Problems awking columns from map file

Question

[Nuthatch]

Hi everyone, I've converted three PACKEDANCESTRYMAP format files (myfile.geno, myfile.snp, myfile.ind) into PED files (myfile.ped, myfile.map, myfile.pedind), using convertf.

myfile.map obtained from the conversion has six columns, and looks like this:

1     rs3094315     0.020130       752566 G A
1    rs12124819     0.020242       776546 A G
1    rs28765502     0.022137       832918 T C
1     rs7419119     0.022518       842013 T G
1      rs950122     0.022720       846864 G C

I want to remove the last two columns of this file. So I've tried with this command:

awk '{print $1" "$2" "$3" "$4"}' myfile.map > myfile_fourcol.map

It worked for other map files in the past, but now I get this message:

awk: cmd. line:1: {print $1" "$2" "$3" "$4"}
awk: cmd. line:1:                         ^ unterminated string
awk: cmd. line:1: {print $1" "$2" "$3" "$4"}
awk: cmd. line:1:                         ^ syntax error

Can anyone help me to fix this? Thank you!

Answer 1

[Bastien Hervé]

The error is clear :

awk: cmd. line:1: {print $1" "$2" "$3" "$4"}
awk: cmd. line:1:                         ^ unterminated string

The " after $4 should be remove

Tabulation is a better delimiter than white spaces

awk -F '\t' '{print $1"\t"$2"\t"$3"\t"$4}' myfile.map > myfile_fourcol.map

[Nuthatch]

I tried with your command, but I got tha same error message. Apparently tabulation is not the delimiter. How to know which is the actual delimiter?

[Nuthatch]

Sorry. I forgot to remove the " after $4! Now it's ok! Problem solved.