Unable To Debug Pacbio Resource (Gfftovcf.Py) Module Error

Question

[Raymond301]

I am just trying to use the gffToVcf.py module. I have already run the cmd to set up the environmental variables. I know that my python_home environment is mapped.

I can successfully run the setup script.

. /data2/labdata/mbcf/pacbio/software/smrtanalysis/etc/setup.sh

But when I try to run:

/data2/labdata/mbcf/pacbio/software/smrtanalysis/analysis/bin/gffToVcf.py --help

- Traceback (most recent call last):
- File "/data2/labdata/mbcf/pacbio/software/smrtanalysis/analysis/bin/gffToVcf.py", line 5, in <module>
    pkg_resources.run_script('pbpy==0.1', 'gffToVcf.py')
- File "/usr/local/biotools/python/2.7/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py", line 489, in run_script
    keys.append(dist.key)
- File "/usr/local/biotools/python/2.7/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py", line 1207, in run_script
    def __init__(self,module):
- File "/data2/labdata/mbcf/pacbio/software/smrtanalysis-1.3.0/analysis/lib/python2.7/pbpy-0.1-py2.7.egg/EGG-INFO/s                         cripts/gffToVcf.py", line 8, in <module>
    from pbpy.io.GffIO import *
- File "/data2/labdata/mbcf/pacbio/software/smrtanalysis/analysis/lib/python2.7/pbpy-0.1-py2.7.egg/pbpy/io/GffIO.py", line 5, in <module>
    import gzip
- File "/usr/local/biotools/python/2.7/lib/python2.7/gzip.py", line 10, in <module>
    import io
- File "/usr/local/biotools/python/2.7/lib/python2.7/io.py", line 60, in <module>
    import _io
- ImportError: /usr/local/biotools/python/2.7/lib/python2.7/lib-dynload/_io.so: undefined symbol: PyUnicodeUCS2_FromObject

I've been playing with environmental variables, and I can't seem to figure out what it is that I'm missing. I'm hoping that it's something obvious, and I'm just missing it.

Answer 1

[Istvan Albert]

I think your Python installation is damaged in some way. Note that your error traces back to a package that is part of Python and is unrelated to the library that you are using.

[Raymond301]

Yes, you are correct! Python 2.5.1 causes FAILURE. Thank you so very much!

Answer 2

[Houkto]

Hi Raymond,

Does the conversion process went well. I am trying to convert gff to vcf.

[Raymond301]

If you have a real gff to begin with then, http://www.smrtcommunity.com/SMRT-Analysis/Tools. The SMRT package is great. But I have a non-standard gff.

[Houkto]

Thanks for the fast reply raymond, I signed up for an account and clicked on the link, however, it says GFF to VCF is available as part of the SMRT Analysis download. and when I click on this link its direct me to SMRT analysis download page which has link to SMRT Analysis Source Code or VMware image or CentOS Binaries or Ubuntu Binaries all of these over 1Gb which one shall i download to get the tool (to run on linux) ? cheers