[Bioperl-l] Bio::SeqIO Genbank + EMBL unquoted values

[Heikki Lehvaslaiho]

Nadeem,

I fixed that only yesterday! Look into cvs.
It was bioperl bugzilla bug # 1516.

	-Heikki

On Thursday 27 Nov 2003 11:04 am, Nadeem Faruque wrote:
> Prompted by a genome submittor that had used BioPerl, I wondered why he
> couldn't get BioPerl to write out unquoted evidence qualifier values.
>
> Maybe I've got this wrong, but I think that the feature table writing
> functions are oversimplified on this point:-
>
> In sub _print_EMBL_FTHelper  (and sub _print_GenBank_FTHelper)
> it appears only to think that only qualifier values that are just numbers
> are unquoted:-
> ...
>             elsif( $always_quote == 1 || $value !~ /^\d+$/ ) {
>                my $pat = $value =~ /\s/ ? '\s|$' : '.|$';
>            $self->_write_line_EMBL_regex("FT                   ",
>                          "FT                   ",
>                          "/$tag=\"$value\"",$pat,80);
>             }
>             else {
>                $self->_write_line_EMBL_regex("FT                   ",
>                          "FT                   ",
>                          "/$tag=$value",'.|$',80); #'
>
>
>
> Each of the folloing qualifiers accepts a non-numeric single token that
> should be unquoted:-
>   /direction=left, right, or both
>   /estimated_length=unknown though an actual number will be accepted next
> year /evidence=experimental or not_experimental
>   /label=*** single token used to permanently tag a feature
>          (for use within EMBL, eg for joins that span entries.
>           External use not advised)
>   /mod_base=m5c for example, the abbreviation for a modified nucleotide
> base /number=1e for example, a single token used as a exon/intron number
> (should be a number but exon numbering is more chaotic than that)
> /rpt_type=tandem, inverted, flanking, terminal, direct, dispersed, and
> other /rpt_unit can either accept quoted text (/rpt_unit="aagggc" )
>           or a location value (/rpt_unit=202..245 )
>
> NB The other qualifiers that are unusual are:-
>   /anticodon=(pos:***,aa:***)
>   /citation=[***] - the number of the citation
>   /codon=(seq:"***", aa:***)
>   /cons_splice=(5'site:***, 3'site:***)
>   /transl_except=(pos:***,aa:***)
>   /usedin=***:*** - like /label, this shouldn't really be created
> externally.
>
>
> Further details are available in teh feature table document or at
> <http://www.ebi.ac.uk/embl/WebFeat/index.html>
>
> Nadeem

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     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
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