Example bracken combining outputs and adding lineage info

Conda install if needed

Program is in my bit toolkit, can be installed in a new environment like so if needed:

conda create -y -n bit -c conda-forge -c bioconda -c defaults -c astrobiomike bit=1.8.08

Getting example data

curl -L -o example-bracken-output-1.tsv https://ndownloader.figshare.com/files/24086822

curl -L -o example-bracken-output-2.tsv https://ndownloader.figshare.com/files/24086822

Combining outputs and adding full lineage info

Script is bit-combine-bracken-and-add-lineage. There is a help menu with -h. It takes as input (-i) a file either with 1 column of input file names only, or 2 tab-delimited columns with input file name in column 1 and the desired sample name in column 2, e.g.:

paste <( ls ex*bracken*.tsv ) <( printf "sample-1\nsample-2\n" ) > bracken-sample-name-map.tsv

cat bracken-sample-name-map.tsv

example-bracken-output-1.tsv	sample-1
example-bracken-output-2.tsv	sample-2

Running the script:

bit-combine-bracken-and-add-lineage -i bracken-sample-name-map.tsv -o Combined-taxonomy.tsv

This has a few things in it, but can be chopped down to what you want:

head Combined-taxonomy.tsv | column -ts $'\t'

domain    phylum      class    order       family        genus        species                      tax_id   tax_level  sample-1_num  sample-1_frac  sample-2_num  sample-2_frac
Bacteria  Firmicutes  Bacilli  Bacillales  Listeriaceae  Listeria     Listeria monocytogenes       1639     S          399031        0.10780        399031        0.10780
Bacteria  Firmicutes  Bacilli  Bacillales  Listeriaceae  Listeria     Listeria grayi               1641     S          204           0.00006        204           0.00006
Bacteria  Firmicutes  Bacilli  Bacillales  Listeriaceae  Listeria     Listeria ivanovii            1638     S          555           0.00015        555           0.00015
Bacteria  Firmicutes  Bacilli  Bacillales  Listeriaceae  Listeria     Listeria welshimeri          1643     S          92            0.00002        92            0.00002
Bacteria  Firmicutes  Bacilli  Bacillales  Listeriaceae  Listeria     Listeria innocua             1642     S          53            0.00001        53            0.00001
Bacteria  Firmicutes  Bacilli  Bacillales  Listeriaceae  Listeria     Listeria seeligeri           1640     S          30            0.00001        30            0.00001
Bacteria  Firmicutes  Bacilli  Bacillales  Listeriaceae  Listeria     Listeria sp. PSOL-1          1844999  S          28            0.00001        28            0.00001
Bacteria  Firmicutes  Bacilli  Bacillales  Listeriaceae  Listeria     Listeria weihenstephanensis  1006155  S          15            0.00000        15            0.00000
Bacteria  Firmicutes  Bacilli  Bacillales  Listeriaceae  Brochothrix  Brochothrix thermosphacta    2756     S          4             0.00000        4             0.00000