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Bonis Sanz, Julio | 2 Mar 2004 18:46
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[BioPython] Martel problems and MS-Windows

Hi everyone, 

I have tried to install biopython. It seem to works propertly, but when
trying the example of the cookbook the Martel module fails (or this is what
I think).

When typing: GenBank.FeatureParser() I get the error: "ImportError: No
module named Martel".

Of course when trying 'import Marvel' it doesnt work.

I have installed: 

python2.3
mx-base 2.0.5 for python 2.3
numarray 0.8 for python 2.3
biopython1.24 for python2.3

following the installation instructions.

I dont find any windows installer for Marvel.

Shoudl I enter in the complex world of compiling py under windows?

Any idea, howto, tutorial?

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ashleigh smythe | 2 Mar 2004 19:05
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[BioPython] problems parsing alignment files

Hello biopythoneers!  I've been having problems parsing alignments, but
I can parse fasta files with no problem so I don't think I'm totally off
base.  I can't get either the NBRF parser or the Clustalw parser to
work.  I have updated biopython on February 27th and just updated Martel
- both via the command "CVS update", but I guess it looks like a Martel
problem.  I think the NBRF (.pir) files and .aln files I'm using are
fine as they open with no problem directly in ClustalX.  

Here's the traceback for NBRF:

>>> from Bio import NBRF
>>> parser=NBRF.RecordParser()
>>> afile=open('allopen6ext2.pir')
>>> iterator=NBRF.Iterator(afile, parser)
>>> cur_record=iterator.next()
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/usr/lib/python2.2/site-packages/Bio/NBRF/__init__.py", line 63,
in next
    return self._parser.parse(File.StringHandle(data))
  File "/usr/lib/python2.2/site-packages/Bio/NBRF/__init__.py", line
158, in parse
    self._scanner.feed(handle, self._consumer)
  File "/usr/lib/python2.2/site-packages/Bio/NBRF/__init__.py", line
108, in feed
    self._parser.parseFile(handle)
  File "/usr/lib/python2.2/site-packages/Martel/Parser.py", line 328, in
parseFile
    self.parseString(fileobj.read())
  File "/usr/lib/python2.2/site-packages/Martel/Parser.py", line 356, in
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Brad Chapman | 2 Mar 2004 20:42
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Re: [BioPython] Martel problems and MS-Windows

Hello;

> I have tried to install biopython. It seem to works propertly, but when
> trying the example of the cookbook the Martel module fails (or this is what
> I think).
> 
> When typing: GenBank.FeatureParser() I get the error: "ImportError: No
> module named Martel".

It looks like you did everything perfectly find -- I believe the
problem is that Martel (the underlying parsing engine) was
accidentally left out of the windows installer.

Michiel kindly provided the installers, so maybe he'd be willing to
double-check if the might have been left out -- since I'm not much
of a Windows person myself.

(As an aside to Michiel -- I think this problem is caused by the way
that the setup.py works. Specifically, only installing Martel if the
version number of the "distributed Martel" is bigger than the
"installed Martel." I put a note in the release instructions and
will fix this in the future by bumping the Martel version on each
release. This also ensures that any fixes/changes to Martel get
installed).

So yes, it looks like a problem on our part, and hopefully we can
get it sorted for you. Thanks for reporting it and sorry for any
confusion.

Brad
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Brad Chapman | 2 Mar 2004 20:48
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Re: [BioPython] problems parsing alignment files

Hi Ashleigh;

> Hello biopythoneers!  I've been having problems parsing alignments, but
> I can parse fasta files with no problem so I don't think I'm totally off
> base.  I can't get either the NBRF parser or the Clustalw parser to
> work.  I have updated biopython on February 27th and just updated Martel
> - both via the command "CVS update", but I guess it looks like a Martel
> problem.  I think the NBRF (.pir) files and .aln files I'm using are
> fine as they open with no problem directly in ClustalX.  
> 
> Here's the traceback for NBRF:
[...]
> And here's the one from Clustalw (I'm not sure if I've got the syntax
> right on this as it doesn't seem to have the same RecordParser as NBRF
> or Fasta):
[...]

Yes, it looks like you are doing everything right -- the tracebacks
are indicating that the underlying Martel parser is having trouble
dealing with the files you are providing, for some reason. If you
could send me the NBRF and ALN files (off-list), I can
have a look and see if I can figure where they are failing and try
to get everything fixed.

Also, that is a good point about the Clustalw parser not having the
same syntax as the other parsers. Thanks for bringing that up.

Please do send the files and thanks for the bug report.
Brad
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Robert Roth | 2 Mar 2004 21:00
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Re: [BioPython] Martel problems and MS-Windows

Hi Julio,

>I have tried to install biopython. It seem to works >propertly, but when
>trying the example of the cookbook the Martel module >fails (or this is what
>I think).
>
>When typing: GenBank.FeatureParser() I get the >error: "ImportError: No
>module named Martel".
>
>I dont find any windows installer for Marvel.
>
>Shoudl I enter in the complex world of compiling py >under windows?

