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Hi,
I am new in python and interested in using this python code to convert the .biom file from hdf5 format to a json one. However it does not sucess:
> python HDF5toJSON.py my_file.biom my_fileJ.biom…
arcys updated
9 years ago
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The recommendation of PEP 8 is to use `UpperCase` for classes, but it does not require it, the typical exception being `under_scores` for callables.
It wouldn't be the craziest thing if they _were_ p…
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Hi @reikopm,
Thank you for the BIOM files and the associated README you so kindly shared! I am looking forward to include MBARI data in our efforts to build a global omics observatory community!
…
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We need classes for many of the core types of data dealt with in QIIME. A lot of these classes may end up in scikit-bio or biom-format, but it'll be useful to get a list started here.
Once implement…
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Hello @tanaes , I tested your pipeline on some data. Here is my experience:
When executing raw_make_links_pe, it said:
`Unable to set utime on symlink data/sample1/Run1/raw/sample1_R1.fq.gz. Your…
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I am following along the Biostar Handbook.
I did 'pip install bio --upgrade' (with and without upgrade) and it says requirement already satisfied. But when I try to use the command is doesn't work…
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Adding a new functionality comes at the cost of complexity and more abstractions. I hereby propose to do a basic review of the current project dependencies.
I.e. a quick search through a codebase r…
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The output from normalize_table.py seems to be in BIOM 1.0.0 format. This causes some really brutal issues, such as preventing the `biom add-metadata` workaround for adding taxonomy data from working …
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Hi,
After formating the biom.df and eqtl.df objects and adding a $type column to each, I got two data frames looking this, which seems fine:
> head(biom.df)
SNPID CHR POS PVAL …
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Dear Developers,
I'm trying this pipeline. However, when I typed
python ./scripts/Master.py -h
, it turned out:
Traceback (most recent call last):
File "./scripts/Master.p…