[Feature] add an option to let taxpasta report relative abundance as fractions instead of only counts

taxprofiler / taxpasta

TAXnomic Profile Aggregation and STAndardisation

https://taxpasta.readthedocs.io/

Apache License 2.0

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[Feature] add an option to let taxpasta report relative abundance as fractions instead of only counts #142

Open Midnighter opened 9 months ago

Midnighter commented 9 months ago

Is there an existing issue for this?

[X] I have searched the existing issues

Problem description

See discussion on Slack reported by @AmaliT.

The following config causes errors:

motus_use_relative_abundance:true
motus_save_mgc_read_counts:true

Code sample

             CRITICAL   schema_context      column           check    merge.py:424
                      check_number failure_case index                             
                      0         Column  read_count  dtype('int64')                
                      None      float64  None

Environment

taxprofiler pipeline

Anything else?

No response

Midnighter commented 6 months ago

After some more discussion on Slack, we decided that we should continue to only read input of integer counts, but add an option to taxpasta to report fractions.