flat file format.
> However, after digging through the LocusLink parsing code (as probably
> the most similar format, etc.), I'm still at a loss for how Martel-based
> parsing works.  I understand the big picture (converting an re-based
> parsing of a file into events), but it is the detail that I am missing.
> I know about pydoc, but the pydoc for much of Martel is not very helpful
> to me, at least not in my current state of knowledge.  Any suggestions
> on how to get started?
>
(Continue reading)

Permalink | Reply | 2 comments |
headers
Sean Davis | 26 Oct 2006 14:09
Picon

Basic python question with regard to Unigene parser

Let me start off by saying that I am a python newbie after working in perl for 
the last few years.  I am working on a Unigene flat file parser.  In my 
scanner, I have a construct that looks like:

        for line in handle:
            tag = line.split(' ')[0]
            line = line.rstrip()
            if tag=='ID':
                consumer.ID(line)
            if tag=='GENE':
                consumer.GENE(line)
            if tag=='TITLE':
                consumer.TITLE(line)
            if tag=='EXPRESS':
                consumer.EXPRESS(line)
            ....

Since I am setting things up so that there is a 1:1 correspondence between the 
"tag" and the consumer method, is there an easy way to reduce this long set 
of IF statements to a simple mapping procedure that maps a tag to the correct 
method?

Sorry for the naive question....

Thanks,
Sean
Permalink | Reply | 2 comments |
headers
Sean Davis | 26 Oct 2006 14:30
Picon

Re: Basic python question with regard to Unigene parser

On Thursday 26 October 2006 08:09, Sean Davis wrote:
> Let me start off by saying that I am a python newbie after working in perl
> for the last few years.  I am working on a Unigene flat file parser.  In my
> scanner, I have a construct that looks like:
>
>         for line in handle:
>             tag = line.split(' ')[0]
>             line = line.rstrip()
>             if tag=='ID':
>                 consumer.ID(line)
>             if tag=='GENE':
>                 consumer.GENE(line)
>             if tag=='TITLE':
>                 consumer.TITLE(line)
>             if tag=='EXPRESS':
>                 consumer.EXPRESS(line)
>             ....
>
> Since I am setting things up so that there is a 1:1 correspondence between
> the "tag" and the consumer method, is there an easy way to reduce this long
> set of IF statements to a simple mapping procedure that maps a tag to the
> correct method?
>
> Sorry for the naive question....

Even more apologies.  I answered my own question.  Something like this seems 
to work:

	exec('consumer.'+tag+'(line)')
(Continue reading)

Permalink | Reply | 1 comment |

Gmane