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You're close, but shell variables aren't known in an awk script unless you explicitly pass them in. And, in awk $var prints the field named by the field number contained in the awk variable var (and...

Hello pathunkathunk,

You can try following code for same.

awk 'FNR==NR{X[$1]=$0;next} ($1 in X){print X[$1]}' file2 file1


Thanks,
R. Singh

I'd say this is some kind of bioinformatics data. Anyway, you can try this in a directory containing your files:
perl -lne '$,="...

sorry.. i didnt understand your question...

so, you mean.. if any of the column sum is less than 8, then it should not print the line ?

---------- Post updated at 12:30 PM ---------- Previous...

I think you're missing a semi-colon. Try this:
sed -n "$line_number { n; p; q;}" en.pep

Many Unix sed have bugs with semicolon - newline works better
sed -n "$line_number {
n
p
q
}
" en.pep

Small variation in the first part:
awk 'NR==FNR{i=$1; $1="_host"; A[i]=$0; next} {print $0 A[$4]}' OFS=_ file2 FS='[|.]' file1

You could try something like:
awk '
FNR == NR {
x[$1] = "_host"
for(i = 2; i <= NF; i++)
x[$1]=x[$1] "_" $i
next
}
{ print $0 x[$4]
}' File2...

$
$ cat f03
>gi|31425523|gb|AY987736.1|_Macrosiphum_rosae
TCCGTGGAGATGCACCACGAAGCT
>gi|512740870|gb|JX507490.1|_Macrosiphum_funestum
GTCGTGTAGAAA-CTGGTCTT...

try..


awk '{lines[NR] = $0}!/>/&&length($0) < 11 {print lines [NR-1]; print lines [NR]} ' example.txt

Do your data always come in pairs? If yes, your code is fine. Try also$ while read HEAD; do read DATA; [ ${#DATA} -lt 10 ] && printf "%s\n%s\n" "$HEAD" "$DATA"; done < file
>gi|bcd| Species two...

Like this?
awk '/^[^>]/ && length($0)<10{print hdr"\n"$0}{hdr=$0}' input

You could try something like:
#!/bin/ksh
# SYNOPSIS:
# colcheck [file [first_column [last_column [threshhold [pass_count]]]]]
# DESCRIPTION:
# Print all lines in the file named by "file"...

try also:
awk '{count=0; for (col=6; col<=20; col++) ($col >= .75) ? count++ : 0; if (count>=8) print}' infile

In your sample code, you don't have identical thresholds for the columns, but in your spec, you do. I'll assume the latter, as it's easier for a start.
For playing around, it might be best to have...

Try:
sed -n '/^>/s/.*)_//;s/:.*//p'

awk '/>/{gsub(/.*\)_|:.*/,x); print}' file

sed 's/.:.=//g'
The g modifier does multiple substitutions in the line.

$ awk ' NR == FNR { arr[$1$2]=1; next } arr[$2$1] {print $1, $2} ' file1 file2
m.160140_g.160140 ACYPI46488-PA_product:GLE

I'm not sure sort can reject non-unique lines like that. But you forgot to actually tell sort which character you wanted to sort by after -t there.

Since it appears to be a single space, you...

Sorry -- I tested it as a multi-line programme, but joined the lines when I posted it and forgot a semicolon.


awk -F \| ' /^>gi/ { printf( ">%s\n", $4 ); getline; print; }' test3.fa

cat file1 | awk '{print $1}' | while read NUM
do
# echo ${NUM}

grep "Gene_${NUM}" file2 2>/dev/null # output to tty or suppress

RC=$?

if [[ ${RC} == 0 ]]...

This will use a bit more memory, but saves heavily on I/O as it requires each file to be read only once. Depending on the size of the files, should run much more quickly.


awk '
NR == FNR {...