[Bioperl-l] use Bio::SeqIO to read Fasta sequence from pipe, or @ARGV, like "while (<>) {....}"

[Haiyan Lin]

Hi, Paul,

Thanks for your quick replay and advice. Soryy for my late feedback, I can't send maill in my location yesterday. I have tried your method. But
it complains that

------------------------------------
[linhy at bioinfo1 Script]$ less try.fa | perl ./fastaLen.pl
Name "main::DATA" used only once: possible typo at ./fastaLen.pl line
42.
Use of uninitialized value in print at ./fastaLen.pl line 49.
------------------------------------


I had also tried the "-fh=>\*STDIN", and "-fh=><>",according to the
documentation returned by "perldoc Bio::SeqIO" at termminal, but I still
haven't got I want.Thanks again.

... ...

   Bio::SeqIO->new()
          $seqIO = Bio::SeqIO->new(-file => 'filename',
-format=>$format);
          $seqIO = Bio::SeqIO->new(-fh   => \*FILEHANDLE,
-format=>$format);
          $seqIO = Bio::SeqIO->new(-format => $format);

       ... ... 

       -fh  You may provide new() with a previously-opened filehandle.
For example, to read from STDIN:

               $seqIO = Bio::SeqIO->new(-fh => \*STDIN);

            Note that you must pass filehandles as references to globs.

            If neither a filehandle nor a filename is specified, then
the module will read from the @ARGV array or STDIN, using the
            familiar <> semantics.

-------------------------------



Regards

Haiyan




On Sat, 2014-07-12 at 10:22 -0400, Paul Cantalupo wrote:
> Hi Haiyan,
> 
> 
> You need to use the '-fh' option in Bio::SeqIO new and have it use
> Perl's DATA filehandle like so:
> my $in = Bio::SeqIO->new(-fh => \*DATA, -format => 'fasta');
> 
> This was taken from
> http://perldoc.perl.org/perldata.html#Special-Literals:
> "Text after __DATA__ may be read via the filehandle PACKNAME::DATA ,
> where PACKNAME is the package that was current when the __DATA__ token
> was encountered."
> 
> 
> 
> Good luck,
> 
> Paul
> 
> 
> 
> 
> Paul Cantalupo
> University of Pittsburgh
> 
> 
> 
> On Sat, Jul 12, 2014 at 8:35 AM, Haiyan Lin <linhy0120 at gmail.com>
> wrote:
>         Hill, dear perlers,
>         
>         I‘m trying to use Bio::SeqIO to read Fasta sequence from pipe,
>         or @ARGV,
>         like "while (<>) {....}". After several trier and error,  I'm
>         failed and
>         need to ask for herp from you. Could you please help me to
>         check or try
>         following code?
>         
>         Thanks in advance.
>         
>         ---------------------------------------
>         use Bio::SeqIO ;
>         use Statistics::Descriptive ;
>         
>         my %opt = () ;
>         my $sta = Statistics::Descriptive::Full->new();
>         
>         ##### here is the key， I think.
>         my $in = Bio::SeqIO->new(-format=>"Fasta");
>         while(my $s = $in->next_seq()){
>             $sta->add_data($s->length()) ;
>         }
>         print $sta->sum() if $opt{sum} ;
>         
>         __DATA__
>         >ct1
>         AGAGAGAGA
>         >ctg2
>         ATATATAT
>         -----------------------------------------------
>         
>         Regards
>         
>         Haiyan
>         
>         
>         
>         
>         
>         
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