Edward Wijaya wrote:
>
> Hi groups,
Hello,
> I have a file which contain many many of this line (Fasta Format):
>
> > YNL331C
> CAATATGCGAGGGACCTACATGTTGA
> CATGACAATGAATTCTATTGAAAAAA
>
> > YKL071W
> ATAATTATTCCTGTTTCTTTAACCTG
> GTAAAAAAAAGTACAAACACTTAAGC
>
> What I would like to do is to concatenate the line below >
> into one single string.
> Such as the output would be:
>
> CAATATGCGAGGGACCTACATGTTGAGCATGACAATGAATTCTATTGAAAAA
> ATAATTATTCCTGTTTCTTTAACCTGGTAAAAAAAAGTACAAACACTTAAGC
>
> The current code I created now seem to work but doesn't
> gie the result I want. Since it concatenates all into 1 single line.
> I thought there must be a very simple way to do this.
> But I can't seem to figure out how to achieve that.
>
> #---My Code --------------
> while (<>) {
> if (/^>/) {
> next;
> }
> chomp;
> $line .= $_;
> }
> push (@crseq, $line);
> print join("\n", @crseq), "\n";
This should do what you want:
$/ = '>';
while ( <> ) {
next unless s/\s+\S.*//;
chomp;
tr/\n//d;
print "$_\n";
}
John
--
use Perl;
program
fulfillment
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