[Bioperl-l] perl one-liner with Bio::SeqIO
Stefan Kirov
stefan.kirov at bms.com
Thu Jul 22 14:30:06 UTC 2010
From what I see in /bioperl-live/Bio/Tools/GuessSeqFormat.pm
if (defined $self->{-file}) {
# Close the file we opened.
close($fh);
} elsif (ref $fh eq 'GLOB') {
# Try seeking to the start position.
>>> seek($fh, $start_pos, 0);
} elsif (defined $fh && $fh->can('setpos')) {
# Seek to the start position.
$fh->setpos($start_pos);
}
return ($done ? $fmt_string : undef);
seek($fh, $start_pos, 0); does not reset as expected- tell $fh after
reset is where the second non-null line starts.
I am not sure why- all manuals claim this should work?
Hope this helps.
Stefan
On 7/22/2010 9:27 AM, Chris Fields wrote:
> cat test.fa | perl -MBio::SeqIO -e 'my $seq=Bio::SeqIO->new(-fh
> >>> =>\*STDIN); while ($myseq=$seq->next_seq){ print
> >>> $myseq->id,"\t",$myseq->seq,"\n"}
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