[Bioperl-l] Bio::DB::Fasta check for ragged line widths

[Hilmar Lapp]

Wouldn't it be easier (and more robust) to just reformat the file to  
meet the constant line width requirement? The code required to do  
that should be fewer lines than your addition below, I think.

For example, one could do a fast first-pass through the file simply  
checking that all sequence lines not followed by a description line  
or eof have the same length, stopping at the first line that fails  
the test. If unequal lengths, use Bio::SeqIO to read and write back  
out the fasta file, then continue as for well-formatted files.

	-hilmar

On Apr 6, 2007, at 11:31 PM, Don Gilbert wrote:

>
> Dear Bioperlers,
>
> There is a hidden issue with Bio::DB::Fasta in that it assumes Fasta
> files have fixed line widths, but that isn't a requirement of Fasta
> format. The documentation notes this package requirement, but I was
> bitten by this, and I'd guess not many people check their data (esp.
> if from someone else) to see it meets this requirement.
>
> Simple tools can easily produce fasta with ragged line formatting:
> e.g. genome assemblers that paste together contig fasta with spacers
> to make assemblies.
>
> It would be nice if B:D:Fasta would check and die when it can't handle
> this ragged input.  Here is a suggested addition:
>
>   package Bio::DB::Fasta;
>
> =head1 DESCRIPTION
>
>   Entries may have any line length up to 65,536 characters, and
>   different line lengths are allowed in the same file.  However,  
> within
>   a sequence entry, all lines must be the same length except for the
>   last.
> + An error will be thrown if this is not the case.
>
> =cut
>
>   use constant DIE_ON_MISSMATCHED_LINES => 1; # if you want
>
>   sub calculate_offsets {
>
>      my ($offset,$id,$linelength,$type,$firstline,$count, 
> $termination_length,%offsets);
>   +  my ($l3_len,$l2_len,$l_len)=(0,0,0);
>
>          $self->_check_linelength($linelength);
>   +      ($l3_len,$l2_len,$l_len)=(0,0,0);
>        } else {
>   +      $l3_len= $l2_len; $l2_len= $l_len; $l_len= length($_); #  
> need to check every line :(
>   +      if(DIE_ON_MISSMATCHED_LINES &&
>   +        $l3_len>0 && $l2_len>0 && $l3_len!=$l2_len) {
>   +         my $fap= substr($_,0,20)."..";
>   +         $self->throw("Each line of the fasta entry must be the  
> same length except the last.
>   +  Line above #$. '$fap' is $l2_len != $l3_len chars.");
>   +         }
>
>          $linelength ||= length($_);
>
> -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
> -- gilbertd at indiana.edu--http://marmot.bio.indiana.edu/
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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