extract first sequence only from a fasta file

Question

I want to extract the first sequence only from a fasta file of multiple sequences. I have this code below but i cant get the loops just right to work with one another.

while (my $line = <$in_fh>) {
    chomp $line;
    for (my $i = 1; $i <= 1; $i++) {
        print $out_fh $line;
    }
}

close $out_fh;

I think its getting mixed up in the while loop but no matter what i try its not correct. I tried moving the for loop outside for example but it didnt work. Is it the type of loop? Thanks very much for all pointers.

Answer 1

Since each fasta record header starts with > and the sequence shouldn't ever have that character in it. It should be safe to keep reading lines until you see the 2nd line that starts with >.

my $line = <$in_fh>;
#print first line no matter what
print $line;

while($line = <$in_fh>){
  #line must start with ">"
  unless( $line =~/^>.+/){
     print $line;
  }else{
    last;  #skip to the end
 }

}