[Bioperl-l] Some more troubles with HTML module?

[Ewan Birney]

On Wed, 25 Oct 2000, Carl Virtanen wrote:

> Hi folks,
> 
> I'm a little new at checking out some of this stuff, so please bear with me. I'm using bioperl 6.2.
> The problem i'm having is that the output from the Blast->to_html routine is not picking up all of the correct references and 'htmlifying' them (see my example near the bottom).  I'm just using the standard kinda usage:
> use Bio::Tools::Blast qw(:obj);
> $Blast->to_html(file=>$ARGV[0]);
> 
>  I've narrowed the problem down to the HTML.pm module.  Now, call me a
> bonehead (if you wish, but that wouldn't be really nice now would it?)
> but the regexps in there are some real bad ass ones (if you'll excuse
> my colourful explanation)! So tracking down where the problem is is
> not so easy for me.  Actually, if somebody would explain to me at
> least one of the regexps,for example:
> 
> s@^ ?(gb|emb|dbj)\|($Word)(\|$Word)?($Descrip)($Int +)($Signif)(.*)$@$1:<a hre
> f="$DbUrl{'gb_n'}$2">$2$3</a>$4$5<A href="\#$2_A">$6</a>$7<a name="$2_H"></a>@o;


Apologies. That looks like a _beast_.


This one is for stevec if he is tuning in. I have to admit, I tend to
generate html files myself by going through the loops

foreach $hit ( ... ){
    foreach $hsp ( ... ) {
     
    }
}

etc. But that is more coding for you....


> 
> 
> then i would be very grateful and would even try to track down the problem myself and possibly contribute a little to all of this. I'm familiar with basic regexps/substitution and so on, but yikes!
> 
> Anyways, here's the output, and you can see that it's missing a bunch of gi's. The search was just a routine peek at some proteins in the nr database:
> 
> Sequences producing significant alignments:                        (bits)  Value
> 
> emb|CAB55683.1| (AL035427) dJ769N13.1 (KIAA0443 protein.) [Homo ...   214  2e-54
> ref|NP_055525.1| KIAA0443 gene product >gi|7512985|pir||T00068 h...   214  2e-54
> dbj|BAB14367.1| (AK023031) unnamed protein product [Homo sapiens]     181  2e-44
> gb:AAF64273.1|AF208859_1 (AF208859) BM-017 [Homo sapiens] >gi|82...   123  6e-27
> 
> 
> 
> Thanks!
> 
> Carl Virtanen
> 
> 
> 

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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
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