Changrong Ge wrote:
Hi guys,
Hello,
Thanks a lot for this issue and with Anjan's help here I got the
wonderful script for my work and I post below, hopefully it would be helpful
for others--works perfectly for fasta file.
Also thanks to others who are interested in the discussion, but I think
it takes time for me to digest those "weird" symbols-----Tack Så Mycket!!!
Have a nice day
Changrong
usage: perl seqComp.pl<input_fasta_file> > <output_file>
#! /usr/bin/perl -w
use strict;
open (S, "$ARGV[0]") || die "cannot open FASTA file to read: $!";
my %s;# a hash of arrays, to hold each line of sequence
my %seq; #a hash to hold the AA sequences.
my $key;
while (<S>){ #Read the FASTA file.
chomp;
if (/>/){
s/>//;
$key= $_;
}else{
push (@{$s{$key}}, $_);
}
}
foreach my $a (keys %s){
my $s= join("", @{$s{$a}});
$seq{$a}=$s;
#print("$a\t$s\n");
}
You don't need two loops for that, you could just do:
while ( <S> ) { #Read the FASTA file.
chomp;
if ( s/>// ) {
$key = $_;
}
else {
$seq{ $key } .= $_;
}
}
John
--
Any intelligent fool can make things bigger and
more complex... It takes a touch of genius -
and a lot of courage to move in the opposite
direction. -- Albert Einstein
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