Eukulele duplicates, and other Eukulele small bugs

[erikrikarddaniel]

Description of the bug

In a project I ran for colleagues I found duplicates in the summary table. It turned out this was due to duplicates in the taxonomy_estimation/prokka-estimated-taxonomy.out.gz file. The ones I've looked at have different scores, so it seems we're not taking that into account:

0       FJKOKEPI_01799  species Bacteria; Gammaproteobacteria; Pseudomonadales; Porticoccaceae; HTCC2207; HTCC2207      HTCC2207        357.8   0
0       FJKOKEPI_01799  order   Bacteria; Gammaproteobacteria; Pseudomonadales  Pseudomonadales 287.0   1
...
0       CJDPECOA_05216  species Bacteria; Alphaproteobacteria; Puniceispirillales; Puniceispirillaceae; UBA8309; UBA8309        UBA8309 594.3   0
0       CJDPECOA_05216  family  Bacteria; Alphaproteobacteria; Puniceispirillales; Puniceispirillaceae; UBA8309; UBA8309        UBA8309 418.3   0

This should make this rather easy to deal with.

(What's a bit interesting above is that the last two lines are identical except for the score and the rank! Must be a Eukulele bug.)

Secondly, I also found that the summary table has capitalized names, e.g. Domain. It would be good to have all lowercase (IMO).

Thirdly, when one doesn't supply a database name, the summary file gets [] in the filename. This also affects the overall summary file in the form of [] in the column header for the eukulele counts.

Command used and terminal output

No response

Relevant files

No response

System information

No response

[danilodileo]

we merged PR #202 so we can close this issue