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