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.