Pedro A Reche wrote:
>
> Hi all,
Hello,
> I have a file that it looks as it follows:
>
> >name1
> ADASDADFSDF
> ADASDADFSDF
> SDFDSFDSDFDF
> >name2
> ASDFDFDFFDF
> ADFEERERREWR
> ADFADFQERQEWR
> >name1
> ADASDADFSDF
> SDFDSFADFDF
> SDFDSFDSDFDF
> >name3
> SDAFSDFDFF
> WERWERER
> WERWERER
>
> and I want to have something like this:
> >name1
> ADASDADFSDFADASDADFSDFSDFDSFDSDFDF
> >name2
> ADASDADFSDFSDFDSFADFDFSDFDSFDSDFDF
> >name3
> SDAFSDFDFFWERWERERWERWERER
>
> Note that ">name1 is repeated in the input but not in the output.
>
> With the script below I can put everything under ">anyname"
> in one line. However, if ">anyname" is repeated I will get a
> concatenation and I do not want that
> Any help welcome and thanks in advance.
> Cheers
>
> #!/usr/sbin/perl
> if (!@ARGV) {
> print STDERR "usage: $0 fasta_file \n";
>
> exit 0;
> }
> my $FILE = shift @ARGV;
> my @ID;
> my %SEQ;
>
> read_alignment($FILE);
> foreach my $key ( keys (%SEQ)){ #defines key for each key
>
> printf "%s\n%s\n", $key, $SEQ{$key};
> }
> sub read_alignment {
> my $line;
> my ($file) = @_;
> #local (*TMP);
> open(TMP, $file) or die "can't open file '$file'\n";
> while ( $line = <TMP> ) {
> chomp($line);
> if ($line =~ /(>\S+)\s*/) {#&& (! $SEQ{$1})) {
> push (@ID, $1);
> }
> else {
> $SEQ{$1}.= $line;
>
> }
> }
> close TMP
> }
#!/usr/sbin/perl -w
use strict;
die "usage: $0 fasta_file\n" unless @ARGV;
my %seq;
$/ = '>';
while ( <> ) {
chomp;
next unless /\S/;
my ( $key, $data ) = split /\n/, $_, 2;
$data =~ s/\s+//g;
$seq{$key} .= $data;
}
for my $key ( keys %seq ) {
print ">$key\n$seq{$key}\n";
}
__END__
John
--
use Perl;
program
fulfillment
--
To unsubscribe, e-mail: [EMAIL PROTECTED]
For additional commands, e-mail: [EMAIL PROTECTED]
