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dputhier / pygtftk

A python package and a set of shell commands to handle GTF files
GNU General Public License v3.0
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[ologram]: FutureWarnings ... #75

Closed yaskermezli closed 5 years ago

yaskermezli commented 5 years ago

After updating (with the command git pull ..) and launching this command gtftk ologram -i Global_gtf_ensbl.gtf.gz -p /gpfs/tagc/home/kermezli/project/ologram_plugin_test/Thymus_H3K27ac.bed -c hg19 / ChromInfo.txt -u 1000 -d 1000 -m set -D -if Thymus_H3K27ac_olog.pdf -k 14

before having results I had this:

/gpfs/tagc/home/kermezli/miniconda2/envs/pygtftk_dev/lib/python3.6/site-packages/pybedtools/bedtool.py:3439: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'. return pandas.read_table(self.fn, *args, kwargs) /gpfs/tagc/home/kermezli/miniconda2/envs/pygtftk_dev/lib/python3.6/site-packages/pybedtools/bedtool.py:3439: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'. return pandas.read_table(self.fn, *args, *kwargs) /gpfs/tagc/home/kermezli/miniconda2/envs/pygtftk_dev/lib/python3.6/site-packages/pybedtools/bedtool.py:3439: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'. return pandas.read_table(self.fn, args, kwargs) /gpfs/tagc/home/kermezli/miniconda2/envs/pygtftk_dev/lib/python3.6/site-packages/pybedtools/bedtool.py:3439: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'. return pandas.read_table(self.fn, *args, kwargs) /gpfs/tagc/home/kermezli/miniconda2/envs/pygtftk_dev/lib/python3.6/site-packages/pybedtools/bedtool.py:3439: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'. return pandas.read_table(self.fn, *args, *kwargs) /gpfs/tagc/home/kermezli/miniconda2/envs/pygtftk_dev/lib/python3.6/site-packages/pybedtools/bedtool.py:3439: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'. return pandas.read_table(self.fn, args, kwargs) /gpfs/tagc/home/kermezli/miniconda2/envs/pygtftk_dev/lib/python3.6/site-packages/pybedtools/bedtool.py:3439: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'. return pandas.read_table(self.fn, *args, kwargs) /gpfs/tagc/home/kermezli/miniconda2/envs/pygtftk_dev/lib/python3.6/site-packages/pybedtools/bedtool.py:3439: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'. return pandas.read_table(self.fn, *args, *kwargs) /gpfs/tagc/home/kermezli/miniconda2/envs/pygtftk_dev/lib/python3.6/site-packages/pybedtools/bedtool.py:3439: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'. return pandas.read_table(self.fn, args, kwargs) /gpfs/tagc/home/kermezli/miniconda2/envs/pygtftk_dev/lib/python3.6/site-packages/pybedtools/bedtool.py:3439: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'. return pandas.read_table(self.fn, *args, *kwargs) /gpfs/tagc/home/kermezli/miniconda2/envs/pygtftk_dev/lib/python3.6/site-packages/pybedtools/bedtool.py:3439: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'. return pandas.read_table(self.fn, args, **kwargs)

qferre commented 5 years ago

Sadly, that's not something we can fix. Those warnings are due to pybedtools. We are debating whether to silence them.

dputhier commented 5 years ago

It seems to have been fixed here https://github.com/daler/pybedtools/pull/274

What is your version of pybedtools ?

pip freeze | grep bedtools

yaskermezli commented 5 years ago

version = '0.8.0'

dputhier commented 5 years ago

In fact I just checked. It seems that this commit (If I'm not wrong) is not included in the current version of pybedtools (0.8.0). So no way, you will have to wait 0.8.1.

yaskermezli commented 5 years ago

Ok! Closing.