Print First Occurence Of A Line

I extracted ORFs from a initial fasta file and now I want to get the longest ORF for each transcript.

After having extracted the size of the ORFs with faSize and sorted them by size, the code I was used to use is:

perl -ane'print unless $x{$F[0]}++'

This time I have a problem using the perl command.

After having extracted the size and sorted the transcripts I have something like this:

Singlet_1000_61 3844

Singlet_2000_73 3508

Singlet_1000_62 3081

Singlet_2000_62 3008

Singlet_3500_48 2973

Singlet_4000_48 2964

Singlet_3500_54 2863

What I want is:

Singlet_1000_61 3844

Singlet_2000_73 3508

Singlet_3500_48 2973

...

The perl command is not working in this case.

Do you have any suggestions on how I can make it work?

Or a awk command?

Thanks for help

perl awk bash fasta

• 2,698 views • link

updated 13.3 years ago by Kenosis

• written 13.3 years ago by federico.gaiti

3 answers

More efficient way using awk:

$ cat input 
Singlet_1000_61 3844
Singlet_2000_73 3508
Singlet_1000_62 3081
Singlet_2000_62 3008
Singlet_3500_48 2973
Singlet_4000_48 2964
Singlet_3500_54 2863

$ awk -F"_" '{if(!tab[$2]){print $0; tab[$2]=1;}}' input 
Singlet_1000_61 3844
Singlet_2000_73 3508
Singlet_3500_48 2973
Singlet_4000_48 2964

• 151 views • link

written 13.3 years ago by Anthony Mathelier

This might not be the most efficient way, but:

$ cat input.txt
Singlet_1000_61 3844
Singlet_2000_73 3508
Singlet_1000_62 3081
Singlet_2000_62 3008
Singlet_3500_48 2973
Singlet_4000_48 2964
Singlet_3500_54 2863

$ cat input.txt | awk -F "_" '{print $1"_"$2"\t" $0}' | sort -u -k1,1 | awk -F "\t" '{print $2}'
Singlet_1000_61 3844
Singlet_2000_73 3508
Singlet_3500_48 2973
Singlet_4000_48 2964

• 1 views • link

written 13.3 years ago by csiu •

Here's another option:

perl -ne 'print if /_(\d+)_/ and !$x{$1}++' inFile

Output on your dataset:

Singlet_1000_61 3844
Singlet_2000_73 3508
Singlet_3500_48 2973
Singlet_4000_48 2964

• 0 views • link

written 13.3 years ago by Kenosis