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OK. It looks like inp1.txt was created on a Windows box. Your matching fields defined in inp2.txt are strings of numbers, but in inp1.txt they are strings of numbers followed by a <carriage-return>...

Now I am confused, what do you expect from your new input ? can you show output sample

Your specification said that field5 had subfields separated by a colon; your real data seems to contain subfields you want to match in fields 5 and 6 separated by a colon and a space. None of the...

Yoda's code will find a match if any subpart of field 4 in file2 is matched by field 2 in file1. Akshay's code will find a match only if the 2nd subpart of field 4 in file 2 is matched by field 2 in...

Try this:
awk '
NR == FNR {
A[$0] = $NF
next
}
{
for ( k in A )
{
n = split (...

Another approach :
$ awk 'FNR==NR{A[$4]=$0;next}{x=0;for(i in A){split(A[i],X,":");if($2==X[2]){x=1;print $0,A[i]}}if(x==0)print}' file2 file1
A B C D L E:B:C
E F
G H G H R H:H:I:J

Not sure why! This is what I get.

Sample input datas:
$ cat file1.txt
[OR] KOG0001 Ubiquitin and ubiquitin-like proteins
ath: At1g31340
ath: At1g53930
ath: At1g53950
[J] KOG0002 60s...

Did you make any modifications in the awk program that I posted?

Another suggestion: If you are on SunOS / Solaris try using nawk or /usr/xpg4/bin/awk

Here is something that you can start working with:
awk '
NR == FNR {
A[$1] = $1
next
}
!/\[/ && FILENAME == "file2.txt" {
...

You can leverage pathname expansion to further simplify:
for dir in *cuff/
do
awk '{...}' "${dir}/xyz.gtf"
done
Regards,
Alister

for dir in *cuff
do
[ -d "$dir" ] && awk '{...}' "${dir}/xyz.gtf"
done

Is it this that you are after?

sort file -k1,1 -k2,2n | awk '
{nbr[$1]++; a[$1]= a[$1] ? a[$1]"@"$2 : $2; sum[$1]+=$2}

END {
for (key in a) {
split(a[key], b, "@")
len =...

* will match directory and file names alike, so you can handle it exactly the same way.

30,000 files may easily be too many to fit into *, however. You could use ls with a read loop instead. ...

@ newbie83: I get:
$ awk '
$1=="collect" {
sub(/.*tbc\</,"");
sub(/;.*/,"");
print FILENAME, $0
} ' file1 file2
file1 A,B,C
file1 D,B,C,A
file2 A
file2 C,A
file2 B,A...

Hi, I just corrected a number of things in what you were trying to do, to give you an idea:
awk '
$1=="collect" {
sub(/.*tbc\</,"");
sub(/;.*/,"");
print FILENAME, $0
}
'...

Might need some performance tuning, but works.

awk -F";" '/collect/ {sub(/tbc</,"");print $2}' File1 | paste -sd , - | awk -F, '{for(i=1;i<=NF;i++) print $i}' |sort -u | tr "\n" "\t"

One way to do this:

for f1 in bam_*.bam
do
mid=${f1#*_}
mid=${mid%.*}
f2=bed_${mid}.bed
awk 'NR==FNR { commands }' $f1 $f2 > out_${mid}.txt
done

That was just an example to set you on your way. Since you didn't display an example of your file, this is just a guess, but it works when applied to a file:


cat file

1.1 . . 2.2 3.3 . ....

FIRST: your file is a DOS file, CR LF (0x0D 0x0A) terminated. To correctly work upon it, remove the CR chars from it (copiously covered in these fora).
Then try: awk '{for (i=1; i<=NF; i++) if...

Now I see that gsub() does not support \1 references.
Also I see one needs 3 cycles to replace a row of dots.
With perl this becomes:
perl -pe 'for ($i=1;$i<=3;$i++) { s/(^|\D)\.(\D|$)/$1 $2/g...

awk '{for (i=1;i<=2;i++) gsub( /(^|[^0-9])\.([^0-9]|$)/ , "\1 \2")} 1'

i would suggest to use a "cut" you can use a loop to move the cut N times across the columns check for a value, then loop through the rows in a loop. The use of a nested loops. I have an example of...

echo "1.1 . . 2.2" | sed 's/ \. \. / /g'

1.1 2.2

for i in `cat file1`
do
grep $i file2 >>output
done

I would highly recommend to avoid using this syntax: for i in `cat file1`

You can find the reason here (http://partmaps.org/era/unix/award.html#backticks)