adding module to query entire lineages, query_taxon_clades.py, in que…

[mtisza1]

Mike's suggestions for minor improvements on this script (query_taxon_clades.py):

1. Change output file format and/or print the result in a more compact format ala the other tool
2. Query the taxdump file to get taxon level "species, genus, family, etc" for each query taxid, similar to other script and set the column names to, for example Genus_816 instead of ID_816 (line 96)\

Other notes: both scripts in this directory use pandas as a dependency the make_hierarchy_table.py script uses pytaxonkit as well.

-- Mike Tisza, 2022-10-12

An example run:

$ cat ../../../few_bacteroides1.txt | python3 query_taxon_clades.py -t stdin
                                 DB  ID_816  ID_817  ID_818  ID_820
0           minikraken_20171019_8GB      13       4       2       0
1  minikraken2_v2_8GB_201904_UPDATE      18       4       2       0
2                   kaiju_db_nr_euk     262      86       4       7
3                     NCBI_nucl_wgs     341      84       3       7
4                      NCBI_nucl_gb     507      14       3       5
5                  MTSV_Oct-28-2019      18       4       2       1
6                        metaphlan3      43       1       1       1
7                        RefSeq_v98     328      79       3       7