Hello, I am merging abundance tables from 6 output table.txt using
merge_metaphlan_tables.py profiled_PB1.txt profiled_PB2.txt profiled_PB3.txt profiled_PB4.txt profiled_PB5.txt profiled_PB6.txt > output/LTS_abundance_table.txt
I am getting different header without “#SampleID” but rather with “clade_name”. See below.
Next, when I am trying to extract only species abundance from this table, using command grep -E “(s__)|(^ID)” LTS_abundance_table.txt | grep -v “t__” | sed ‘s/^.*s__//g’ > LTS_abundance_table_species.txt.
I am getting no header at all in the output file (output below). I see there is no ID head in the input file probably that is why this is happening.
It worked now, but I have another issue in creating the heatmap. I am using the following command.
-s --fperc 99
The version previously I was using was matplotlib 3.6.2 but than I downgraded to 2.2.3. In both cases it didnt work.
Currently, I can also see matplotlib-base 3.6.2 and metplotlib 2.2.3 in the conda list.