Combine count_presence and count_abundance

[pommevilla]

MetaFunPrimer/src/mfpcount

Line 123 in 997c15e

join -j 1 -t ' ' <(count_presence $input_dir | sort -k 1) <(count_abundance $input_dir | sort -k 1) > "$shortdir.summary.tsv"

count_presence and count_abundance can be combined into a single function that summarizes the presence and abundance of the genes within a directory in a single pass.

Tasks

• Write new function summarize_results_directory that combines count_presence and count_abundance. The quoted line above should look like:
  summarize_results_directory $input_dir > "shortdir.summary.tsv"

Affected files

• mfpcount, in the line quoted at the top
• count_presence and count_abundance will be replaced with the new summarize_directory