biom-format

biom-format copied to clipboard

take column names from all metadata not just first entry

1

When converting observation metadata to dataframe the column names were taken from the first row. When the first row had missing values (i.e. incomplete taxonomic assignment) then the number of...

asafpr

Clarification about ID type in the docs for Table.update_ids

3

I'm not sure if non-string IDs were ever officially supported for BIOM tables, but some of the Empress test code ([these lines, in particular](https://github.com/biocore/empress/blob/bf6f755c5187e543ff13c2c624b153fb97918b23/tests/python/test_tools.py#L143-L145)) involved setting IDs to integers. It...

fedarko

wasade

Failing tests

7

Hi, Thanks for your work on biom-format. While running tests on the latest version(2.1.10) of corresponding package, two tests are failing with: ``` =================================== FAILURES =================================== ___________________ TableTests.test_from_hdf5_custom_parsers ___________________ args...

nileshpatra

it would be nice to easily remove blanks

2

Something like `biom filter-blanks -i foo -o bar`, where any sample containing "blank" case insensitive is dropped

wasade

metadata_to_dataframe order matters

3

Hi, When you have this: [good.txt](https://github.com/biocore/biom-format/files/5957980/good.txt) it'ok When the order of metadata is different : [bad.txt](https://github.com/biocore/biom-format/files/5957946/bad.txt) You have : `ValueError: 2 columns passed, passed data had 6 columns` Maybe, taking...

guillaume-gricourt

Issue on big-endian architectures

1

Hi, there is a long standing bug open in [Debian bug tracking system](https://bugs.debian.org/820060) which I simply want to document here since there is no sign that this will be solved...

tillea

add script to export sample/observation metadata from a biom file to a sample/observation mapping file

2

this would be useful for any bash-type processing, and for working with QIIME

gregcaporaso

In unit tests where the same exception can be raised by multiple different cases it would be handy to also check for the error message. Since biom provides py2/py3 support...

ElDeveloper

Add examples of using BIOM executable to the website

4

Thanks to #3, there are excellent examples of using the `biom` API. There are also excellent examples in the manpage, but not on the website! For example, the command `biom...

colinbrislawn