Processing a tab delimited file with shell script processing - bash

Question

normally I would use Python/Perl for this procedure but I find myself (for political reasons) having to pull this off using a bash shell.
I have a large tab delimited file that contains six columns and the second column is integers. I need to shell script a solution that would verify that the file indeed is six columns and that the second column is indeed integers. I am assuming that I would need to use sed/awk here somewhere. Problem is that I'm not that familiar with sed/awk. Any advice would be appreciated.
Many thanks!
Lilly

Answer 1

gawk:
BEGIN {
FS="\t"
}
(NF != 6) || ($2 != int($2)) {
exit 1
}
Invoke as follows:
if awk -f colcheck.awk somefile
then
# is valid
else
# is not valid
fi

Answer 2

Well you can directly tell awk what the field delimiter is (the -F option). Inside your awk script you can tell how many fields are present in each record with the NF variable.
Oh, and you can check the second field with a regex. The whole thing might look something like this:
awk < thefile -F\\t '
{ if (NF != 6 || $2 ~ /[^0123456789]/) print "Format error, line " NR; }
'
That's probably close but I need to check the regex because Linux regex syntax variation is so insane. (edited because grrrr)

Answer 3

here's how to do it with awk
awk 'NF!=6||$2+0!=$2{print "error"}' file

Answer 4

Pure Bash:
infile='column6.dat'
lno=0
while read -a line ; do
((lno++))
if [ ${#line[#]} -ne 6 ] ; then
echo -e "line $lno has ${#line[#]} elements"
fi
if ! [[ ${line[1]} =~ ^[0-9]+$ ]] ; then
echo -e "line $lno column 2 : not an integer"
fi
done < "$infile"
Possible output:
line 19 has 5 elements
line 36 column 2 : not an integer
line 38 column 2 : not an integer
line 51 has 3 elements