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Perl script to read multi fasta sequence one by one
By Jit 2425 days ago
#!/usr/bin/env perl
use strict;
use warnings;
#USAGE
#perl rohanRun.pl seq.fa
my $outfile='tmp.fa';
my $fastaSeq_ref = readfasta ("$ARGV[0]");
my %fastaSeq = %$fastaSeq_ref;
foreach my $key ( keys %fastaSeq) {
open (OUT, ">$outfile") or die "couldn't open the file $outfile $!";
print OUT "$key\n$fastaSeq{$key}\n";
}
sub readfasta
{
(my $file)=@_;
my %sequence;
my $header;
my $temp_seq;
#suppose fasta files contains multiple sequences;
open (IN, "<$file") or die "couldn't open the file $file $!";
while (<IN>)
{
chop;
next if /^\s*$/; #skip empty line
if ($_ =~ /^>/) #when see head line
{
$header= $_;
if ($sequence{$header}){print colored("#CAUTION: SAME FASTA HAS BEEN READ MULTIPLE TIMES.\n#CAUTION: PLEASE CHECK FASTA SEQUENCE:$header\n","red")};
if ($temp_seq) {$temp_seq=""} # If there is alreay sequence in temp_seq, empty the sequence file
}
else # when see the sequence line
{
s/\s+//g;
$temp_seq .= $_;
$sequence{$header}=$temp_seq; #update the contents
}
}
return \%sequence;
}
