mjhjmtu

I have a file which looks like this:

latitude Chr01 0.85
latitude Chr05 0.25
latitude Chr11 0.07
latitude Chr13_a 0.26
latitude Chr13_b 0.00
latitude Chr14_a 0.00
latitude Chr14_b 1
latitude Chr15 1
latitude Chr16_a 0.01
latitude Chr16_b 1
latitude Chr17 0.62
MCMT Chr01 1
MCMT Chr05 0.30
MCMT Chr11 0.018
MCMT Chr13_a 0.34
MCMT Chr13_b 0.00
MCMT Chr14_a 0.00
MCMT Chr14_b 1
MCMT Chr15 1
MCMT Chr16_a 0.00
MCMT Chr16_b 1
MCMT Chr17 0.18
tD Chr01 0.09
tD Chr05 0.00
tD Chr11 0.02
tD Chr13_a 0.04
tD Chr13_b 2.88
tD Chr14_a 5.25
tD Chr14_b 1
tD Chr15 1
tD Chr16_a 0.00
tD Chr16_b 1
tD Chr17 0.00

I want to convert my file into this format

env chr01 chr05 chr11 chr13_a chr13_b chr14_a chr14_b chr15 chr16_a chr16_b chr17
latitude 0.85 0.25 0.07 0.26 0 0 1 1 0.01 1 0.62
MCMT 1 0.3 0 0.34 0 0 1 1 0 1 0.18
TD 0.09 0 0.02 0.04 2.88 5.25 1 1 0 1 0

How can I do this?

There may be bioinformatics-specific tools for this - but otherwise you can use GNU datamash

$ datamash -s crosstab 1,2 unique 3 < file
 Chr01 Chr05 Chr11 Chr13_a Chr13_b Chr14_a Chr14_b Chr15 Chr16_a Chr16_b Chr17
MCMT 1 0.30 0.018 0.34 0.00 0.00 1 1 0.00 1 0.18
latitude 0.85 0.25 0.07 0.26 0.00 0.00 1 1 0.01 1 0.62
tD 0.09 0.00 0.02 0.04 2.88 5.25 1 1 0.00 1 0.00

If the order of output lines is important, pipe the result through sort

BTW this isn't really transposition - it's cross-tabulation (sometimes known as a pivot table).

With miller (http://johnkerl.org/miller/doc)

mlr --inidx --ifs " " --opprint rename 1,env,2,key,3,value then reshape -s key,value input.txt

gives you

env Chr01 Chr05 Chr11 Chr13_a Chr13_b Chr14_a Chr14_b Chr15 Chr16_a Chr16_b Chr17
latitude 0.85 0.25 0.07 0.26 0.00 0.00 1 1 0.01 1 0.62
MCMT 1 0.30 0.018 0.34 0.00 0.00 1 1 0.00 1 0.18
tD 0.09 0.00 0.02 0.04 2.88 5.25 1 1 0.00 1 0.00