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Created 2016-02-05 21:30:50 | Updated | Tags: install error python oncotator
Comments (0)

Hi,

I installed Oncotator v1.8.0.0 on RHEL.

I am getting following error when running the command oncotator -h

Traceback (most recent call last): File "/usr/bin/oncotator", line 9, in load_entry_point('Oncotator==v1.8.0.0', 'console_scripts', 'oncotator')() File "/usr/lib/python2.6/site-packages/distribute-0.6.15-py2.6.egg/pkg_resources.py", line 305, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/usr/lib/python2.6/site-packages/distribute-0.6.15-py2.6.egg/pkg_resources.py", line 2244, in load_entry_point return ep.load() File "/usr/lib/python2.6/site-packages/distribute-0.6.15-py2.6.egg/pkg_resources.py", line 1954, in load entry = import(self.module_name, globals(),globals(), ['name']) File "/usr/lib/python2.6/site-packages/Oncotator-v1.8.0.0-py2.6.egg/oncotator/Oncotator.py", line 52, in from oncotator.utils.RunSpecificationFactory import RunSpecificationFactory File "/usr/lib/python2.6/site-packages/Oncotator-v1.8.0.0-py2.6.egg/oncotator/utils/RunSpecificationFactory.py", line 2, in from oncotator.DatasourceFactory import DatasourceFactory File "/usr/lib/python2.6/site-packages/Oncotator-v1.8.0.0-py2.6.egg/oncotator/DatasourceFactory.py", line 53, in from oncotator.datasources.EnsemblTranscriptDatasource import EnsemblTranscriptDatasource File "/usr/lib/python2.6/site-packages/Oncotator-v1.8.0.0-py2.6.egg/oncotator/datasources/EnsemblTranscriptDatasource.py", line 75 POPULATED_ANNOTATION_NAMES = {'transcript_exon', 'variant_type', 'variant_classification', 'other_transcripts', ^ SyntaxError: invalid syntax

What am i doing wrong.

LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch Distributor ID: RedHatEnterpriseServer Description: Red Hat Enterprise Linux Server release 6.5 (Santiago) Release: 6.5 Codename: Santiago

Linux 2.6.32-431.17.1.el6.x86_64 x86_64


Created 2014-09-29 15:28:12 | Updated | Tags: parallelism python
Comments (3)

Hi, I have 190 samples that I am running through the GATK DNAseq pipeline following the Best Practices. Since only a few genes have been sequenced for each sample, the alignment files are very small (0.5 GB BAM files), but even then processing each samples takes about 3 hours. Is there a way to parallelize the processing of the individual samples on a mutli-core machine (since processing each sample is independent of each other it should not make a difference). There is a feature in Python using Pool in the multiprocessing module that could be used. I tried it but it does not seem to work for me. Does the GATK team have any guidance or information on this issue. Thanks,

  • Pankaj

Created 2012-12-28 07:08:02 | Updated 2013-01-07 19:14:29 | Tags: developer python wrappers
Comments (5)

Hi all,

Wouldn't it be useful to have GATK wrapped into a Python API? pygatk. As pysam is for samtools or pybedtools is for bedtools. Is anybody developing this?

Regards, Pablo.