http://www.perlmonks.org?node_id=833659


in reply to simple perl script to trim a FASTA file

Generally, FASTA files contain multiple sequence lines (wrapped at n? chars), per header line, which means your example could be misleading. If that is the case, then something like this may be needed: 

#! perl -slw
use strict;

my( $x, $y ) = ( 3, 5 );

while( <DATA> ) {
    chomp;
    print ">$_";
    local $/ = '>';
    $_ = <DATA>;
    chomp;
    tr[\n][]d;
    print for unpack '(A36)*', substr $_, $x, length() - $x - $y;
}

__DATA__
>HWI-EAS158_40_3_1_46_535
GTGAATGCGTGATACAGGAATGTTCGTTGTGACCAT
>HWI-EAS158_40_3_1_47_579
AAAGTGAATGCGTGATACAGGAATGTTCGTTGTGAC
AAAGTGAATGCGTGATACAGGAATGTTCGTTGTGAC
AAAGTGAATGCGTGATACAGGAATGTTCGTTGTGAC
AAAGTGAATGCGTGATACAGGAATGTTCGTTGTGAC
>HWI-EAS158_40_3_1_46_731
GTGTCATGCGTGATACAGGAATGTTCGTTGTGAAAA
GTGTCATGCGTGATACAGGAATGTTCGTTGTGAAAA
GTGTCATGCGTGATACAGGAATGTTCGTTGTGAAAA

[download]

Produces:

c:\test>junk46
>>HWI-EAS158_40_3_1_46_535
AATGCGTGATACAGGAATGTTCGTTGTG
>HWI-EAS158_40_3_1_47_579
GTGAATGCGTGATACAGGAATGTTCGTTGTGACAAA
GTGAATGCGTGATACAGGAATGTTCGTTGTGACAAA
GTGAATGCGTGATACAGGAATGTTCGTTGTGACAAA
GTGAATGCGTGATACAGGAATGTTCGTT
>HWI-EAS158_40_3_1_46_731
TCATGCGTGATACAGGAATGTTCGTTGTGAAAAGTG
TCATGCGTGATACAGGAATGTTCGTTGTGAAAAGTG
TCATGCGTGATACAGGAATGTTCGTTGT

[download]
Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
"Science is about questioning the status quo. Questioning authority".
In the absence of evidence, opinion is indistinguishable from prejudice.

In Section Seekers of Perl Wisdom