print first occurence of a line

[uqfgaiti]

Hi all,

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

[bruce01]

Try stackoverflow.com, they love this sort of thing, but put your thick-skin on.

[westerman]

Or, as a hint, use a hash to keep track of if a transcript has been printed or not. Hashes are a wonderful data structure to know about.

[syfo]

I don't get it. What do the numbers in your input refer to? If the first one is the ID of the transcript and the last one the length I would do

tac list | awk -F "_" '{t[$2]=$0}END{for (i in t)print t[i]}'

If the ID of each transcript is the first column then it is even simpler

tac list | awk '{t[$1]=$0}END{for (i in t)print t[i]}'

Pipe sort the output if needed.
Since you already sorted them by size the script starts by the end (tac) and only remembers the last occurrence of each ID.