Pooling
This is a nice example to show the pooling script included with THAPBI PICT, here pooling on the first two columns of the sample report:
$ ../../scripts/pooling.py -i summary/430_bats.COI.samples.onebp.tsv -c 1,2
<SEE TABLE BELOW>
You can specify an output stem like -o pooled
and get pooled.tsv
and
matching pooled.xlsx
files, but by default the plain text table is printed
to the terminal:
Rare |
Ratio |
Samples-sequenced |
Corynorhinus townsendii |
Eptesicus fuscus |
Tadarida brasiliensis |
Unknown |
---|---|---|---|---|---|---|
COTO |
1:192 |
10 |
58948 |
99888 |
82587 |
19059 |
COTO |
1:64 |
10 |
45632 |
51977 |
0 |
148446 |
EPFU |
1:192 |
10 |
99840 |
9668 |
103545 |
21191 |
EPFU |
1:64 |
10 |
91018 |
52574 |
21507 |
65809 |
TABR |
1:192 |
10 |
149636 |
73958 |
1563 |
52279 |
TABR |
1:64 |
10 |
128019 |
106581 |
773 |
50833 |
As discussed earlier, where Corynorhinus townsendii (COTO) is the rare species at a 1:64 ratio there is no Tadarida brasiliensis matched with the initial database, but it is found with the extended database:
$ ../../scripts/pooling.py -i summary/ext_bats.COI.samples.onebp.tsv -c 1,2
<SEE TABLE BELOW>
Again, shown as a table:
Rare |
Ratio |
Samples-sequenced |
Corynorhinus townsendii |
Eptesicus fuscus |
Tadarida brasiliensis |
Unknown |
---|---|---|---|---|---|---|
COTO |
1:192 |
10 |
61727 |
100185 |
92815 |
5755 |
COTO |
1:64 |
10 |
70121 |
68495 |
101333 |
6106 |
EPFU |
1:192 |
10 |
100822 |
9668 |
108264 |
15490 |
EPFU |
1:64 |
10 |
91242 |
68322 |
67690 |
3654 |
TABR |
1:192 |
10 |
154907 |
98791 |
1563 |
22175 |
TABR |
1:64 |
10 |
133876 |
140456 |
773 |
11101 |
One of the options in this script is -b
or --boolean
for a yes/no
summary rather than showing the sum of the reads:
$ ../../scripts/pooling.py -i summary/ext_bats.COI.samples.onebp.tsv -c 1,2 -b
<SEE TABLE BELOW>
All three species (and unknowns) are found in at least one of the 10 samples sequenced in each of the six groups:
Rare |
Ratio |
Samples-sequenced |
Corynorhinus townsendii |
Eptesicus fuscus |
Tadarida brasiliensis |
Unknown |
---|---|---|---|---|---|---|
COTO |
1:192 |
10 |
Y |
Y |
Y |
Y |
COTO |
1:64 |
10 |
Y |
Y |
Y |
Y |
EPFU |
1:192 |
10 |
Y |
Y |
Y |
Y |
EPFU |
1:64 |
10 |
Y |
Y |
Y |
Y |
TABR |
1:192 |
10 |
Y |
Y |
Y |
Y |
TABR |
1:64 |
10 |
Y |
Y |
Y |
Y |
In the Excel output the species labels are rotated 90 degrees allowing a very compact display.