How to merge two files genotype and ped In Linux? I sample files as follows.

Question

[mm]

How to merge two files genotype and pre-ped In Linux? I sample files as follows.

S949C08 111071 900533 900409 Susceptible 2
S949G08 111064 900533 900469 Susceptible 2
S949E09 111051 910054 890231 Susceptible 2
S949209 111049 910054 910087 Susceptible 2
R949C06 111034 920283 920207 Susceptible 1

genotype file: One example of an animal's genotype

R949C06 TC TT CC TC CC TT GG CC AG TT AA GG AA TT CC TC -- CC TC GC TC AA TC AG AG TC AA AA AA AG TC CC AT AA TT AA TT GG AA TC AG TC TA TA AG -- TG TT -- AA -- TT TT CC AG GG TC GG CC AA -- CC AC AA GG -- AA CC CC AA TC AG AA TC CG TT GG CC TT GG AG GG TT AA CC AA CC TC AG GG TC AG AG AG GC CC AG GG AA TC GG AA AA GG TC AG CC AG CC TC AA CC CC CC GG CC AG CC CC AG AC CC GG TT CC AG CC AA TC TT GG AG GG CC TC TC AA GG CC TC AG AG TT GG TG AG AA TG

[Devon Ryan]

man join, noting that you need to sort the files before use.

[mm]

I do not understand what are you saying?

[Pierre Lindenbaum]

Devon asks you to read the manual for the linux command 'join'. https://linux.die.net/man/1/join

"join - join lines of two files on a common field "

noting that you need to sort the files before use.

"Important: FILE1 and FILE2 must be sorted on the join fields. "

[mm]

I SNP Chip id ,common in both files. That is done I want to join

Answer 1

[mittu1602]

You can try awk one-liner

cat Test1.txt

S949C08 111071 900533 900409 Susceptible 2
S949G08 111064 900533 900469 Susceptible 2
S949E09 111051 910054 890231 Susceptible 2
S949209 111049 910054 910087 Susceptible 2
R949C06 111034 920283 920207 Susceptible 1

cat Test2.txt

R949C06 TC TT CC TC CC TT GG CC AG TT AA GG AA TT CC TC -- CC TC GC TC AA TC AG AG TC AA AA AA AG TC CC AT AA TT AA TT GG AA TC AG TC TA TA AG -- TG TT -- AA -- TT TT CC AG GG TC GG CC AA -- CC AC AA GG -- AA CC CC AA TC AG AA TC CG TT GG CC TT GG AG GG TT AA CC AA CC TC AG GG TC AG AG AG GC CC AG GG AA TC GG AA AA GG TC AG CC AG CC TC AA CC CC CC GG CC AG CC CC AG AC CC GG TT CC AG CC AA TC TT GG AG GG CC TC TC AA GG CC TC AG AG TT GG TG AG AA TG

awk 'FNR==NR{a[$1]=$2 FS $3 FS $4 FS $5 FS $6;next}{ print $0, a[$1]}' Test1.txt Test2.txt > result.txt

cat result.txt

R949C06 TC TT CC TC CC TT GG CC AG TT AA GG AA TT CC TC -- CC TC GC TC AA TC AG AG TC AA AA AA AG TC CC AT AA TT AA TT GG AA TC AG TC TA TA AG -- TG TT -- AA -- TT TT CC AG GG TC GG CC AA -- CC AC AA GG -- AA CC CC AA TC AG AA TC CG TT GG CC TT GG AG GG TT AA CC AA CC TC AG GG TC AG AG AG GC CC AG GG AA TC GG AA AA GG TC AG CC AG CC TC AA CC CC CC GG CC AG CC CC AG AC CC GG TT CC AG CC AA TC TT GG AG GG CC TC TC AA GG CC TC AG AG TT GG TG AG AA TG 111034 920283 920207 Susceptible 1