This is shorter and I'd be surprised if it's not also faster. I've cut down the data for demo purposes.

Input file:

$ cat pm_1076056_in.fasta
>gi|321257144|ref|XP_003193485.1| flap ...
MGIKGLTG
RTIRMVDH
ECK
>gi|321473340|gb|EFX84308.1| hypothetical ...
MGIKGLTQ
TIRMVDNG
CKQ

[download]

Script:

$ cat oneline.pl 
use strict;
use warnings;

while (<>) {
    /^>/ ? ($. > 1 && print "\n") : chomp;
    print;
}

print "\n";

[download]

Sample run:

$ perl oneline.pl pm_1076056_in.fasta > pm_1076056_out.fasta

[download]

Output file:

$ cat pm_1076056_out.fasta
>gi|321257144|ref|XP_003193485.1| flap ...
MGIKGLTGRTIRMVDHECK
>gi|321473340|gb|EFX84308.1| hypothetical ...
MGIKGLTQTIRMVDNGCKQ

[download]

-- Ken

In reply to Re: Can you make this code shorter and/or quicker as well? by kcott
in thread Can you make this code shorter and/or quicker as well? by Anonymous Monk

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