seq.Newbler2SAM

[FCicconardi]

Dear all, I'm trying desperately to convert the 454PailAlign file into
a SAM file. So I run the glu script Newbler2SAM, but this is what I
get...

[fracicco@mrsmith02 scripts]$ /work/adt/gmancini/Software/Python-2.6.4/
python /work/adt/gmancini/Software/PythonLibs/glu-genetics/bin/glu -v
seq.Newbler2SAM -o /work/adt/fracicco/454data/454PairAlign.sam /work/
adt/fracicco/454data/454PairAlign.txt /work/adt/fracicco/454data/
GVLEKQS01.sff
GLU (unknown) module: seq.Newbler2SAM
Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health
& Human Services. Funded by NCI under Contract N01-CO-12400.

Loading SFF index for /work/adt/fracicco/454data/GVLEKQS01.sff
/work/adt/fracicco/libs/biopython-1.56/Bio/SeqIO/SffIO.py:441:
DeprecationWarning: Private function _sff_read_roche_index_xml is
deprecated. Use new public function ReadRocheXmlManifest instead
DeprecationWarning)
Generating alignment from /work/adt/fracicco/454data/454PairAlign.txt
to /work/adt/fracicco/454data/454PairAlign.sam


Well, that could have gone better.

Execution aborted due to a problem with the program input, parameters
supplied, an error in the program. Please examine the following
failure
trace for clues as to what may have gone wrong. When in doubt, please
send
this message and a complete description of the analysis you are
attempting
to perform to the software developers.

Error: global name 'SeqIO' is not defined

Command line:
glu seq.Newbler2SAM -o /work/adt/fracicco/454data/454PairAlign.sam /
work/adt/fracicco/454data/454PairAlign.txt /work/adt/fracicco/454data/
GVLEKQS01.sff

Well, this is embarrassing.

Traceback: Traceback (most recent call last):
File "/work/adt/gmancini/pkg/python/lib/python2.6/site-packages/
glu-1.0b2_dev-py2.6-linux-x86_64.egg/glu/lib/glu_launcher.py", line
212, in main
progmain()
File "/work/adt/gmancini/pkg/python/lib/python2.6/site-packages/
glu-1.0b2_dev-py2.6-linux-x86_64.egg/glu/modules/seq/Newbler2SAM.py",
line 457, in main
out.writerows(alignment)
File "/work/adt/gmancini/pkg/python/lib/python2.6/site-packages/
glu-1.0b2_dev-py2.6-linux-x86_64.egg/glu/modules/seq/Newbler2SAM.py",
line 306, in handle_unaligned
for read in SeqIO.parse(open(filename,'rb'), 'sff'):
NameError: global name 'SeqIO' is not defined


[Tue Feb 8 13:17:38 2011] Execution aborted due to a fatal error



Does anybody could help me??
Thanks anyway
Francesco

[Kevin Jacobs <jacobs@bioinformed.com>]

On Tue, Feb 8, 2011 at 7:29 AM, FCicconardi <fran...@gmail.com> wrote:

Dear all, I'm trying desperately to convert the 454PailAlign file into
a SAM file. So I run the glu script Newbler2SAM, but this is what I
get...

Hi Francesco,

It appears that you are using GLU with a newer version of BioPython than I am running.  I'll upgrade my dev box and make the necessary changes to get it to work.

-Kevin

[Francesco Cicconardi]

It sounds very good indeed! Do I wait for your update?
cheers
Francesco




Francesco Cicconardi, Ph.D
___________________________________________________
Department of Biochemical Sciences
Sapienza University
P.le A. Moro, 5
00185 Rome
Italy
phone: +390649914297

CASPUR - Inter University Consortium for Supercomputing Applications
for University and Research
Via dei Tizii, 6/b
00185 Roma
Italy

e-mail: fran...@gmail.com
            frac...@caspur.it

2011/2/8 Kevin Jacobs <jac...@bioinformed.com> <bioin...@gmail.com>

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[Francesco Cicconardi]

I may use and older version of Biopython. Which one should I use?
F

Francesco Cicconardi, Ph.D
___________________________________________________
Department of Biochemical Sciences
Sapienza University
P.le A. Moro, 5
00185 Rome
Italy
phone: +390649914297

CASPUR - Inter University Consortium for Supercomputing Applications
for University and Research
Via dei Tizii, 6/b
00185 Roma
Italy

e-mail: fran...@gmail.com
            frac...@caspur.it

2011/2/8 Francesco Cicconardi <fran...@gmail.com>

[Jacobs, Kevin (NIH/NCI) [C]]

I’m using 1.54 locally, so that should work for you in the meantime.  I’ll hopefully have an update later today to add support for 1.56.

 

-Kevin

[Francesco Cicconardi]

I tried also the 1.54 version, but it doesn't work...

F




Francesco Cicconardi, Ph.D
___________________________________________________
Department of Biochemical Sciences
Sapienza University
P.le A. Moro, 5
00185 Rome
Italy
phone: +390649914297

CASPUR - Inter University Consortium for Supercomputing Applications
for University and Research
Via dei Tizii, 6/b
00185 Roma
Italy

e-mail: fran...@gmail.com
            frac...@caspur.it

2011/2/8 Jacobs, Kevin (NIH/NCI) [C] <jaco...@mail.nih.gov>

[Jacobs, Kevin (NIH/NCI) [C]]

Hi Francesco,

 

I’ve loaded 1.56 and it does seem to work for me too.  Can you verify the version of Python and BioPython?  The clues suggest that you may also have a pre-release version in your Python path.  One way to check is to run: “glu –path” and use that interpreter to import BioPython “import Bio; print Bio.__version__”.

[Francesco Cicconardi]

ok Kevin,

I’ve loaded 1.56 and it does seem to work for me too.  Can you verify the version of Python and BioPython? 

 

The clues suggest that you may also have a pre-release version in your Python path.  One way to check is to run: “glu –path” and use that interpreter to import BioPython “import Bio; print Bio.__version__”.

Typing glu --path it gives me

GLU interpreter version: 2.6.4 (r264:75706, Sep  9 2010, 12:54:47)
[GCC 4.4.3]
GLU import path: /work/adt/gmancini/pkg/python/lib/python2.6/site-packages/glu-1.0b2_dev-py2.6-linux-x86_64.egg/glu/__init__.pyc

Biopython version is 1.56 while python version is 2.6.4

F



 

[Kevin Jacobs <jacobs@bioinformed.com>]

Hi Francesco,

Please update your source tree and try once more.  I believe I have fixed the bug that you observed.

-Kevin

[Francesco Cicconardi]

Thank you very much! I'll give a try!

F




Francesco Cicconardi, Ph.D
___________________________________________________
Department of Biochemical Sciences
Sapienza University
P.le A. Moro, 5
00185 Rome
Italy
phone: +390649914297

CASPUR - Inter University Consortium for Supercomputing Applications
for University and Research
Via dei Tizii, 6/b
00185 Roma
Italy

e-mail: fran...@gmail.com
            frac...@caspur.it

2011/2/9 Kevin Jacobs <jac...@bioinformed.com> <bioin...@gmail.com>

Hi Francesco,

Please update your source tree and try once more.  I believe I have fixed the bug that you observed.

-Kevin