[Bioperl-l] Some more troubles with HTML module?
Carl Virtanen
carl@cimmed.com
Wed, 25 Oct 2000 18:17:51 +1000
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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);
$Blast->to_html(file=3D>$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 =
+)($Signif)(.*)$@$1:<a hre
f=3D"$DbUrl{'gb_n'}$2">$2$3</a>$4$5<A href=3D"\#$2_A">$6</a>$7<a =
name=3D"$2_H"></a>@o;
then i would be very grateful and would even try to track down the =
problem myself and possibly contribute a little to all of this. I'm =
familiar with basic regexps/substitution and so on, but yikes!
Anyways, here's the output, and you can see that it's missing a bunch of =
gi's. The search was just a routine peek at some proteins in the nr =
database:
Sequences producing significant alignments: =
(bits) Value
emb|CAB55683.1| (AL035427) dJ769N13.1 (KIAA0443 protein.) [Homo ... =
214 2e-54
ref|NP_055525.1| KIAA0443 gene product >gi|7512985|pir||T00068 h... =
214 2e-54
dbj|BAB14367.1| (AK023031) unnamed protein product [Homo sapiens] =
181 2e-44
gb:AAF64273.1|AF208859_1 (AF208859) BM-017 [Homo sapiens] >gi|82... =
123 6e-27
Thanks!
Carl Virtanen
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=3DContent-Type content=3D"text/html; =
charset=3Diso-8859-1">
<META content=3D"MSHTML 5.50.4134.600" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT face=3DArial size=3D2>Hi folks,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>I'm a little new at checking out some =
of this=20
stuff, so please bear with me. I'm using bioperl 6.2.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>The problem i'm having is that the =
output from the=20
Blast->to_html routine is not picking up all of the correct =
references and=20
'htmlifying' them (see my example near the bottom). I'm just using =
the=20
standard kinda usage:</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>use Bio::Tools::Blast =
qw(:obj);</FONT></DIV>
<DIV><FONT face=3DArial =
size=3D2>$Blast->to_html(file=3D>$ARGV[0]);</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2> I've narrowed the problem down to =
the HTML.pm=20
module. Now, call me a bonehead (if you wish, but that wouldn't be =
really=20
nice now would it?) but the regexps in there are some real bad ass ones =
(if=20
you'll excuse my colourful explanation)!</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>So tracking down where the problem is =
is not=20
so easy for me. Actually, if somebody would explain to me at least =
one of=20
the regexps,</FONT><FONT face=3DArial size=3D2>for example:</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>s@^ =
?(gb|emb|dbj)\|($Word)(\|$Word)?($Descrip)($Int=20
+)($Signif)(.*)$@$1:<a =
hre<BR>f=3D"$DbUrl{'gb_n'}$2">$2$3</a>$4$5<A=20
href=3D"\#$2_A">$6</a>$7<a =
name=3D"$2_H"></a>@o;</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>then i would be very grateful and would =
even try to=20
track down the problem myself and possibly contribute a little to all of =
this.=20
I'm familiar with basic regexps/substitution and so on, but =
yikes!</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Anyways, here's the output, and you can =
see that=20
it's missing a bunch of gi's. The search was just a routine peek at some =
proteins in the nr database:</FONT></DIV>
<DIV><BR>Sequences producing significant=20
alignments: &n=
bsp; &nb=
sp;=20
(bits) Value<BR><BR>emb|CAB55683.1| (AL035427) dJ769N13.1 =
(KIAA0443=20
protein.) [Homo ... 214 2e-54<BR>ref|NP_055525.1| =
KIAA0443=20
gene product >gi|7512985|pir||T00068 h... 214 =20
2e-54<BR>dbj|BAB14367.1| (AK023031) unnamed protein product [Homo=20
sapiens] 181 2e-44<BR>gb:<A=20
href=3D"http://www3.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=3Dn&f=
orm=3D6&dopt=3Dg&uid=3DAAF64273.1">AAF64273.1|AF208859_1</A>=20
(AF208859) BM-017 [Homo sapiens] >gi|82... 123 <A=20
href=3D"http://zeus/~carl/FJtest.html#AAF64273.1_A">6e-27</A><A=20
name=3DAAF64273.1_H></A><BR></DIV>
<DIV> </DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Thanks!</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Carl =
Virtanen</FONT></DIV><PRE> </PRE></BODY></HTML>
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