I ran in to similar problems when running some tests after installing biopython 1.24 on windows. The tests
fails and give a dead link (dont remember the link exactly, www.biopython.org/~dalke/Martel
something). 

I solved this by downloading the source for Martel from the CVS and installing by, 

python setup.py install

Not very complex and all tests worked after this. 
Hope this helps. 

/Robert

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Brad Chapman | 3 Mar 2004 00:15
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Re: [BioPython] problems parsing alignment files

Hey all;

[Ashleigh reports errors in parsing Clustalw and PIR files]

Me:
> If you could send me the NBRF and ALN files (off-list), I can
> have a look and see if I can figure where they are failing and try
> to get everything fixed.

To follow up to the list -- I got the files and just now squished
the bugs. Here were the problems:

=> The clustalw format didn't accept question marks in title names.

=> The NBRF/PIR parser didn't handle Clustalw format PIR, which is
valid but different then the PIR files you can download.

Fixes for both of these are in CVS and I also squashed some other
bugs in the PIR parsing that I found.

Thanks again to Asleigh for the report.
Brad
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Michiel Jan Laurens de Hoon | 3 Mar 2004 02:43
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Re: [BioPython] Martel problems and MS-Windows

You are right, Martel did get skipped because it was already present on my 
machine. Why is it necessary to check version number of Martel? Is it possible 
that a version of Martel is already present that is newer than the one included 
with Biopython?

--Michiel.

Brad Chapman wrote:

> Hello;
> 
> 
>>I have tried to install biopython. It seem to works propertly, but when
>>trying the example of the cookbook the Martel module fails (or this is what
>>I think).
>>
>>When typing: GenBank.FeatureParser() I get the error: "ImportError: No
>>module named Martel".
> 
> 
> It looks like you did everything perfectly find -- I believe the
> problem is that Martel (the underlying parsing engine) was
> accidentally left out of the windows installer.
> 
> Michiel kindly provided the installers, so maybe he'd be willing to
> double-check if the might have been left out -- since I'm not much
> of a Windows person myself.
> 
> (As an aside to Michiel -- I think this problem is caused by the way
> that the setup.py works. Specifically, only installing Martel if the
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Jeffrey Chang | 3 Mar 2004 14:56

Re: [BioPython] Martel problems and MS-Windows

This was my doing.  At the time (and still now, I believe), Andrew 
wanted also to distribute Martel as a separate package, that people can 
use outside of Biopython.  So thus, the CVS version, and possible 
distributions, were ahead of Biopython.  But now that it appears that 
Martel development is stabilizing, perhaps it is time to revisit that 
decision.

Jeff

On Mar 2, 2004, at 8:43 PM, Michiel Jan Laurens de Hoon wrote:

> You are right, Martel did get skipped because it was already present 
> on my machine. Why is it necessary to check version number of Martel? 
> Is it possible that a version of Martel is already present that is 
> newer than the one included with Biopython?
>
> --Michiel.
>
> Brad Chapman wrote:
>
>> Hello;
>>> I have tried to install biopython. It seem to works propertly, but 
>>> when
>>> trying the example of the cookbook the Martel module fails (or this 
>>> is what
>>> I think).
>>>
>>> When typing: GenBank.FeatureParser() I get the error: "ImportError: 
>>> No
>>> module named Martel".
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Brad Chapman | 3 Mar 2004 17:00
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Re: [BioPython] Martel problems and MS-Windows

Hey guys;

Michiel:
> >You are right, Martel did get skipped because it was already present 
> >on my machine. Why is it necessary to check version number of Martel? 
> >Is it possible that a version of Martel is already present that is 
> >newer than the one included with Biopython?

Jeff:
> This was my doing.  At the time (and still now, I believe), Andrew 
> wanted also to distribute Martel as a separate package, that people can 
> use outside of Biopython.  So thus, the CVS version, and possible 
> distributions, were ahead of Biopython.  But now that it appears that 
> Martel development is stabilizing, perhaps it is time to revisit that 
> decision.

My vote is that it's not really necessary, since I thought that
distutils would already do the work of determining if the files to
be installed are newer than the stuff in site-packages. Of course, I
guess this based on time-stamps so it's not a perfect system, but
should work for most cases and make things a little less confusing.

On the other hand, it's not too tough to bump the version on making
new releases or if new changes go into CVS -- I think I was just
sleeping (well, really studying for exams) during the whole Martel
install debate a while back, so I didn't know to do this on the last
release. I added it to the build release directions, so it shouldn't
be a problem in the future if we leave things the way they are.

By the way, Michiel -- the quick fix is to just remove Martel from
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Ralf Sigmund | 3 Mar 2004 19:21
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[BioPython] wu-blast 2.0 standalone parser?

Hi,
are there any efforts to build a pythonic parser for the licensed 
version of wahington university wu-blast 2.0 standalone?
should this be done using the event based martel parser architecture?
is there a martel - based parser for ncbi blast?
there are production quality parsers for theese formats in BioPerl. 
Would You favour to call Bioperl from Biopython over reimplementing a 
wu-blast parser in biopython?
slightly off topic - does it still make sense to support both wu and 
ncbi blast?

cheers Ralf

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