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Thanks bipinajith. That worked perfectly.

I have data that looks like this:

chr1 mm9_knownGene exon 155747075 155747189 0.000000 + . gene_id "Glul"; transcript_id "uc007daq.1";
chr1 mm9_knownGene...

Thanks for the help everyone!

All the options worked except for bipinajith's.
It turns out this was the fastest option:
awk '{p=$2; getline<f} !A[$2=p $2]++' f=file2 file1

It churned through...

I have two text files that look something like this:

A:B:C 123
D:E:F 234
G:H:I 345
J:K:L 123
M:N:O 456
P:Q:R 567


A:B:C 456
D:E:F 567
G:H:I 678
J:K:L 456
M:N:O 789
P:Q:R 890

I...

Thank you! I'm glad it was something so simple.

I apologize, I should have been more clear. This is what I meant when I said "I can add more columns and get more of that first line" in my original post. I'm more concerned about why the first line...

I have an input that looks like this:


chr1 mm9_knownGene utr3 3204563 3206102 0 - . gene_id "Xkr4"; transcript_id "uc007aeu.1";
chr1 mm9_knownGene utr3 4280927...

You're a wizard.

CPU time : 3.88 sec.
Max Memory : 2 MB
Max Swap : 25 MB
Max Processes : 1
Max Threads : 1

:eek:

This involves...

Sure. These were all submitted to an LSF queue, and each node has a minimum of 8 cores with 2.8Ghz+ Intel Xeon CPUs and 16GB RAM running RHEL 5.3. Here is some extra info about each job, with the...

Thanks for the suggestions everyone. Here's how it went.
My original method: 99,640 CPU seconds
hergp's method: 207,613 CPU seconds
alister's awk method: 42,552 CPU seconds

Thanks alister for...

Hello,
I am using sed in a for loop to replace text in a 100MB file. I have about 55,000 entries to convert in a csv file with two entries per line. The following script works to search file.txt for...