Update to include multisample tables #7
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Support for humann2 multi-sample merged tables. How to generate and normalize merged tables: https://bitbucket.org/biobakery/biobakery/wiki/humann2#rst-header-humann2-for-multiple-samples
Added multisample table for test data
Update format_humann2_output.py
remove blank line after header
remove blank line after header
remove blank line after header
remove blank line after header
Ignore differences in whitespace representations of Tabs
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Thank you for this very useful function! I have been using it to trim down some humann2 data involving comparisons between samples. For input I have a merged and normalized table humann2 output. I've made some changes to format_humann2_output.py to accept this file type as input and thought others might find them useful.
This branch supports humann2 multi-sample merged tables as input and writes a column for each sample abundance in the output files. Additionally, this branch supports input files that contain additional information after the "UNGROUPED" designation or are labeled "UNMAPPED". I have attached a test input table.
I've fixed the modified the format_humann2_output.py script to round to the nearest integer. This prevents inconsistency between environments but can be modified. I've also modified the test script to allow differences in conversion of tab spacing to white space.
More info on humann2 multi-sample merged tables: https://bitbucket.org/biobakery/biobakery/wiki/humann2#rst-header-humann2-for-multiple-samples