[Bioperl-l] perl one-liner with Bio::SeqIO
Stefan Kirov
stefan.kirov at bms.com
Thu Jul 22 17:51:59 UTC 2010
Sorry for copying you all, but my posts to bioperl list do not go
through (my headers seem suspicious).
I proposed (comment on the bug) that seek throws an IO error, I think
this would be good practice in general (device gets disconnected, etc.)
I agree with Aaron that one option would be that if STDIN is the input
format MUST be specified or parser dies.
Another option is to right to a temp file or slurp into memory. This
could be dangerous though...
On 7/22/2010 1:15 PM, Aaron Mackey wrote:
> You cannot seek on a pipe, unfortunately. SeqIO should probably try
> to detect this, and die rather than invoking GuessSeqFormat.
>
> -Aaron
>
> On Thu, Jul 22, 2010 at 10:30 AM, Stefan Kirov <stefan.kirov at bms.com
> <mailto:stefan.kirov at bms.com>> wrote:
>
> 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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>
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